Result

Search results for the GEO ID: GSE22367

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM556593

GPL3921

Untreated-rep1

Primary human erythroid progenitor cells

treatment: Untreated cell type: Primary human erythroid progenitor cells

Primary human erythroid progenitor cells replicate 1

Sample_geo_accession	GSM556593
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 left untreated or treated with 0.5uM SAHA.
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/GSM556593/suppl/GSM556593_5500024037498121108439.E06.CEL.gz
Sample_series_id	GSE22367
Sample_series_id	GSE22369
Sample_data_row_count	22277

GSM556594

GPL3921

Untreated-rep2

Primary human erythroid progenitor cells

treatment: Untreated cell type: Primary human erythroid progenitor cells

Primary human erythroid progenitor cells replicate 2

Sample_geo_accession	GSM556594
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 left untreated or treated with 0.5uM SAHA.
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/GSM556594/suppl/GSM556594_5500024037498121108439.E09.CEL.gz
Sample_series_id	GSE22367
Sample_series_id	GSE22369
Sample_data_row_count	22277

GSM556595

GPL3921

Untreated-rep3

Primary human erythroid progenitor cells

treatment: Untreated cell type: Primary human erythroid progenitor cells

Primary human erythroid progenitor cells replicate 3

Sample_geo_accession	GSM556595
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 left untreated or treated with 0.5uM SAHA.
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/GSM556595/suppl/GSM556595_5500024037498121108439.F03.CEL.gz
Sample_series_id	GSE22367
Sample_series_id	GSE22369
Sample_data_row_count	22277

GSM556596

GPL3921

SAHA-rep1

Primary human erythroid progenitor cells treated with 0.5uM SAHA

treatment: 0.5uM SAHA cell type: Primary human erythroid progenitor cells

Primary human erythroid progenitor cells treated with 0.5uM SAHA replicate 1

Sample_geo_accession	GSM556596
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 left untreated or treated with 0.5uM SAHA.
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/GSM556596/suppl/GSM556596_5500024037498121108439.F12.CEL.gz
Sample_series_id	GSE22367
Sample_series_id	GSE22369
Sample_data_row_count	22277

GSM556597

GPL3921

SAHA-rep2

Primary human erythroid progenitor cells treated with 0.5uM SAHA

treatment: 0.5uM SAHA cell type: Primary human erythroid progenitor cells

Primary human erythroid progenitor cells treated with 0.5uM SAHA replicate 2

Sample_geo_accession	GSM556597
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 left untreated or treated with 0.5uM SAHA.
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/GSM556597/suppl/GSM556597_5500024037498121108439.F02.CEL.gz
Sample_series_id	GSE22367
Sample_series_id	GSE22369
Sample_data_row_count	22277

GSM556598

GPL3921

SAHA-rep3

Primary human erythroid progenitor cells treated with 0.5uM SAHA

treatment: 0.5uM SAHA cell type: Primary human erythroid progenitor cells

Primary human erythroid progenitor cells treated with 0.5uM SAHA replicate 3

Sample_geo_accession	GSM556598
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 left untreated or treated with 0.5uM SAHA.
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/GSM556598/suppl/GSM556598_5500024037498121108439.E11.CEL.gz
Sample_series_id	GSE22367
Sample_series_id	GSE22369
Sample_data_row_count	22277

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