Search results for the GEO ID: GSE28050  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM693927 | GPL570 |
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HEK293T_BACH1-esiRNA_24h_rep1
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HEK 293T cells, BACH1 knockdown, 24h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: esiRNA (e)
genotype/variation: BACH1 knockdown
time: 24h
|
Sample name: BACH1_e_1_24
BACH1_e_1_200ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with esiRNA.
|
| Sample_geo_accession | GSM693927
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693927/suppl/GSM693927.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693927/suppl/GSM693927.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693928 | GPL570 |
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HEK293T_BACH1-esiRNA_24h_rep2
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HEK 293T cells, BACH1 knockdown, 24h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: esiRNA (e)
genotype/variation: BACH1 knockdown
time: 24h
|
Sample name: BACH1_e_2_24
BACH1_e_2_200ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with esiRNA.
|
| Sample_geo_accession | GSM693928
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693928/suppl/GSM693928.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693928/suppl/GSM693928.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
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GSM693929 | GPL570 |
|
HEK293T_BACH1-esiRNA_24h_rep3
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HEK 293T cells, BACH1 knockdown, 24h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: esiRNA (e)
genotype/variation: BACH1 knockdown
time: 24h
|
Sample name: BACH1_e_3_24
BACH1_e_3_200ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with esiRNA.
|
| Sample_geo_accession | GSM693929
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693929/suppl/GSM693929.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693929/suppl/GSM693929.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693930 | GPL570 |
|
HEK293T_BACH1-siRNA1_24h_rep1
|
HEK 293T cells, BACH1 knockdown, 24h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: siRNA1 SI00309876 (q)
genotype/variation: BACH1 knockdown
time: 24h
|
Sample name: BACH1_q_1_24
BACH1_q_1_300ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with Qiagen siRNA.
|
| Sample_geo_accession | GSM693930
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693930/suppl/GSM693930.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693930/suppl/GSM693930.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693931 | GPL570 |
|
HEK293T_BACH1-siRNA1_24h_rep2
|
HEK 293T cells, BACH1 knockdown, 24h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: siRNA1 SI00309876 (q)
genotype/variation: BACH1 knockdown
time: 24h
|
Sample name: BACH1_q_2_24
BACH1_q_2_300ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with Qiagen siRNA.
|
| Sample_geo_accession | GSM693931
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693931/suppl/GSM693931.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693931/suppl/GSM693931.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693932 | GPL570 |
|
HEK293T_BACH1-siRNA1_24h_rep3
|
HEK 293T cells, BACH1 knockdown, 24h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: siRNA1 SI00309876 (q)
genotype/variation: BACH1 knockdown
time: 24h
|
Sample name: BACH1_q_3_24
BACH1_q_3_300ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with Qiagen siRNA.
|
| Sample_geo_accession | GSM693932
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693932/suppl/GSM693932.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693932/suppl/GSM693932.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693933 | GPL570 |
|
HEK293T_BACH1-siRNA2_24h_rep1
|
HEK 293T cells, BACH1 knockdown, 24h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: siRNA2 HSS100910 (s)
genotype/variation: BACH1 knockdown
time: 24h
|
Sample name: BACH1_s_1_24
BACH1_s_1_300ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with Stealth siRNA.
|
| Sample_geo_accession | GSM693933
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693933/suppl/GSM693933.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693933/suppl/GSM693933.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693934 | GPL570 |
|
HEK293T_BACH1-siRNA2_24h_rep2
|
HEK 293T cells, BACH1 knockdown, 24h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: siRNA2 HSS100910 (s)
genotype/variation: BACH1 knockdown
time: 24h
|
Sample name: BACH1_s_2_24
BACH1_s_2_300ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with Stealth siRNA.
|
| Sample_geo_accession | GSM693934
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693934/suppl/GSM693934.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693934/suppl/GSM693934.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693935 | GPL570 |
|
HEK293T_BACH1-siRNA2_24h_rep3
|
HEK 293T cells, BACH1 knockdown, 24h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: siRNA2 HSS100910 (s)
genotype/variation: BACH1 knockdown
time: 24h
|
Sample name: BACH1_s_3_24
BACH1_s_3_300ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after knockdown of BACH1 with Stealth siRNA.
|
| Sample_geo_accession | GSM693935
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693935/suppl/GSM693935.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693935/suppl/GSM693935.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693936 | GPL570 |
|
HEK293T_mock-transfection_24h_rep1
|
HEK 293T cells, mock transfection, 24h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: mock (without siRNA)
genotype/variation: control
time: 24h
|
Sample name: BACH1_m_1_24
MOCK_m_1_0ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after mock transfection without siRNA.
|
| Sample_geo_accession | GSM693936
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693936/suppl/GSM693936.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693936/suppl/GSM693936.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693937 | GPL570 |
|
HEK293T_mock-transfection_24h_rep2
|
HEK 293T cells, mock transfection, 24h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: mock (without siRNA)
genotype/variation: control
time: 24h
|
Sample name: BACH1_m_2_24
MOCK_m_2_0ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after mock transfection without siRNA.
|
| Sample_geo_accession | GSM693937
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693937/suppl/GSM693937.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693937/suppl/GSM693937.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693938 | GPL570 |
|
HEK293T_mock-transfection_24h_rep3
|
HEK 293T cells, mock transfection, 24h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: mock (without siRNA)
genotype/variation: control
time: 24h
|
Sample name: BACH1_m_3_24
MOCK_m_3_0ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after mock transfection without siRNA.
|
| Sample_geo_accession | GSM693938
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693938/suppl/GSM693938.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693938/suppl/GSM693938.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693939 | GPL570 |
|
HEK293T_mock-transfection_24h_rep4
|
HEK 293T cells, mock transfection, 24h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: mock (without siRNA)
genotype/variation: control
time: 24h
|
Sample name: BACH1_m_4_24
MOCK_m_4_0ng_24h_293T.CEL
Gene expression data from HEK 293T cells 24h after mock transfection without siRNA.
|
| Sample_geo_accession | GSM693939
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693939/suppl/GSM693939.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693939/suppl/GSM693939.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693940 | GPL570 |
|
HEK293T_BACH1-esiRNA_72h_rep1
|
HEK 293T cells, BACH1 knockdown, 72h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: esiRNA (e)
genotype/variation: BACH1 knockdown
time: 72h
|
Sample name: BACH1_e_1_72
BACH1_e_1_200ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with esiRNA.
|
| Sample_geo_accession | GSM693940
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693940/suppl/GSM693940.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693940/suppl/GSM693940.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693941 | GPL570 |
|
HEK293T_BACH1-esiRNA_72h_rep2
|
HEK 293T cells, BACH1 knockdown, 72h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: esiRNA (e)
genotype/variation: BACH1 knockdown
time: 72h
|
Sample name: BACH1_e_2_72
BACH1_e_2_200ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with esiRNA.
|
| Sample_geo_accession | GSM693941
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693941/suppl/GSM693941.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693941/suppl/GSM693941.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693942 | GPL570 |
|
HEK293T_BACH1-esiRNA_72h_rep3
|
HEK 293T cells, BACH1 knockdown, 72h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: esiRNA (e)
genotype/variation: BACH1 knockdown
time: 72h
|
Sample name: BACH1_e_3_72
BACH1_e_3_200ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with esiRNA.
|
| Sample_geo_accession | GSM693942
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693942/suppl/GSM693942.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693942/suppl/GSM693942.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693943 | GPL570 |
|
HEK293T_BACH1-siRNA1_72h_rep1
|
HEK 293T cells, BACH1 knockdown, 72h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: siRNA1 SI00309876 (q)
genotype/variation: BACH1 knockdown
time: 72h
|
Sample name: BACH1_q_1_72
BACH1_q_1_300ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with Qiagen siRNA.
|
| Sample_geo_accession | GSM693943
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693943/suppl/GSM693943.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693943/suppl/GSM693943.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693944 | GPL570 |
|
HEK293T_BACH1-siRNA1_72h_rep2
|
HEK 293T cells, BACH1 knockdown, 72h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: siRNA1 SI00309876 (q)
genotype/variation: BACH1 knockdown
time: 72h
|
Sample name: BACH1_q_2_72
BACH1_q_2_300ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with Qiagen siRNA.
|
| Sample_geo_accession | GSM693944
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693944/suppl/GSM693944.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693944/suppl/GSM693944.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693945 | GPL570 |
|
HEK293T_BACH1-siRNA1_72h_rep3
|
HEK 293T cells, BACH1 knockdown, 72h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: siRNA1 SI00309876 (q)
genotype/variation: BACH1 knockdown
time: 72h
|
Sample name: BACH1_q_3_72
BACH1_q_3_300ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with Qiagen siRNA.
|
| Sample_geo_accession | GSM693945
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693945/suppl/GSM693945.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693945/suppl/GSM693945.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693946 | GPL570 |
|
HEK293T_BACH1-siRNA2_72h_rep1
|
HEK 293T cells, BACH1 knockdown, 72h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: siRNA2 HSS100910 (s)
genotype/variation: BACH1 knockdown
time: 72h
|
Sample name: BACH1_s_1_72
BACH1_s_1_300ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with Stealth siRNA.
|
| Sample_geo_accession | GSM693946
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693946/suppl/GSM693946.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693946/suppl/GSM693946.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693947 | GPL570 |
|
HEK293T_BACH1-siRNA2_72h_rep2
|
HEK 293T cells, BACH1 knockdown, 72h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: siRNA2 HSS100910 (s)
genotype/variation: BACH1 knockdown
time: 72h
|
Sample name: BACH1_s_2_72
BACH1_s_2_300ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with Stealth siRNA.
|
| Sample_geo_accession | GSM693947
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693947/suppl/GSM693947.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693947/suppl/GSM693947.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693948 | GPL570 |
|
HEK293T_BACH1-siRNA2_72h_rep3
|
HEK 293T cells, BACH1 knockdown, 72h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: siRNA2 HSS100910 (s)
genotype/variation: BACH1 knockdown
time: 72h
|
Sample name: BACH1_s_3_72
BACH1_s_3_300ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after knockdown of BACH1 with Stealth siRNA.
|
| Sample_geo_accession | GSM693948
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693948/suppl/GSM693948.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693948/suppl/GSM693948.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693949 | GPL570 |
|
HEK293T_mock-transfection_72h_rep1
|
HEK 293T cells, mock transfection, 72h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: mock (without siRNA)
genotype/variation: control
time: 72h
|
Sample name: BACH1_m_1_72
MOCK_m_1_0ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after mock transfection without siRNA.
|
| Sample_geo_accession | GSM693949
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693949/suppl/GSM693949.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693949/suppl/GSM693949.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693950 | GPL570 |
|
HEK293T_mock-transfection_72h_rep2
|
HEK 293T cells, mock transfection, 72h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: mock (without siRNA)
genotype/variation: control
time: 72h
|
Sample name: BACH1_m_2_72
MOCK_m_2_0ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after mock transfection without siRNA.
|
| Sample_geo_accession | GSM693950
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693950/suppl/GSM693950.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693950/suppl/GSM693950.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
GSM693951 | GPL570 |
|
HEK293T_mock-transfection_72h_rep3
|
HEK 293T cells, mock transfection, 72h
|
cell line: embryonic kidney cell line HEK 293T
sirna transfection: mock (without siRNA)
genotype/variation: control
time: 72h
|
Sample name: BACH1_m_3_72
MOCK_m_3_0ng_72h_293T.CEL
Gene expression data from HEK 293T cells 72h after mock transfection without siRNA.
|
| Sample_geo_accession | GSM693951
| | Sample_status | Public on May 13 2011
| | Sample_submission_date | Mar 21 2011
| | Sample_last_update_date | May 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For transfection, ca. 18,000 cells/cm² were seeded in 12-well plates together with esiRNA/HiPerFect complexes (200 ng esiRNA/6 µl HiPerFect per well) or siRNA/HiPerFect complexes (300 ng siRNA/6 µl HiPerFect per well) according to the HiPerFect fast-forward protocol (Qiagen). For the mock transfections, cells were treated with HiPerFect reagent only.
| | Sample_growth_protocol_ch1 | The human embryonic kidney cell line HEK 293T/17 (CRL-11268 from ATCC) was cultured in DMEM low glucose (Invitrogen) supplemented with 100 U/ml Penicillin/G-Streptomycin (Invitrogen) and 10% heat-inactivated FBS (Biochrom) at 37°C and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells at 24h and 72h post transfection using the RNeasy Mini Kit (Qiagen) following the manufacturers instructions. All RNA samples were treated on-column with RNase-free DNase I, quantified by UV spectrophotometry and controlled for integrity by gel electrophoresis and capillary electrophoresis using the Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Reverse transcription reactions were performed with random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). Complementary DNA for quantitative real-time PCR analysis was prepared from 1 µg of total RNA of each sample in 20 µl reactions and diluted to 12.5 ng/µl equivalent of total RNA. For hybridizations on microarrays, 1 µg of DNA-free total RNA from each sample was used to synthetize biotinylated cRNA using the GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagents kit from Affymetrix (P/N 900493).
| | Sample_hyb_protocol | Following integrity control using an Agilent 2100 bioanalyzer, the cRNA was fragmented and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 (HG-U133Plus2).
| | Sample_scan_protocol | The arrays were washed, stained, and scanned by the German Resource Center for Genome Research (RZPD) following recommended protocols from Affymetrix.
| | Sample_data_processing | The array probe intensities from the knock-down samples were normalized together with those from the control samples using GC-RMA from the R/Bioconductor package to give p-values from a Student’s t-test. The expression ratios for each probe were calculated as average of the ratios of the treated samples divided by the average of the ratios of the control samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hans-Jörg,,Warnatz
| | Sample_contact_email | warnatz@molgen.mpg.de
| | Sample_contact_laboratory | Gene Expression and Regulation
| | Sample_contact_department | Vertebrate Genomics
| | Sample_contact_institute | Max Planck Institute for Molecular Genetics
| | Sample_contact_address | Ihnestrasse 63-73
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 14195
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://chr21.molgen.mpg.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693951/suppl/GSM693951.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM693nnn/GSM693951/suppl/GSM693951.EXP.gz
| | Sample_series_id | GSE28050
| | Sample_series_id | GSE28053
| | Sample_data_row_count | 54675
| | |
|
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