Search results for the GEO ID: GSE7955  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM190915 | GPL1355 |
|
Frontal_Cerebrocortex_Vehicle_6hr_rep1
|
Frontal cerebrocortex, vehicle control (corn oil), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM190915
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test compound: Corn Oil
| | Sample_treatment_protocol_ch1 | CAS: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg
| | Sample_treatment_protocol_ch1 | Exposure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 = First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer (200mM Tris acetate - pH | 8.1, 100 mM KOAc, 150 mM MgOAc).
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_hyb_protocol | Breifly, fragmented biotin-labeled cRNA was diluted in a hybridization cocktail containing hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20), 0.5 mg/mL acetylated BSA, 0.1 mg/mL herring sperm DNA, 50 pM of control oligonucleotide B2, and 1.5, 5, 25 and 100 pM of BioB, BioC, BioD and Cre eukaryotic hybridization controls, respectively. Hybridization cocktails were incubated for 5 min at 99°C followed by incubation for 5 min at 45°C and then injected into the GeneChip® arrays. Loaded GeneChips® were then incubated in an Affymetrix hybridization oven for 16 hours at 45°C and 60 RPM. GeneChips® were then washed under a series of non-stringent (buffer A: 0.9 M NaCl, 0.06 M NaH2PO4, 6 mM EDTA, 0.01% Tween-20 at 25°C) and stringent (buffer B: 100 mM MES, 0.1 M NaCl, 0.05% Tween-20 at 50°C) conditions on an Affymetrix fluidics module using the EukGE-WS2v4-450 fluidics script. GeneChips® were then stained with SAPE solution (100 mM MES, 1 M NaCl, 0.05 % Tween-20, 10 µg/mL streptavidin-phycoerythrin, 2 mg/mL acetylated BSA) and subjected to another series of washes in buffer A.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190915/suppl/GSM190915.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190915/suppl/GSM190915.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195231 | GPL1355 |
|
Frontal_Cerebrocortex_Vehicle_6hr_rep2
|
Frontal Cerebrocortex, vehicle control (corn oil), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195231
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Corn Oil
| | Sample_treatment_protocol_ch1 | CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1mL/kg
| | Sample_treatment_protocol_ch1 | Exposure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195231/suppl/GSM195231.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195231/suppl/GSM195231.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195232 | GPL1355 |
|
Frontal_Cerebrocortex_Vehicle_6hr_rep3
|
Frontal cerebrocortex, vehicle control (corn oil), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195232
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Corn Oil
| | Sample_treatment_protocol_ch1 | CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1mL/kg
| | Sample_treatment_protocol_ch1 | Exposure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195232/suppl/GSM195232.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195232/suppl/GSM195232.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195233 | GPL1355 |
|
Frontal_Cerebrocortex_Vehicle_6hr_rep4
|
Frontal cerebrocortex, vehicle control (corn oil), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195233
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Corn Oil
| | Sample_treatment_protocol_ch1 | CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1mL/kg
| | Sample_treatment_protocol_ch1 | Exposure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195233/suppl/GSM195233.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195233/suppl/GSM195233.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195234 | GPL1355 |
|
Frontal_Cerebrocortex_Vehicle_6hr_rep5
|
Frontal cerebrocortex, vehicle control (corn oil), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195234
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Corn Oil
| | Sample_treatment_protocol_ch1 | CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1mL/kg
| | Sample_treatment_protocol_ch1 | Exposure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195234/suppl/GSM195234.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195234/suppl/GSM195234.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195235 | GPL1355 |
|
Frontal_Cerebrocortex_Vehicle_6hr_rep6
|
Frontal cerebrocortex, vehicle control (corn oil), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195235
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Corn Oil
| | Sample_treatment_protocol_ch1 | CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1mL/kg
| | Sample_treatment_protocol_ch1 | Exposure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195235/suppl/GSM195235.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195235/suppl/GSM195235.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195236 | GPL1355 |
|
Frontal_Cerebrocortex_Vehicle_6hr_rep7
|
Frontal cerebrocortex, vehicle control (corn oil), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195236
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Corn Oil
| | Sample_treatment_protocol_ch1 | CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1mL/kg
| | Sample_treatment_protocol_ch1 | Exposure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195236/suppl/GSM195236.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195236/suppl/GSM195236.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195237 | GPL1355 |
|
Frontal_Cerebrocortex_Vehicle_6hr_rep8
|
Frontal cerebrocortex, vehicle control (corn oil), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195237
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Corn Oil
| | Sample_treatment_protocol_ch1 | CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1mL/kg
| | Sample_treatment_protocol_ch1 | Exposure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195237/suppl/GSM195237.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195237/suppl/GSM195237.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195238 | GPL1355 |
|
Frontal_Cerebrocortex_Vehicle_6hr_rep9
|
Frontal cerebrocortex, vehicle control (corn oil), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195238
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Corn Oil
| | Sample_treatment_protocol_ch1 | CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1mL/kg
| | Sample_treatment_protocol_ch1 | Exposure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195238/suppl/GSM195238.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195238/suppl/GSM195238.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195239 | GPL1355 |
|
Frontal_Cerebrocortex_Vehicle_6hr_rep10
|
Frontal cerebrocortex, vehicle control (corn oil), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195239
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Corn Oil
| | Sample_treatment_protocol_ch1 | CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1mL/kg
| | Sample_treatment_protocol_ch1 | Exposure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195239/suppl/GSM195239.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195239/suppl/GSM195239.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195240 | GPL1355 |
|
Frontal_Cerebrocortex_Vehicle_6hr_rep11
|
Frontal cerebrocortex, vehicle control (corn oil), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195240
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Corn Oil
| | Sample_treatment_protocol_ch1 | CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1mL/kg
| | Sample_treatment_protocol_ch1 | Exposure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195240/suppl/GSM195240.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195240/suppl/GSM195240.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195241 | GPL1355 |
|
Frontal_Cerebrocortex_Vehicle_6hr_rep12
|
Frontal cerebrocortex, vehicle control (corn oil), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195241
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Corn Oil
| | Sample_treatment_protocol_ch1 | CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1mL/kg
| | Sample_treatment_protocol_ch1 | Exposure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195241/suppl/GSM195241.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195241/suppl/GSM195241.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195242 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep1
|
Frontal cerebrocortex, permethrin (1mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195242
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195242/suppl/GSM195242.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195242/suppl/GSM195242.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195243 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep2
|
Frontal cerebrocortex, Permethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195243
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195243/suppl/GSM195243.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195243/suppl/GSM195243.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195248 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep3
|
Frontal cerebrocortex, permethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195248
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195248/suppl/GSM195248.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195248/suppl/GSM195248.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195249 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep4
|
Frontal cerebrocortex, permethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195249
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195249/suppl/GSM195249.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195249/suppl/GSM195249.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195250 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep5
|
Frontal cerebrocortex, permethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195250
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195250/suppl/GSM195250.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195250/suppl/GSM195250.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195251 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep6
|
Frontal Cerebrocortex, permethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195251
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195251/suppl/GSM195251.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195251/suppl/GSM195251.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195252 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep7
|
Frontal cerebrocortex, permethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195252
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195252/suppl/GSM195252.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195252/suppl/GSM195252.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195253 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep8
|
Frontal Cerebrocortex, permethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195253
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195253/suppl/GSM195253.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195253/suppl/GSM195253.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195254 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep1
|
Frontal Cerebrocortex, permethrin (10 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195254
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 10 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195254/suppl/GSM195254.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195254/suppl/GSM195254.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195255 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep2
|
Frontal Cerebrocortex, permethrin (10 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195255
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 10 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195255/suppl/GSM195255.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195255/suppl/GSM195255.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195256 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep3
|
Frontal Cerebrocortex, permethrin (10 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195256
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 10 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195256/suppl/GSM195256.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195256/suppl/GSM195256.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195257 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep4
|
Frontal Cerebrocortex, permethrin (10 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195257
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 10 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195257/suppl/GSM195257.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195257/suppl/GSM195257.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195258 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep5
|
Frontal cerebrocortex, permethrin (10 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195258
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 10 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195258/suppl/GSM195258.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195258/suppl/GSM195258.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195259 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep6
|
Frontal Cerebrocortex, permethrin (10mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195259
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 10 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195259/suppl/GSM195259.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195259/suppl/GSM195259.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195260 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep7
|
Frontal Cerebrocortex, permethrin (10 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195260
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 10 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195260/suppl/GSM195260.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195260/suppl/GSM195260.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195261 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep8
|
Frontal cerebrocortex, permethrin (10 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195261
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 10 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195261/suppl/GSM195261.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195261/suppl/GSM195261.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195263 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep1
|
Frontal cerebrocortex, permethrin 100 mg/kg, 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195263
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 100 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195263/suppl/GSM195263.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195263/suppl/GSM195263.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195264 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep2
|
Frontal Cerebrocortex, permethrin (100 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195264
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 100 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195264/suppl/GSM195264.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195264/suppl/GSM195264.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195265 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep3
|
Frontal cerebrocortex, permethrin (100 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195265
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 100 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195265/suppl/GSM195265.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195265/suppl/GSM195265.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195266 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep4
|
Frontal Cerebrocortex, permethrin (100 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195266
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 100 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195266/suppl/GSM195266.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195266/suppl/GSM195266.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195267 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep5
|
Frontal cerebrocortex, permethrin (100 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195267
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 100 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195267/suppl/GSM195267.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195267/suppl/GSM195267.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195269 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep6
|
Frontal cerebrocortex, permethrin (100 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195269
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 100 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195269/suppl/GSM195269.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195269/suppl/GSM195269.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195270 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep7
|
Frontal cerebrocortex, permethrin (100 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195270
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 100 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195270/suppl/GSM195270.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195270/suppl/GSM195270.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195272 | GPL1355 |
|
Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep8
|
Frontal cerebrocortex, permethrin (100 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195272
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Permethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52645-53-1
| | Sample_treatment_protocol_ch1 | Isomer Composition: 40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
| | Sample_treatment_protocol_ch1 | Purity: 92.0 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 100 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL/kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195272/suppl/GSM195272.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195272/suppl/GSM195272.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195276 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep1
|
Frontal cerebrocortex, deltamethrin (0.3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195276
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 0.3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195276/suppl/GSM195276.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195276/suppl/GSM195276.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195278 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep2
|
Frontal cerebrocortex, deltamethrin (0.3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195278
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 0.3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195278/suppl/GSM195278.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195278/suppl/GSM195278.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195280 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep3
|
Frontal cerebrocortex, deltamethrin (0.3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195280
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 0.3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195280/suppl/GSM195280.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195280/suppl/GSM195280.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195281 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep4
|
Frontal cerebrocortex, deltamethrin (0.3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195281
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 0.3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195281/suppl/GSM195281.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195281/suppl/GSM195281.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195283 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep5
|
Frontal cerebrocortex, deltamethrin (0.3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195283
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 0.3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195283/suppl/GSM195283.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195283/suppl/GSM195283.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195285 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep6
|
Frontal cerebrocortex, deltamethrin (0.3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195285
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 0.3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195285/suppl/GSM195285.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195285/suppl/GSM195285.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195286 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep7
|
Frontal cerebrocortex, deltamethrin (0.3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195286
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 0.3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195286/suppl/GSM195286.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195286/suppl/GSM195286.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195288 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep8
|
Frontal Cerebrocortex, deltamethrin (0.3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195288
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 0.3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195288/suppl/GSM195288.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195288/suppl/GSM195288.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195289 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep1
|
Frontal cerebrocortex, deltamethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195289
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195289/suppl/GSM195289.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195289/suppl/GSM195289.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195290 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep2
|
Frontal Cerebrocortex, deltamethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195290
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195290/suppl/GSM195290.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195290/suppl/GSM195290.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195291 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep3
|
Frontal cerebrocortex, deltamethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195291
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195291/suppl/GSM195291.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195291/suppl/GSM195291.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195292 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep4
|
Frontal cerebrocortex, deltamethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195292
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195292/suppl/GSM195292.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195292/suppl/GSM195292.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195293 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep5
|
Frontal cerebrocortex, deltamethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195293
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195293/suppl/GSM195293.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195293/suppl/GSM195293.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195295 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep6
|
Frontal Cerebrocortex, deltamethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195295
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195295/suppl/GSM195295.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195295/suppl/GSM195295.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195296 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep7
|
Frontal cerebrocortex, deltamethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195296
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195296/suppl/GSM195296.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195296/suppl/GSM195296.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195297 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep8
|
Frontal cerebrocortex, deltamethrin (1 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195297
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 1 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195297/suppl/GSM195297.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195297/suppl/GSM195297.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195298 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep1
|
Frontal cerebrocortex, deltamethrin (3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195298
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195298/suppl/GSM195298.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195298/suppl/GSM195298.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195299 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep2
|
Frontal cerebrocortex, deltamethrin (3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195299
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195299/suppl/GSM195299.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195299/suppl/GSM195299.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195300 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep3
|
Frontal cerebrocortex, deltamethrin (3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195300
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195300/suppl/GSM195300.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195300/suppl/GSM195300.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195301 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep4
|
Frontal cerebrocortex, deltamethrin (3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195301
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195301/suppl/GSM195301.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195301/suppl/GSM195301.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195302 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep5
|
Frontal cerebrocortex, deltamethrin (3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195302
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_hyb_protocol | Breifly, fragmented biotin-labeled cRNA was diluted in a hybridization cocktail containing hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20), 0.5 mg/mL acetylated BSA, 0.1 mg/mL herring sperm DNA, 50 pM of control oligonucleotide B2, and 1.5, 5, 25 and 100 pM of BioB, BioC, BioD and Cre eukaryotic hybridization controls, respectively. Hybridization cocktails were incubated for 5 min at 99°C followed by incubation for 5 min at 45°C and then injected into the GeneChip® arrays. Loaded GeneChips® were then incubated in an Affymetrix hybridization oven for 16 hours at 45°C and 60 RPM. GeneChips® were then washed under a series of non-stringent (buffer A: 0.9 M NaCl, 0.06 M NaH2PO4, 6 mM EDTA, 0.01% Tween-20 at 25°C) and stringent (buffer B: 100 mM MES, 0.1 M NaCl, 0.05% Tween-20 at 50°C) conditions on an Affymetrix fluidics module using the EukGE-WS2v4-450 fluidics script. GeneChips® were then stained with SAPE solution (100 mM MES, 1 M NaCl, 0.05 % Tween-20, 10 µg/mL streptavidin-phycoerythrin, 2 mg/mL acetylated BSA) and subjected to another series of washes in buffer A.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195302/suppl/GSM195302.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195302/suppl/GSM195302.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195303 | GPL1355 |
|
Frontal_cerebrocortex_Deltamethrin_3mg/kg_6hr_rep6
|
Frontal cerebrocortex, deltamethrin (3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195303
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_hyb_protocol | Breifly, fragmented biotin-labeled cRNA was diluted in a hybridization cocktail containing hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20), 0.5 mg/mL acetylated BSA, 0.1 mg/mL herring sperm DNA, 50 pM of control oligonucleotide B2, and 1.5, 5, 25 and 100 pM of BioB, BioC, BioD and Cre eukaryotic hybridization controls, respectively. Hybridization cocktails were incubated for 5 min at 99°C followed by incubation for 5 min at 45°C and then injected into the GeneChip® arrays. Loaded GeneChips® were then incubated in an Affymetrix hybridization oven for 16 hours at 45°C and 60 RPM. GeneChips® were then washed under a series of non-stringent (buffer A: 0.9 M NaCl, 0.06 M NaH2PO4, 6 mM EDTA, 0.01% Tween-20 at 25°C) and stringent (buffer B: 100 mM MES, 0.1 M NaCl, 0.05% Tween-20 at 50°C) conditions on an Affymetrix fluidics module using the EukGE-WS2v4-450 fluidics script. GeneChips® were then stained with SAPE solution (100 mM MES, 1 M NaCl, 0.05 % Tween-20, 10 µg/mL streptavidin-phycoerythrin, 2 mg/mL acetylated BSA) and subjected to another series of washes in buffer A.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195303/suppl/GSM195303.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195303/suppl/GSM195303.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195304 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep7
|
Frontal cerebrocortex, deltamethrin (3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195304
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_hyb_protocol | Breifly, fragmented biotin-labeled cRNA was diluted in a hybridization cocktail containing hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20), 0.5 mg/mL acetylated BSA, 0.1 mg/mL herring sperm DNA, 50 pM of control oligonucleotide B2, and 1.5, 5, 25 and 100 pM of BioB, BioC, BioD and Cre eukaryotic hybridization controls, respectively. Hybridization cocktails were incubated for 5 min at 99°C followed by incubation for 5 min at 45°C and then injected into the GeneChip® arrays. Loaded GeneChips® were then incubated in an Affymetrix hybridization oven for 16 hours at 45°C and 60 RPM. GeneChips® were then washed under a series of non-stringent (buffer A: 0.9 M NaCl, 0.06 M NaH2PO4, 6 mM EDTA, 0.01% Tween-20 at 25°C) and stringent (buffer B: 100 mM MES, 0.1 M NaCl, 0.05% Tween-20 at 50°C) conditions on an Affymetrix fluidics module using the EukGE-WS2v4-450 fluidics script. GeneChips® were then stained with SAPE solution (100 mM MES, 1 M NaCl, 0.05 % Tween-20, 10 µg/mL streptavidin-phycoerythrin, 2 mg/mL acetylated BSA) and subjected to another series of washes in buffer A.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195304/suppl/GSM195304.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195304/suppl/GSM195304.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
|
GSM195305 | GPL1355 |
|
Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep8
|
Frontal cerebrocortex, deltamethrin (3 mg/kg), 6 hours
|
Strain: Long-Evans
Gender: Male
Age: Adult (PND62-PND64)
Tissue: Cerebrocortex
|
This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.
|
| Sample_geo_accession | GSM195305
| | Sample_status | Public on Oct 15 2007
| | Sample_submission_date | May 29 2007
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Charles River, Inc.
| | Sample_treatment_protocol_ch1 | Test Compound: Deltamethrin
| | Sample_treatment_protocol_ch1 | Test Compound CAS#: 52918-63-5
| | Sample_treatment_protocol_ch1 | Isomer Composition: 100 % (1R, 3R, alpha-S)
| | Sample_treatment_protocol_ch1 | Purity: 98.9 %
| | Sample_treatment_protocol_ch1 | Vehicle: Corn Oil
| | Sample_treatment_protocol_ch1 | Vehicle CAS #: 8001-30-07
| | Sample_treatment_protocol_ch1 | Administration Route: Oral Gavage
| | Sample_treatment_protocol_ch1 | Test Compound Concentration: 3 mg/mL
| | Sample_treatment_protocol_ch1 | Delivery Volume: 1 mL / kg body weight
| | Sample_treatment_protocol_ch1 | Expsoure Duration: Single, Acute
| | Sample_treatment_protocol_ch1 | Sampling Time: 6 Hours post-exposure
| | Sample_growth_protocol_ch1 | Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding. Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment. Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%. Purina 5001 Rat Chow and tap water were provided ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions. Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour. DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7. Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min. Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH | 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min. Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021). Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol. Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol. Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.
| | Sample_hyb_protocol | Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).
| | Sample_hyb_protocol | Breifly, fragmented biotin-labeled cRNA was diluted in a hybridization cocktail containing hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20), 0.5 mg/mL acetylated BSA, 0.1 mg/mL herring sperm DNA, 50 pM of control oligonucleotide B2, and 1.5, 5, 25 and 100 pM of BioB, BioC, BioD and Cre eukaryotic hybridization controls, respectively. Hybridization cocktails were incubated for 5 min at 99°C followed by incubation for 5 min at 45°C and then injected into the GeneChip® arrays. Loaded GeneChips® were then incubated in an Affymetrix hybridization oven for 16 hours at 45°C and 60 RPM. GeneChips® were then washed under a series of non-stringent (buffer A: 0.9 M NaCl, 0.06 M NaH2PO4, 6 mM EDTA, 0.01% Tween-20 at 25°C) and stringent (buffer B: 100 mM MES, 0.1 M NaCl, 0.05% Tween-20 at 50°C) conditions on an Affymetrix fluidics module using the EukGE-WS2v4-450 fluidics script. GeneChips® were then stained with SAPE solution (100 mM MES, 1 M NaCl, 0.05 % Tween-20, 10 µg/mL streptavidin-phycoerythrin, 2 mg/mL acetylated BSA) and subjected to another series of washes in buffer A.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.
| | Sample_data_processing | Signal intensities calculated using RMA algorithm
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Joshua,A,Harrill
| | Sample_contact_email | harrill.josh@epa.gov
| | Sample_contact_phone | 919-541-4606
| | Sample_contact_laboratory | NBTB/NTD/NHEERL/ORD/USEPA
| | Sample_contact_department | Curriculum in Toxicology
| | Sample_contact_institute | University of North Carolina
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195305/suppl/GSM195305.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM195nnn/GSM195305/suppl/GSM195305.CHP.gz
| | Sample_series_id | GSE7955
| | Sample_data_row_count | 31042
| | |
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