Search results for the GEO ID: GSE22366  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM556579 | GPL3921 |
|
Luciferase-rep1
|
Primary human erythroid progenitor cells expressing a luciferase control shRNA
|
construct: Luciferase Control shRNA
cell type: Primary human erythroid progenitor cells
|
Primary human erythroid progenitor cells expressing a luciferase control shRNA biological replicate 1
|
| Sample_geo_accession | GSM556579
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 15 2010
| | Sample_last_update_date | Jun 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.
| | Sample_growth_protocol_ch1 | Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex). Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol. Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec). Erythroid differentiation was induced in vitro in two steps.(1) For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3), 40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo). After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Benjamin,L,Ebert
| | Sample_contact_email | Benjamin_Ebert@dfci.harvard.edu
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556579/suppl/GSM556579_5500024037498121108439.F09.CEL.gz
| | Sample_series_id | GSE22366
| | Sample_series_id | GSE22369
| | Sample_data_row_count | 22277
| | |
|
GSM556580 | GPL3921 |
|
Luciferase-rep2
|
Primary human erythroid progenitor cells expressing a luciferase control shRNA
|
construct: Luciferase Control shRNA
cell type: Primary human erythroid progenitor cells
|
Primary human erythroid progenitor cells expressing a luciferase control shRNA biological replicate 2
|
| Sample_geo_accession | GSM556580
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 15 2010
| | Sample_last_update_date | Jun 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.
| | Sample_growth_protocol_ch1 | Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex). Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol. Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec). Erythroid differentiation was induced in vitro in two steps.(1) For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3), 40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo). After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Benjamin,L,Ebert
| | Sample_contact_email | Benjamin_Ebert@dfci.harvard.edu
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556580/suppl/GSM556580_5500024037498121108439.F11.CEL.gz
| | Sample_series_id | GSE22366
| | Sample_series_id | GSE22369
| | Sample_data_row_count | 22277
| | |
|
GSM556581 | GPL3921 |
|
Luciferase-rep3
|
Primary human erythroid progenitor cells expressing a luciferase control shRNA
|
construct: Luciferase Control shRNA
cell type: Primary human erythroid progenitor cells
|
Primary human erythroid progenitor cells expressing a luciferase control shRNA biological replicate 3
|
| Sample_geo_accession | GSM556581
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 15 2010
| | Sample_last_update_date | Jun 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.
| | Sample_growth_protocol_ch1 | Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex). Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol. Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec). Erythroid differentiation was induced in vitro in two steps.(1) For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3), 40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo). After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Benjamin,L,Ebert
| | Sample_contact_email | Benjamin_Ebert@dfci.harvard.edu
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556581/suppl/GSM556581_5500024037498121108439.E01.CEL.gz
| | Sample_series_id | GSE22366
| | Sample_series_id | GSE22369
| | Sample_data_row_count | 22277
| | |
|
GSM556582 | GPL3921 |
|
HDAC1_A3-rep1
|
Primary human erythroid progenitor cells expressing HDAC1 A3 shRNA
|
construct: HDAC1 A3 shRNA
cell type: Primary human erythroid progenitor cells
|
Primary human erythroid progenitor cells expressing HDAC1 A3 shRNA biological replicate 1
|
| Sample_geo_accession | GSM556582
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 15 2010
| | Sample_last_update_date | Jun 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.
| | Sample_growth_protocol_ch1 | Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex). Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol. Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec). Erythroid differentiation was induced in vitro in two steps.(1) For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3), 40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo). After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Benjamin,L,Ebert
| | Sample_contact_email | Benjamin_Ebert@dfci.harvard.edu
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556582/suppl/GSM556582_5500024037498121108439.E08.CEL.gz
| | Sample_series_id | GSE22366
| | Sample_series_id | GSE22369
| | Sample_data_row_count | 22277
| | |
|
GSM556583 | GPL3921 |
|
HDAC1_A3-rep3
|
Primary human erythroid progenitor cells expressing HDAC1 A3 shRNA
|
construct: HDAC1 A3 shRNA
cell type: Primary human erythroid progenitor cells
|
Primary human erythroid progenitor cells expressing HDAC1 A3 shRNA biological replicate 3
|
| Sample_geo_accession | GSM556583
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 15 2010
| | Sample_last_update_date | Jun 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.
| | Sample_growth_protocol_ch1 | Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex). Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol. Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec). Erythroid differentiation was induced in vitro in two steps.(1) For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3), 40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo). After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Benjamin,L,Ebert
| | Sample_contact_email | Benjamin_Ebert@dfci.harvard.edu
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556583/suppl/GSM556583_5500024037498121108439.F04.CEL.gz
| | Sample_series_id | GSE22366
| | Sample_series_id | GSE22369
| | Sample_data_row_count | 22277
| | |
|
GSM556584 | GPL3921 |
|
HDAC1_G10-rep1
|
Primary human erythroid progenitor cells expressing HDAC1 G10 shRNA
|
construct: HDAC1 G10 shRNA
cell type: Primary human erythroid progenitor cells
|
Primary human erythroid progenitor cells expressing HDAC1 G10 shRNA biological replicate 1
|
| Sample_geo_accession | GSM556584
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 15 2010
| | Sample_last_update_date | Jun 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.
| | Sample_growth_protocol_ch1 | Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex). Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol. Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec). Erythroid differentiation was induced in vitro in two steps.(1) For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3), 40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo). After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Benjamin,L,Ebert
| | Sample_contact_email | Benjamin_Ebert@dfci.harvard.edu
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556584/suppl/GSM556584_5500024037498121108439.F10.CEL.gz
| | Sample_series_id | GSE22366
| | Sample_series_id | GSE22369
| | Sample_data_row_count | 22277
| | |
|
GSM556585 | GPL3921 |
|
HDAC1_G10-rep2
|
Primary human erythroid progenitor cells expressing HDAC1 G10 shRNA
|
construct: HDAC1 G10 shRNA
cell type: Primary human erythroid progenitor cells
|
Primary human erythroid progenitor cells expressing HDAC1 G10 shRNA biological replicate 2
|
| Sample_geo_accession | GSM556585
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 15 2010
| | Sample_last_update_date | Jun 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.
| | Sample_growth_protocol_ch1 | Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex). Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol. Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec). Erythroid differentiation was induced in vitro in two steps.(1) For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3), 40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo). After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Benjamin,L,Ebert
| | Sample_contact_email | Benjamin_Ebert@dfci.harvard.edu
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556585/suppl/GSM556585_5500024037498121108439.F06.CEL.gz
| | Sample_series_id | GSE22366
| | Sample_series_id | GSE22369
| | Sample_data_row_count | 22277
| | |
|
GSM556586 | GPL3921 |
|
HDAC1_G10-rep3
|
Primary human erythroid progenitor cells expressing HDAC1 G10 shRNA
|
construct: HDAC1 G10 shRNA
cell type: Primary human erythroid progenitor cells
|
Primary human erythroid progenitor cells expressing HDAC1 G10 shRNA biological replicate 3
|
| Sample_geo_accession | GSM556586
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 15 2010
| | Sample_last_update_date | Jun 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.
| | Sample_growth_protocol_ch1 | Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex). Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol. Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec). Erythroid differentiation was induced in vitro in two steps.(1) For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3), 40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo). After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Benjamin,L,Ebert
| | Sample_contact_email | Benjamin_Ebert@dfci.harvard.edu
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556586/suppl/GSM556586_5500024037498121108439.E12.CEL.gz
| | Sample_series_id | GSE22366
| | Sample_series_id | GSE22369
| | Sample_data_row_count | 22277
| | |
|
GSM556587 | GPL3921 |
|
HDAC2_B10-rep1
|
Primary human erythroid progenitor cells expressing HDAC2 B10 shRNA
|
construct: HDAC2 B10 shRNA
cell type: Primary human erythroid progenitor cells
|
Primary human erythroid progenitor cells expressing HDAC2 B10 shRNA biological replicate 1
|
| Sample_geo_accession | GSM556587
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 15 2010
| | Sample_last_update_date | Jun 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.
| | Sample_growth_protocol_ch1 | Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex). Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol. Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec). Erythroid differentiation was induced in vitro in two steps.(1) For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3), 40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo). After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Benjamin,L,Ebert
| | Sample_contact_email | Benjamin_Ebert@dfci.harvard.edu
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556587/suppl/GSM556587_5500024037498121108439.E05.CEL.gz
| | Sample_series_id | GSE22366
| | Sample_series_id | GSE22369
| | Sample_data_row_count | 22277
| | |
|
GSM556588 | GPL3921 |
|
HDAC2_B10-rep2
|
Primary human erythroid progenitor cells expressing HDAC2 B10 shRNA
|
construct: HDAC2 B10 shRNA
cell type: Primary human erythroid progenitor cells
|
Primary human erythroid progenitor cells expressing HDAC2 B10 shRNA biological replicate 2
|
| Sample_geo_accession | GSM556588
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 15 2010
| | Sample_last_update_date | Jun 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.
| | Sample_growth_protocol_ch1 | Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex). Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol. Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec). Erythroid differentiation was induced in vitro in two steps.(1) For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3), 40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo). After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Benjamin,L,Ebert
| | Sample_contact_email | Benjamin_Ebert@dfci.harvard.edu
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556588/suppl/GSM556588_5500024037498121108439.E04.CEL.gz
| | Sample_series_id | GSE22366
| | Sample_series_id | GSE22369
| | Sample_data_row_count | 22277
| | |
|
GSM556589 | GPL3921 |
|
HDAC2_B10-rep3
|
Primary human erythroid progenitor cells expressing HDAC2 B10 shRNA
|
construct: HDAC2 B10 shRNA
cell type: Primary human erythroid progenitor cells
|
Primary human erythroid progenitor cells expressing HDAC2 B10 shRNA biological replicate 3
|
| Sample_geo_accession | GSM556589
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 15 2010
| | Sample_last_update_date | Jun 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.
| | Sample_growth_protocol_ch1 | Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex). Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol. Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec). Erythroid differentiation was induced in vitro in two steps.(1) For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3), 40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo). After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Benjamin,L,Ebert
| | Sample_contact_email | Benjamin_Ebert@dfci.harvard.edu
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556589/suppl/GSM556589_5500024037498121108439.F05.CEL.gz
| | Sample_series_id | GSE22366
| | Sample_series_id | GSE22369
| | Sample_data_row_count | 22277
| | |
|
GSM556590 | GPL3921 |
|
HDAC2_H6-rep1
|
Primary human erythroid progenitor cells expressing HDAC2 H6 shRNA
|
construct: HDAC2 H6 shRNA
cell type: Primary human erythroid progenitor cells
|
Primary human erythroid progenitor cells expressing HDAC2 H6 shRNA biological replicate 1
|
| Sample_geo_accession | GSM556590
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 15 2010
| | Sample_last_update_date | Jun 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.
| | Sample_growth_protocol_ch1 | Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex). Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol. Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec). Erythroid differentiation was induced in vitro in two steps.(1) For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3), 40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo). After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Benjamin,L,Ebert
| | Sample_contact_email | Benjamin_Ebert@dfci.harvard.edu
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556590/suppl/GSM556590_5500024037498121108439.E03.CEL.gz
| | Sample_series_id | GSE22366
| | Sample_series_id | GSE22369
| | Sample_data_row_count | 22277
| | |
|
GSM556591 | GPL3921 |
|
HDAC2_H6-rep2
|
Primary human erythroid progenitor cells expressing HDAC2 H6 shRNA
|
construct: HDAC2 H6 shRNA
cell type: Primary human erythroid progenitor cells
|
Primary human erythroid progenitor cells expressing HDAC2 H6 shRNA biological replicate 2
|
| Sample_geo_accession | GSM556591
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 15 2010
| | Sample_last_update_date | Jun 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.
| | Sample_growth_protocol_ch1 | Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex). Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol. Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec). Erythroid differentiation was induced in vitro in two steps.(1) For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3), 40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo). After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Benjamin,L,Ebert
| | Sample_contact_email | Benjamin_Ebert@dfci.harvard.edu
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556591/suppl/GSM556591_5500024037498121108439.E07.CEL.gz
| | Sample_series_id | GSE22366
| | Sample_series_id | GSE22369
| | Sample_data_row_count | 22277
| | |
|
GSM556592 | GPL3921 |
|
HDAC2_H6-rep3
|
Primary human erythroid progenitor cells expressing HDAC2 H6 shRNA
|
construct: HDAC2 H6 shRNA
cell type: Primary human erythroid progenitor cells
|
Primary human erythroid progenitor cells expressing HDAC2 H6 shRNA biological replicate 3
|
| Sample_geo_accession | GSM556592
| | Sample_status | Public on Jun 28 2010
| | Sample_submission_date | Jun 15 2010
| | Sample_last_update_date | Jun 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.
| | Sample_growth_protocol_ch1 | Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex). Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol. Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec). Erythroid differentiation was induced in vitro in two steps.(1) For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3), 40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo). After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Benjamin,L,Ebert
| | Sample_contact_email | Benjamin_Ebert@dfci.harvard.edu
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556592/suppl/GSM556592_5500024037498121108439.F01.CEL.gz
| | Sample_series_id | GSE22366
| | Sample_series_id | GSE22369
| | Sample_data_row_count | 22277
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