Search results for the GEO ID: GSE10411  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM263056 | GPL1355 |
|
2552 Control 0ppm Liver
|
2552 Control 0ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
Control_01
|
| Sample_geo_accession | GSM263056
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263056/suppl/GSM263056.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263057 | GPL1355 |
|
2553 Control 0ppm Liver
|
2553 Control 0ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
Control_02
|
| Sample_geo_accession | GSM263057
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263057/suppl/GSM263057.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263058 | GPL1355 |
|
2558 Control 0ppm Liver
|
2558 Control 0ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
Control_03
|
| Sample_geo_accession | GSM263058
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263058/suppl/GSM263058.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263059 | GPL1355 |
|
2561 Control 0ppm Liver
|
2561 Control 0ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
Control_04
|
| Sample_geo_accession | GSM263059
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263059/suppl/GSM263059.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263060 | GPL1355 |
|
3144 Control 0ppm Liver
|
3144 Control 0ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
Control_05
|
| Sample_geo_accession | GSM263060
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263060/suppl/GSM263060.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263061 | GPL1355 |
|
3145 Control 0ppm Liver
|
3145 Control 0ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
Control_06
|
| Sample_geo_accession | GSM263061
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263061/suppl/GSM263061.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263062 | GPL1355 |
|
3156 Control 0ppm Liver
|
3156 Control 0ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
Control_07
|
| Sample_geo_accession | GSM263062
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263062/suppl/GSM263062.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263063 | GPL1355 |
|
2582 Myclobutanil 500ppm Liver
|
2582 Myclobutanil 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
M500_01
|
| Sample_geo_accession | GSM263063
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263063/suppl/GSM263063.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263064 | GPL1355 |
|
2583 Myclobutanil 500ppm Liver
|
2583 Myclobutanil 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
M500_02
|
| Sample_geo_accession | GSM263064
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263064/suppl/GSM263064.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263065 | GPL1355 |
|
2585 Myclobutanil 500ppm Liver
|
2585 Myclobutanil 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
M500_03
|
| Sample_geo_accession | GSM263065
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263065/suppl/GSM263065.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263066 | GPL1355 |
|
2588 Myclobutanil 500ppm Liver
|
2588 Myclobutanil 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
M500_04
|
| Sample_geo_accession | GSM263066
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263066/suppl/GSM263066.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263067 | GPL1355 |
|
2591 Myclobutanil 500ppm Liver
|
2591 Myclobutanil 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
M500_05
|
| Sample_geo_accession | GSM263067
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263067/suppl/GSM263067.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263068 | GPL1355 |
|
2597 Myclobutanil 2000ppm Liver
|
2597 Myclobutanil 2000ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
M2000_01
Processed data not available because this sample was not included in the final analysis.
|
| Sample_geo_accession | GSM263068
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263068/suppl/GSM263068.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 0
| | |
|
GSM263069 | GPL1355 |
|
2598 Myclobutanil 2000ppm Liver
|
2598 Myclobutanil 2000ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
M2000_02
|
| Sample_geo_accession | GSM263069
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263069/suppl/GSM263069.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263070 | GPL1355 |
|
2600 Myclobutanil 2000ppm Liver
|
2600 Myclobutanil 2000ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
M2000_03
|
| Sample_geo_accession | GSM263070
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263070/suppl/GSM263070.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263071 | GPL1355 |
|
2603 Myclobutanil 2000ppm Liver
|
2603 Myclobutanil 2000ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
M2000_04
|
| Sample_geo_accession | GSM263071
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263071/suppl/GSM263071.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263072 | GPL1355 |
|
2606 Myclobutanil 2000ppm Liver
|
2606 Myclobutanil 2000ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
M2000_05
|
| Sample_geo_accession | GSM263072
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263072/suppl/GSM263072.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263073 | GPL1355 |
|
2627 Propiconazole 500ppm Liver
|
2627 Propiconazole 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
P500_01
|
| Sample_geo_accession | GSM263073
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263073/suppl/GSM263073.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263074 | GPL1355 |
|
2628 Propiconazole 500ppm Liver
|
2628 Propiconazole 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
P500_02
|
| Sample_geo_accession | GSM263074
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263074/suppl/GSM263074.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263075 | GPL1355 |
|
2630 Propiconazole 500ppm Liver
|
2630 Propiconazole 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
P500_03
Processed data not available because this sample was not included in the final analysis.
|
| Sample_geo_accession | GSM263075
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263075/suppl/GSM263075.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 0
| | |
|
GSM263076 | GPL1355 |
|
2633 Propiconazole 500ppm Liver
|
2633 Propiconazole 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
P500_04
Processed data not available because this sample was not included in the final analysis.
|
| Sample_geo_accession | GSM263076
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263076/suppl/GSM263076.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 0
| | |
|
GSM263077 | GPL1355 |
|
2636 Propiconazole 500ppm Liver
|
2636 Propiconazole 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
P500_05
|
| Sample_geo_accession | GSM263077
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263077/suppl/GSM263077.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263078 | GPL1355 |
|
2642 Propiconazole 2500ppm Liver
|
2642 Propiconazole 2500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
P2500_01
|
| Sample_geo_accession | GSM263078
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263078/suppl/GSM263078.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263079 | GPL1355 |
|
2643 Propiconazole 2500ppm Liver
|
2643 Propiconazole 2500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
P2500_02
|
| Sample_geo_accession | GSM263079
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263079/suppl/GSM263079.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263080 | GPL1355 |
|
2645 Propiconazole 2500ppm Liver
|
2645 Propiconazole 2500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
P2500_03
|
| Sample_geo_accession | GSM263080
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263080/suppl/GSM263080.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263081 | GPL1355 |
|
2654 Propiconazole 2500ppm Liver
|
2654 Propiconazole 2500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
P2500_04
|
| Sample_geo_accession | GSM263081
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263081/suppl/GSM263081.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263082 | GPL1355 |
|
2672 Triadimefon 500ppm Liver
|
2672 Triadimefon 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
T500_01
|
| Sample_geo_accession | GSM263082
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263082/suppl/GSM263082.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263083 | GPL1355 |
|
2673 Triadimefon 500ppm Liver
|
2673 Triadimefon 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
T500_02
|
| Sample_geo_accession | GSM263083
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263083/suppl/GSM263083.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263084 | GPL1355 |
|
2675 Triadimefon 500ppm Liver
|
2675 Triadimefon 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
T500_03
|
| Sample_geo_accession | GSM263084
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263084/suppl/GSM263084.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263085 | GPL1355 |
|
2678 Triadimefon 500ppm Liver
|
2678 Triadimefon 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
T500_04
|
| Sample_geo_accession | GSM263085
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263085/suppl/GSM263085.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263086 | GPL1355 |
|
2681 Triadimefon 500ppm Liver
|
2681 Triadimefon 500ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
T500_05
|
| Sample_geo_accession | GSM263086
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263086/suppl/GSM263086.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263087 | GPL1355 |
|
2696 Triadimefon 1800ppm Liver
|
2696 Triadimefon 1800ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
T1800_01
|
| Sample_geo_accession | GSM263087
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263087/suppl/GSM263087.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263088 | GPL1355 |
|
3153 Triadimefon 1800ppm Liver
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3153 Triadimefon 1800ppm Liver
|
liver
Wistar Han rat, PND92 adult
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T1800_02
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| Sample_geo_accession | GSM263088
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263088/suppl/GSM263088.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263089 | GPL1355 |
|
3154 Triadimefon 1800ppm Liver
|
3154 Triadimefon 1800ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
T1800_03
|
| Sample_geo_accession | GSM263089
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263089/suppl/GSM263089.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
| | |
|
GSM263090 | GPL1355 |
|
3170 Triadimefon 1800ppm Liver
|
3170 Triadimefon 1800ppm Liver
|
liver
Wistar Han rat, PND92 adult
|
T1800_04
|
| Sample_geo_accession | GSM263090
| | Sample_status | Public on Feb 07 2008
| | Sample_submission_date | Feb 06 2008
| | Sample_last_update_date | Feb 06 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Feeding study, exposure from gestation day 6 through to post natal day 92
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PND92 testis of individual Wistar Han IGS rats of the mid dose (M500, P500, T500 ppm) and high dose (M2000, P2500, T1800 ppm) treatment groups using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer’s protocol and subjected to quality control measures before application to microarrays. For quality control, RNA A260:A280 ratios were assessed via NanoDrop Fluorospectrometer (NanoDrop Technologies, Inc. Wilmington, DE). RNA absorbance readings with a range 1.8 – 2.1 were followed with DNase treatment, Total RNA Cleanup (Qiagen RNeasy), and then checked for RNA quality using the model 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Those samples with a ratio of 28S:18S rRNA >1.6 were accepted for subsequent use in DNA microarrays. RNA was stored at -80ºC until labeling for microarray hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms or purified total RNA from each liver of 3-7 individual rats per treatment group was hybridized to Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Briefly, after purified RNA passed quantity and quality assessment, double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization.
| | Sample_hyb_protocol | cRNA was combined with the hybridization cocktail, containing 3nM B2 control oligo, 10 mg/ml Herring Sperm DNA, 50 mg/ml BSA, 100% DMSO, and 2X hybridization buffer (NaCL 5M, MES hydrate Sigma Ultra, MES Sodium Salt, EDTA Disodium Salt 0.5M, 10% Tween-20). GeneChips were hybridized at 45ºC for 16 h. After hybridization the chip was washed and stained with fluorescent streptavidin-phycoerythrin, binding to biotin for detection.
| | Sample_scan_protocol | Signal amplification using anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody was used to bind biotin and provide an amplified fluor that emitted light when the chip is scanned with the GeneChip Scanner 3000.
| | Sample_data_processing | To minimize non-biological factors, e.g. total amount of target hybridized to each array, signal values for each hybridization were multiplied by a scaling factor (SF) to get a trimmed mean intensity equal to 500. Converted .cel files were loaded into JMP Genomics (SAS Inc., Cary, NC), Log2 transformed, normalized using interquartile normalization, and analyzed for significant changes in transcript levels through row-by-row modeling using one-way ANOVA. For initial exploratory analysis, principle component analysis (PCA) was applied using JMP Genomics. Comparisons were made between controls and each treatment group with statistical cut-offs applied at a p-value adjusted false discovery rate (FDR) of 25% for testis (p<0.000229), and an absolute difference of |1.2| or greater. Probe sets representing transcribed loci, unknown genes, and image clones were removed from the final list of each analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | David,,Dix
| | Sample_contact_email | dix.david@epa.gov
| | Sample_contact_phone | 919-541-2701
| | Sample_contact_department | ORD/NCCT
| | Sample_contact_institute | US EPA
| | Sample_contact_address | 109 TW Alexander Drive
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27711
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM263nnn/GSM263090/suppl/GSM263090.CEL.gz
| | Sample_series_id | GSE10411
| | Sample_data_row_count | 31099
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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