Search results for the GEO ID: GSE20952  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM523888 | GPL10226 |
|
Testis, Cmpd1, biological rep1
|
Rat testes, mock
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: mock
harmfulness: Negative control
labelblock: Label block 1
hybblock: Hybridization block 1
|
Gene expression data from rat testes isolated at 24 h after Mock (no chemical substance) treatment of rat.
|
| Sample_geo_accession | GSM523888
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523888/suppl/GSM523888.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523889 | GPL10226 |
|
Testis, Cmpd1, biological rep2
|
Rat testes, mock
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: mock
harmfulness: Negative control
labelblock: Label block 1
hybblock: Hybridization block 2
|
Gene expression data from rat testes isolated at 24 h after Mock (no chemical substance) treatment of rat.
|
| Sample_geo_accession | GSM523889
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523889/suppl/GSM523889.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523890 | GPL10226 |
|
Testis, Cmpd1, biological rep3
|
Rat testes, mock
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: mock
harmfulness: Negative control
labelblock: Label block 2
hybblock: Hybridization block 3
|
Gene expression data from rat testes isolated at 24 h after Mock (no chemical substance) treatment of rat.
|
| Sample_geo_accession | GSM523890
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523890/suppl/GSM523890.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523891 | GPL10226 |
|
Testis, Cmpd1, biological rep4
|
Rat testes, mock
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: mock
harmfulness: Negative control
labelblock: Label block 2
hybblock: Hybridization block 4
|
Gene expression data from rat testes isolated at 24 h after Mock (no chemical substance) treatment of rat.
|
| Sample_geo_accession | GSM523891
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523891/suppl/GSM523891.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523892 | GPL10226 |
|
Testis, Cmpd1, biological rep5
|
Rat testes, mock
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: mock
harmfulness: Negative control
labelblock: Label block 3
hybblock: Hybridization block 5
|
Gene expression data from rat testes isolated at 24 h after Mock (no chemical substance) treatment of rat.
|
| Sample_geo_accession | GSM523892
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523892/suppl/GSM523892.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523893 | GPL10226 |
|
Testis, Cmpd2, biological rep1
|
Rat testes, 2-ME
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: 2-ME
harmfulness: Positive control
labelblock: Label block 1
hybblock: Hybridization block 1
|
Gene expression data from testes isolated at 24 h after 2-ME treatment of rat.
|
| Sample_geo_accession | GSM523893
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523893/suppl/GSM523893.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523894 | GPL10226 |
|
Testis, Cmpd2, biological rep2
|
Rat testes, 2-ME
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: 2-ME
harmfulness: Positive control
labelblock: Label block 1
hybblock: Hybridization block 2
|
Gene expression data from testes isolated at 24 h after 2-ME treatment of rat.
|
| Sample_geo_accession | GSM523894
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523894/suppl/GSM523894.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523895 | GPL10226 |
|
Testis, Cmpd2, biological rep3
|
Rat testes, 2-ME
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: 2-ME
harmfulness: Positive control
labelblock: Label block 2
hybblock: Hybridization block 3
|
Gene expression data from testes isolated at 24 h after 2-ME treatment of rat.
|
| Sample_geo_accession | GSM523895
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523895/suppl/GSM523895.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523896 | GPL10226 |
|
Testis, Cmpd2, biological rep4
|
Rat testes, 2-ME
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: 2-ME
harmfulness: Positive control
labelblock: Label block 2
hybblock: Hybridization block 4
|
Gene expression data from testes isolated at 24 h after 2-ME treatment of rat.
|
| Sample_geo_accession | GSM523896
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523896/suppl/GSM523896.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523897 | GPL10226 |
|
Testis, Cmpd2, biological rep5
|
Rat testes, 2-ME
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: 2-ME
harmfulness: Positive control
labelblock: Label block 3
hybblock: Hybridization block 5
|
Gene expression data from testes isolated at 24 h after 2-ME treatment of rat.
|
| Sample_geo_accession | GSM523897
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523897/suppl/GSM523897.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523898 | GPL10226 |
|
Testis, Cmpd3, biological rep1
|
Rat testes, DEHP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DEHP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 1
|
Gene expression data from testes isolated at 24 h after DEHP treatment of rat.
|
| Sample_geo_accession | GSM523898
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523898/suppl/GSM523898.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523899 | GPL10226 |
|
Testis, Cmpd3, biological rep2
|
Rat testes, DEHP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DEHP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 2
|
Gene expression data from testes isolated at 24 h after DEHP treatment of rat.
|
| Sample_geo_accession | GSM523899
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523899/suppl/GSM523899.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523900 | GPL10226 |
|
Testis, Cmpd3, biological rep3
|
Rat testes, DEHP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DEHP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 3
|
Gene expression data from testes isolated at 24 h after DEHP treatment of rat.
|
| Sample_geo_accession | GSM523900
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523900/suppl/GSM523900.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523901 | GPL10226 |
|
Testis, Cmpd3, biological rep4
|
Rat testes, DEHP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DEHP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 4
|
Gene expression data from testes isolated at 24 h after DEHP treatment of rat.
|
| Sample_geo_accession | GSM523901
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523901/suppl/GSM523901.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523902 | GPL10226 |
|
Testis, Cmpd3, biological rep5
|
Rat testes, DEHP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DEHP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 3
hybblock: Hybridization block 5
|
Gene expression data from testes isolated at 24 h after DEHP treatment of rat.
|
| Sample_geo_accession | GSM523902
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523902/suppl/GSM523902.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523903 | GPL10226 |
|
Testis, Cmpd4, biological rep1
|
Rat testes, DHP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DHP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 1
|
Gene expression data from testes isolated at 24 h after DHP treatment of rat.
|
| Sample_geo_accession | GSM523903
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523903/suppl/GSM523903.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523904 | GPL10226 |
|
Testis, Cmpd4, biological rep2
|
Rat testes, DHP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DHP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 2
|
Gene expression data from testes isolated at 24 h after DHP treatment of rat.
|
| Sample_geo_accession | GSM523904
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523904/suppl/GSM523904.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523905 | GPL10226 |
|
Testis, Cmpd4, biological rep3
|
Rat testes, DHP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DHP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 3
|
Gene expression data from testes isolated at 24 h after DHP treatment of rat.
|
| Sample_geo_accession | GSM523905
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523905/suppl/GSM523905.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523906 | GPL10226 |
|
Testis, Cmpd4, biological rep4
|
Rat testes, DHP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DHP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 4
|
Gene expression data from testes isolated at 24 h after DHP treatment of rat.
|
| Sample_geo_accession | GSM523906
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523906/suppl/GSM523906.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523907 | GPL10226 |
|
Testis, Cmpd4, biological rep5
|
Rat testes, DHP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DHP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 3
hybblock: Hybridization block 5
|
Gene expression data from testes isolated at 24 h after DHP treatment of rat.
|
| Sample_geo_accession | GSM523907
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523907/suppl/GSM523907.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523908 | GPL10226 |
|
Testis, Cmpd5, biological rep1
|
Rat testes, DPeP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DPeP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 1
|
Gene expression data from testes isolated at 24 h after DPeP treatment of rat.
|
| Sample_geo_accession | GSM523908
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523908/suppl/GSM523908.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523909 | GPL10226 |
|
Testis, Cmpd5, biological rep2
|
Rat testes, DPeP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DPeP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 2
|
Gene expression data from testes isolated at 24 h after DPeP treatment of rat.
|
| Sample_geo_accession | GSM523909
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523909/suppl/GSM523909.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523910 | GPL10226 |
|
Testis, Cmpd5, biological rep3
|
Rat testes, DPeP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DPeP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 3
|
Gene expression data from testes isolated at 24 h after DPeP treatment of rat.
|
| Sample_geo_accession | GSM523910
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523910/suppl/GSM523910.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523911 | GPL10226 |
|
Testis, Cmpd5, biological rep4
|
Rat testes, DPeP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DPeP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 4
|
Gene expression data from testes isolated at 24 h after DPeP treatment of rat.
|
| Sample_geo_accession | GSM523911
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523911/suppl/GSM523911.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523912 | GPL10226 |
|
Testis, Cmpd6, biological rep1
|
Rat testes, DBP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DBP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 1
|
Gene expression data from testes isolated at 24 h after DBP treatment of rat.
|
| Sample_geo_accession | GSM523912
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523912/suppl/GSM523912.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523913 | GPL10226 |
|
Testis, Cmpd6, biological rep2
|
Rat testes, DBP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DBP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 2
|
Gene expression data from testes isolated at 24 h after DBP treatment of rat.
|
| Sample_geo_accession | GSM523913
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523913/suppl/GSM523913.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523914 | GPL10226 |
|
Testis, Cmpd6, biological rep3
|
Rat testes, DBP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DBP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 3
|
Gene expression data from testes isolated at 24 h after DBP treatment of rat.
|
| Sample_geo_accession | GSM523914
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523914/suppl/GSM523914.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523915 | GPL10226 |
|
Testis, Cmpd6, biological rep4
|
Rat testes, DBP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DBP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 4
|
Gene expression data from testes isolated at 24 h after DBP treatment of rat.
|
| Sample_geo_accession | GSM523915
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523915/suppl/GSM523915.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523916 | GPL10226 |
|
Testis, Cmpd6, biological rep5
|
Rat testes, DBP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DBP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 3
hybblock: Hybridization block 5
|
Gene expression data from testes isolated at 24 h after DBP treatment of rat.
|
| Sample_geo_accession | GSM523916
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523916/suppl/GSM523916.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523917 | GPL10226 |
|
Testis, Cmpd7, biological rep1
|
Rat testes, DPrP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DPrP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 1
|
Gene expression data from testes isolated at 24 h after DPrP treatment of rat.
|
| Sample_geo_accession | GSM523917
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523917/suppl/GSM523917.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523918 | GPL10226 |
|
Testis, Cmpd7, biological rep2
|
Rat testes, DPrP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DPrP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 2
|
Gene expression data from testes isolated at 24 h after DPrP treatment of rat.
|
| Sample_geo_accession | GSM523918
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523918/suppl/GSM523918.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523919 | GPL10226 |
|
Testis, Cmpd7, biological rep3
|
Rat testes, DPrP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DPrP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 3
|
Gene expression data from testes isolated at 24 h after DPrP treatment of rat.
|
| Sample_geo_accession | GSM523919
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523919/suppl/GSM523919.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523920 | GPL10226 |
|
Testis, Cmpd7, biological rep4
|
Rat testes, DPrP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DPrP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 4
|
Gene expression data from testes isolated at 24 h after DPrP treatment of rat.
|
| Sample_geo_accession | GSM523920
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523920/suppl/GSM523920.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523921 | GPL10226 |
|
Testis, Cmpd8, biological rep1
|
Rat testes, DOP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DOP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 1
|
Gene expression data from testes isolated at 24 h after DOP treatment of rat.
|
| Sample_geo_accession | GSM523921
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523921/suppl/GSM523921.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523922 | GPL10226 |
|
Testis, Cmpd8, biological rep2
|
Rat testes, DOP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DOP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 2
|
Gene expression data from testes isolated at 24 h after DOP treatment of rat.
|
| Sample_geo_accession | GSM523922
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523922/suppl/GSM523922.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523923 | GPL10226 |
|
Testis, Cmpd8, biological rep3
|
Rat testes, DOP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DOP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 3
|
Gene expression data from testes isolated at 24 h after DOP treatment of rat.
|
| Sample_geo_accession | GSM523923
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523923/suppl/GSM523923.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523924 | GPL10226 |
|
Testis, Cmpd8, biological rep4
|
Rat testes, DOP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DOP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 4
|
Gene expression data from testes isolated at 24 h after DOP treatment of rat.
|
| Sample_geo_accession | GSM523924
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523924/suppl/GSM523924.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523925 | GPL10226 |
|
Testis, Cmpd8, biological rep5
|
Rat testes, DOP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DOP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 3
hybblock: Hybridization block 5
|
Gene expression data from testes isolated at 24 h after DOP treatment of rat.
|
| Sample_geo_accession | GSM523925
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523925/suppl/GSM523925.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523926 | GPL10226 |
|
Testis, Cmpd9, biological rep1
|
Rat testes, DEP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DEP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 1
|
Gene expression data from testes isolated at 24 h after DEP treatment of rat.
|
| Sample_geo_accession | GSM523926
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523926/suppl/GSM523926.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523927 | GPL10226 |
|
Testis, Cmpd9, biological rep2
|
Rat testes, DEP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DEP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 2
|
Gene expression data from testes isolated at 24 h after DEP treatment of rat.
|
| Sample_geo_accession | GSM523927
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523927/suppl/GSM523927.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523928 | GPL10226 |
|
Testis, Cmpd9, biological rep3
|
Rat testes, DEP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DEP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 3
|
Gene expression data from testes isolated at 24 h after DEP treatment of rat.
|
| Sample_geo_accession | GSM523928
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523928/suppl/GSM523928.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523929 | GPL10226 |
|
Testis, Cmpd9, biological rep4
|
Rat testes, DEP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DEP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 4
|
Gene expression data from testes isolated at 24 h after DEP treatment of rat.
|
| Sample_geo_accession | GSM523929
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523929/suppl/GSM523929.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523930 | GPL10226 |
|
Testis, Cmpd9, biological rep5
|
Rat testes, DEP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DEP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 3
hybblock: Hybridization block 5
|
Gene expression data from testes isolated at 24 h after DEP treatment of rat.
|
| Sample_geo_accession | GSM523930
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523930/suppl/GSM523930.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523931 | GPL10226 |
|
Testis, Cmpd10, biological rep1
|
Rat testes, DMP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DMP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 1
|
Gene expression data from testes isolated at 24 h after DMP treatment of rat.
|
| Sample_geo_accession | GSM523931
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523931/suppl/GSM523931.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523932 | GPL10226 |
|
Testis, Cmpd10, biological rep2
|
Rat testes, DMP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DMP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 2
|
Gene expression data from testes isolated at 24 h after DMP treatment of rat.
|
| Sample_geo_accession | GSM523932
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523932/suppl/GSM523932.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523933 | GPL10226 |
|
Testis, Cmpd10, biological rep3
|
Rat testes, DMP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DMP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 3
|
Gene expression data from testes isolated at 24 h after DMP treatment of rat.
|
| Sample_geo_accession | GSM523933
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523933/suppl/GSM523933.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523934 | GPL10226 |
|
Testis, Cmpd10, biological rep4
|
Rat testes, DMP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DMP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 4
|
Gene expression data from testes isolated at 24 h after DMP treatment of rat.
|
| Sample_geo_accession | GSM523934
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523934/suppl/GSM523934.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523935 | GPL10226 |
|
Testis, Cmpd10, biological rep5
|
Rat testes, DMP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: DMP
harmfulness: Non-reprotoxic Phthalate
labelblock: Label block 3
hybblock: Hybridization block 5
|
Gene expression data from testes isolated at 24 h after DMP treatment of rat.
|
| Sample_geo_accession | GSM523935
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523935/suppl/GSM523935.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523936 | GPL10226 |
|
Testis, Cmpd11, biological rep1
|
Rat testes, MEHP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: MEHP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 1
hybblock: Hybridization block 2
|
Gene expression data from testes isolated at 24 h after MEHP treatment of rat.
|
| Sample_geo_accession | GSM523936
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523936/suppl/GSM523936.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523937 | GPL10226 |
|
Testis, Cmpd11, biological rep2
|
Rat testes, MEHP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: MEHP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 3
|
Gene expression data from testes isolated at 24 h after MEHP treatment of rat.
|
| Sample_geo_accession | GSM523937
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523937/suppl/GSM523937.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523938 | GPL10226 |
|
Testis, Cmpd11, biological rep3
|
Rat testes, MEHP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: MEHP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 2
hybblock: Hybridization block 4
|
Gene expression data from testes isolated at 24 h after MEHP treatment of rat.
|
| Sample_geo_accession | GSM523938
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523938/suppl/GSM523938.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
GSM523939 | GPL10226 |
|
Testis, Cmpd11, biological rep4
|
Rat testes, MEHP
|
tissue: testes
strain: HsdCpb:WU
gender: male
age: 10 weeks old
compound: MEHP
harmfulness: Reprotoxic Phthalate
labelblock: Label block 3
hybblock: Hybridization block 5
|
Gene expression data from testes isolated at 24 h after MEHP treatment of rat.
|
| Sample_geo_accession | GSM523939
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Mar 18 2010
| | Sample_last_update_date | Mar 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After three weeks of acclimation, rats were treated by oral gavage with 2,000 mg/kg bodyweight DMP, DEP, DPrP, DBP, DPeP, DHP, DOP, DEHP, MEHP, 2-ME or with the vehicle (corn oil). Each treatment group consisted of 5 rats. Rats were killed by CO2/O2 suffocation 24h after the treatment. Testes were isolated for RNA extraction.
| | Sample_growth_protocol_ch1 | Seven-week-old male HsdCpb:WU rats supplied by Harlan (Horst, the Netherlands) were housed in the animal facility in a climate controlled room with a 12h on/off light cycle. Tap water and standard diets were provided ad libitum. Animals were monitored daily for general health. Studies were approved and performed in accordance with the appropriate institutional and federal regulations.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from testis was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA), followed by a DNase treatment with RNase-Free DNase Set (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
| | Sample_data_processing | Probes were re-annotated according to de Leeuw et al., (2008), which resulted in 27,630 probe-sets including 49 controls instead of the 31,099 probe-sets containing 57 controls defined by Affymetrix. Probe-set expression values were calculated using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003).
| | Sample_platform_id | GPL10226
| | Sample_contact_name | Xiaolian,,Yuan
| | Sample_contact_email | x.yuan@uva.nl
| | Sample_contact_phone | +31 20 5257383
| | Sample_contact_fax | +31 20 5257762
| | Sample_contact_laboratory | Microarray department
| | Sample_contact_department | Microarray department
| | Sample_contact_institute | Amsterdam University
| | Sample_contact_address | Science Park 904
| | Sample_contact_city | Amsterdam
| | Sample_contact_state | North Holland
| | Sample_contact_zip/postal_code | 1098 XH
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | www.micro-array.nl
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM523nnn/GSM523939/suppl/GSM523939.CEL.gz
| | Sample_series_id | GSE20952
| | Sample_data_row_count | 27630
| | |
|
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