Search results for the GEO ID: GSE13793  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM346998 | GPL341 |
|
Cerebellum PND14. Mother (12M) dosed
|
Cerebellum from pup on PND14. Mother (12M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14
|
strain: Long Evans
Sex: male
|
Gene expression data from Cerebellum from pup on PND14. Mother (12M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14
|
| Sample_geo_accession | GSM346998
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346998/suppl/GSM346998.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347000 | GPL341 |
|
Cerebellum PND14. Mother (15M) dosed
|
Cerebellum from pup on PND14. Mother (15M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14
|
strain: Long Evans
Sex: male
|
Gene expression data from Cerebellum from pup on PND14. Mother (15M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14
|
| Sample_geo_accession | GSM347000
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347000/suppl/GSM347000.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347001 | GPL341 |
|
Cerebellum PND14. Mother (18M) dosed
|
Cerebellum from pup on PND14. Mother (18M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14
|
strain: Long Evans
Sex: male
|
Gene expression data from Cerebellum from pup on PND14. Mother (18M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14
|
| Sample_geo_accession | GSM347001
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347001/suppl/GSM347001.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347002 | GPL341 |
|
Cerebellum PND14. Mother (1M) not dosed
|
Cerebellum from pup on PND14. Mother (1M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14
|
strain: Long Evans
Sex: male
|
Gene expression data from Cerebellum from pup on PND14. Mother (1M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14
|
| Sample_geo_accession | GSM347002
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347002/suppl/GSM347002.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347003 | GPL341 |
|
Cerebellum PND14. Mother (7M) not dosed
|
Cerebellum from pup on PND14. Mother (7M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14
|
strain: Long Evans
Sex: male
|
Gene expression data from Cerebellum from pup on PND14. Mother (7M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14
|
| Sample_geo_accession | GSM347003
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347003/suppl/GSM347003.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347004 | GPL341 |
|
Cerebellum PND7. Mother (12M) dosed
|
Cerebellum from pup on PND7. Mother (12M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7
|
strain: Long Evans
Sex: male
|
Gene expression data from Cerebellum from pup on PND7. Mother (12M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7
|
| Sample_geo_accession | GSM347004
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347004/suppl/GSM347004.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347005 | GPL341 |
|
Cerebellum PND7. Mother (13M) not dosed
|
Cerebellum from pup on PND7. Mother (13M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7
|
strain: Long Evans
Sex: male
|
Gene expression data from Cerebellum from pup on PND7. Mother (13M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7
|
| Sample_geo_accession | GSM347005
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347005/suppl/GSM347005.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347006 | GPL341 |
|
Cerebellum PND7. Mother (15M) dosed
|
Cerebellum from pup on PND7. Mother (15M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7
|
strain: Long Evans
Sex: male
|
Gene expression data from Cerebellum from pup on PND7. Mother (15M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7
|
| Sample_geo_accession | GSM347006
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347006/suppl/GSM347006.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347007 | GPL341 |
|
Cerebellum PND7. Mother (18M) dosed
|
Cerebellum from pup on PND7. Mother (18M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7
|
strain: Long Evans
Sex: male
|
Gene expression data from Cerebellum from pup on PND7. Mother (18M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7
|
| Sample_geo_accession | GSM347007
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347007/suppl/GSM347007.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347008 | GPL341 |
|
Cerebellum PND7. Mother (1M) not dosed
|
Cerebellum from pup on PND7. Mother (1M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7
|
strain: Long Evans
Sex: male
|
Gene expression data from Cerebellum from pup on PND7. Mother (1M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7
|
| Sample_geo_accession | GSM347008
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347008/suppl/GSM347008.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347009 | GPL341 |
|
Cerebellum PND7. Mother (7M) not dosed
|
Cerebellum from pup on PND7. Mother (7M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7
|
strain: Long Evans
Sex: male
|
Gene expression data from Cerebellum from pup on PND7. Mother (7M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7
|
| Sample_geo_accession | GSM347009
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347009/suppl/GSM347009.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347010 | GPL341 |
|
Hippocampus PND14. Mother (12M) dosed
|
Hippocampus from pup on PND14. Mother (12M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14
|
strain: Long Evans
Sex: male
|
Gene expression data from Hippocampus from pup on PND14. Mother (12M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14
|
| Sample_geo_accession | GSM347010
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347010/suppl/GSM347010.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347011 | GPL341 |
|
Hippocampus PND14. Mother (13M) not dosed
|
Hippocampus from pup on PND14. Mother (13M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14
|
strain: Long Evans
Sex: male
|
Gene expression data from Hippocampus from pup on PND14. Mother (13M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14
|
| Sample_geo_accession | GSM347011
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347011/suppl/GSM347011.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347012 | GPL341 |
|
Hippocampus PND14. Mother (15M) dosed
|
Hippocampus from pup on PND14. Mother (15M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14
|
strain: Long Evans
Sex: male
|
Gene expression data from Hippocampus from pup on PND14. Mother (15M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14
|
| Sample_geo_accession | GSM347012
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347012/suppl/GSM347012.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347013 | GPL341 |
|
Hippocampus PND14. Mother (18M) dosed
|
Hippocampus from pup on PND14. Mother (18M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14
|
strain: Long Evans
Sex: male
|
Gene expression data from Hippocampus from pup on PND14. Mother (18M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14
|
| Sample_geo_accession | GSM347013
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347013/suppl/GSM347013.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347014 | GPL341 |
|
Hippocampus PND14. Mother (1M) not dosed
|
Hippocampus from pup on PND14. Mother (1M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14
|
strain: Long Evans
Sex: male
|
Gene expression data from Hippocampus from pup on PND14. Mother (1M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14
|
| Sample_geo_accession | GSM347014
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347014/suppl/GSM347014.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347015 | GPL341 |
|
Hippocampus PND14. Mother (7M) not dosed
|
Hippocampus from pup on PND14. Mother (7M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14
|
strain: Long Evans
Sex: male
|
Gene expression data from Hippocampus from pup on PND14. Mother (7M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14
|
| Sample_geo_accession | GSM347015
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347015/suppl/GSM347015.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347016 | GPL341 |
|
Hippocampus PND7. Mother (12M) dosed
|
Hippocampus from pup on PND7. Mother (12M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7
|
strain: Long Evans
Sex: male
|
Gene expression data from Hippocampus from pup on PND7. Mother (12M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7
|
| Sample_geo_accession | GSM347016
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347016/suppl/GSM347016.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347017 | GPL341 |
|
Hippocampus PND7. Mother (13M) not dosed
|
Hippocampus from pup on PND7. Mother (13M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7
|
strain: Long Evans
Sex: male
|
Gene expression data from Hippocampus from pup on PND7. Mother (13M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7
|
| Sample_geo_accession | GSM347017
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347017/suppl/GSM347017.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347018 | GPL341 |
|
Hippocampus PND7. Mother (15M) dosed
|
Hippocampus from pup on PND7. Mother (15M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7
|
strain: Long Evans
Sex: male
|
Gene expression data from Hippocampus from pup on PND7. Mother (15M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7
|
| Sample_geo_accession | GSM347018
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347018/suppl/GSM347018.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347019 | GPL341 |
|
Hippocampus PND7. Mother (18M) dosed
|
Hippocampus from pup on PND7. Mother (18M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7
|
strain: Long Evans
Sex: male
|
Gene expression data from Hippocampus from pup on PND7. Mother (18M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7
|
| Sample_geo_accession | GSM347019
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347019/suppl/GSM347019.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347020 | GPL341 |
|
Hippocampus PND7. Mother (1M) not dosed
|
Hippocampus from pup on PND7. Mother (1M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7
|
strain: Long Evans
Sex: male
|
Gene expression data from Hippocampus from pup on PND7. Mother (1M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7
|
| Sample_geo_accession | GSM347020
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347020/suppl/GSM347020.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
|
GSM347021 | GPL341 |
|
Hippocampus PND7. Mother (7M) not dosed
|
Hippocampus from pup on PND7. Mother (7M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7
|
strain: Long Evans
Sex: male
|
Gene expression data from Hippocampus from pup on PND7. Mother (7M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7
|
| Sample_geo_accession | GSM347021
| | Sample_status | Public on Jan 31 2009
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.
| | Sample_growth_protocol_ch1 | The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.
| | Sample_hyb_protocol | Chips were incubated at 42 degree C for ≥ 16 h, washed with a series of non-stringent (25 degree C) and stringent (50 degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).
| | Sample_data_processing | Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed
| | Sample_platform_id | GPL341
| | Sample_contact_name | Jennifer,,Fostel
| | Sample_contact_email | fostel@niehs.nih.gov
| | Sample_contact_phone | 919 541 5055
| | Sample_contact_department |
| | Sample_contact_institute | NIEHS
| | Sample_contact_address |
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM347nnn/GSM347021/suppl/GSM347021.CEL.gz
| | Sample_series_id | GSE13793
| | Sample_data_row_count | 15923
| | |
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