Search results for the GEO ID: GSE7579  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM179757 | GPL8300 |
|
Erythroid progenitor cells. SCF+Epo cells 0hr 1.
|
Cord blood derived erythroid progenitors cultured in SCF+Epo.
|
Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells).
|
Drug treatment of human red blood precursor cells. Human red blood precursor cells (SCF/Epo cells), differentiated SCF/Epo cells and differentiated SCF/Epo cells in the presence of thyroid hormone (T3/T4), 9-cis retinoic acid (9cRA) or T3 plus 9cRA.
|
| Sample_geo_accession | GSM179757
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Apr 02 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l b-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M Dexamethasone (Dex). Growth factors were added every 2 days and cells were maintained at 2 million cells/ml cell density.
| | Sample_growth_protocol_ch1 | After 8 days of culture progenitor cells were induced to fully differentiate into erythrocytes in modified S13 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO Invitrogen Corporation, Paisley, UK) and 1U/ml Epo and 10 ng/ml insulin for 4 days (1 million cells/ml). Those cytokine/hormone were added every day and cells were maintained at 1 million cells/ml cell density.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the maufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 mg total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription employing double stranded cDNA as template and biotinylated UTP and CTP (Perkin Elmer/ENZO) as label was performed with the MEGAscript kit from Ambion according to the manufacturer's instructions.
| | Sample_label_protocol_ch1 | Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 ml MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 mg of labeled cRNA in 200 ml MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Affymetrix-HP GeneArray scanner. Scanned arrays were processed with Affymetrix MicroArray Suite 5.0. This includes automatic background and noise subtraction and calculation of “Average Difference” number values and ‘P’ (present, expressed) or ‘A’ (absent, not expressed) calls. Please refer to www.affymetrix.com for detailed information. Default Affymetrix settings and global scaling to 300 was used.
| | Sample_data_processing | Data were normalized using MAS5 algorithm (scaled to 300) and further analyzed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductor. Control probe sets were removed from global gene lists before normalization.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM179nnn/GSM179757/suppl/GSM179757.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM179nnn/GSM179757/suppl/GSM179757.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM179nnn/GSM179757/suppl/GSM179757.EXP.gz
| | Sample_series_id | GSE7579
| | Sample_data_row_count | 12625
| | |
|
GSM180044 | GPL8300 |
|
Erythroid progenitor cells. SCF+Epo cells 0hr 2.
|
Cord blood derived erythroid progenitors cultured in SCF+Epo
|
Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells)
|
Drug treatment of human red blood precursor cells. Human red blood precursor cells (SCF/Epo cells), differentiated SCF/Epo cells and differentiated SCF/Epo cells in the presence of thyroid hormone (T3/T4), 9-cis retinoic acid (9cRA) or T3 plus 9cRA.
|
| Sample_geo_accession | GSM180044
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Apr 03 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l _-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the maufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 _g total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription employing double stranded cDNA as template and biotinylated UTP and CTP (Perkin Elmer/ENZO) as label was performed with the MEGAscript kit from Ambion according to the manufacturer's instructions.
| | Sample_label_protocol_ch1 | Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 _l MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 _g of labeled cRNA in 200 _l MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Affymetrix-HP GeneArray scanner. Scanned arrays were processed with Affymetrix MicroArray Suite 5.0. This includes automatic background and noise subtraction and calculation of “Average Difference” number values and ‘P’ (present, expressed) or ‘A’ (absent, not expressed) calls. Please refer to www.affymetrix.com for detailed information. Default Affymetrix settings and global scaling to 300 was used.
| | Sample_data_processing | Data were normalized using MAS5 algorithm (scaled to 300) and further analysed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductur. Control probe sets were removed from global gene lists before normalization.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180044/suppl/GSM180044.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180044/suppl/GSM180044.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180044/suppl/GSM180044.EXP.gz
| | Sample_series_id | GSE7579
| | Sample_data_row_count | 12625
| | |
|
GSM180045 | GPL8300 |
|
Erythroid progenitor cells. Epo+insulin cells 8hr 1.
|
Cord blood derived erythroid progenitors. differentiation for 8hrs in Epo+insulin
|
Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) for 8 hrs.
|
Drug treatment of human red blood precursor cells. Human red blood precursor cells (SCF/Epo cells), differentiated SCF/Epo cells and differentiated SCF/Epo cells in the presence of thyroid hormone (T3/T4), 9-cis retinoic acid (9cRA) or T3 plus 9cRA.
|
| Sample_geo_accession | GSM180045
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Apr 03 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l _-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M. Growth factors were added every 2 days and cells were maintained at 2 million cells/ml cell density.
| | Sample_growth_protocol_ch1 | After 8 days of culture progenitor cells were induced to fully differentiate into erythrocytes in modified S13 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO Invitrogen Corporation, Paisley, UK) and 1U/ml Epo and 10 ng/ml insulin for 4 days (1 million cells/ml). Those cytokine/hormone were added every day and cells were maintained at 1 million cells/ml cell density.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the maufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 _g total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription employing double stranded cDNA as template and biotinylated UTP and CTP (Perkin Elmer/ENZO) as label was performed with the MEGAscript kit from Ambion according to the manufacturer's instructions.
| | Sample_label_protocol_ch1 | Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 _l MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 _g of labeled cRNA in 200 _l MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Affymetrix-HP GeneArray scanner. Scanned arrays were processed with Affymetrix MicroArray Suite 5.0. This includes automatic background and noise subtraction and calculation of “Average Difference” number values and ‘P’ (present, expressed) or ‘A’ (absent, not expressed) calls. Please refer to www.affymetrix.com for detailed information. Default Affymetrix settings and global scaling to 300 was used.
| | Sample_data_processing | Data were normalized using MAS5 algorithm (scaled to 300) and further analysed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductur. Control probe sets were removed from global gene lists before normalization.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180045/suppl/GSM180045.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180045/suppl/GSM180045.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180045/suppl/GSM180045.EXP.gz
| | Sample_series_id | GSE7579
| | Sample_data_row_count | 12625
| | |
|
GSM180046 | GPL8300 |
|
Erythroid progenitor cells. Epo+insulin cells 8hr 2.
|
Cord blood derived erythroid progenitors. differentiation for 8hrs in Epo+insulin
|
Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) for 8 hrs.
|
Drug treatment of human red blood precursor cells. Human red blood precursor cells (SCF/Epo cells), differentiated SCF/Epo cells and differentiated SCF/Epo cells in the presence of thyroid hormone (T3/T4), 9-cis retinoic acid (9cRA) or T3 plus 9cRA.
|
| Sample_geo_accession | GSM180046
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Apr 03 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l _-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M. Growth factors were added every 2 days and cells were maintained at 2 million cells/ml cell density.
| | Sample_growth_protocol_ch1 | After 8 days of culture progenitor cells were induced to fully differentiate into erythrocytes in modified S13 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO Invitrogen Corporation, Paisley, UK) and 1U/ml Epo and 10 ng/ml insulin for 4 days (1 million cells/ml). Those cytokine/hormone were added every day and cells were maintained at 1 million cells/ml cell density.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the maufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 _g total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription employing double stranded cDNA as template and biotinylated UTP and CTP (Perkin Elmer/ENZO) as label was performed with the MEGAscript kit from Ambion according to the manufacturer's instructions.
| | Sample_label_protocol_ch1 | Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 _l MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 _g of labeled cRNA in 200 _l MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Affymetrix-HP GeneArray scanner. Scanned arrays were processed with Affymetrix MicroArray Suite 5.0. This includes automatic background and noise subtraction and calculation of “Average Difference” number values and ‘P’ (present, expressed) or ‘A’ (absent, not expressed) calls. Please refer to www.affymetrix.com for detailed information. Default Affymetrix settings and global scaling to 300 was used.
| | Sample_data_processing | Data were normalized using MAS5 algorithm (scaled to 300) and further analysed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductur. Control probe sets were removed from global gene lists before normalization.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180046/suppl/GSM180046.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180046/suppl/GSM180046.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180046/suppl/GSM180046.EXP.gz
| | Sample_series_id | GSE7579
| | Sample_data_row_count | 12625
| | |
|
GSM180047 | GPL8300 |
|
Erythroid progenitor cells. Epo+insulin cells 24hr 1.
|
Cord blood derived erythroid progenitors. differentiation for 24 hrs in Epo+insulin
|
Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) for 24 hrs.
|
Drug treatment of human red blood precursor cells. Human red blood precursor cells (SCF/Epo cells), differentiated SCF/Epo cells and differentiated SCF/Epo cells in the presence of thyroid hormone (T3/T4), 9-cis retinoic acid (9cRA) or T3 plus 9cRA.
|
| Sample_geo_accession | GSM180047
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Apr 03 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l _-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M. Growth factors were added every 2 days and cells were maintained at 2 million cells/ml cell density.
| | Sample_growth_protocol_ch1 | After 8 days of culture progenitor cells were induced to fully differentiate into erythrocytes in modified S13 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO Invitrogen Corporation, Paisley, UK) and 1U/ml Epo and 10 ng/ml insulin for 4 days (1 million cells/ml). Those cytokine/hormone were added every day and cells were maintained at 1 million cells/ml cell density.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the maufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 _g total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription employing double stranded cDNA as template and biotinylated UTP and CTP (Perkin Elmer/ENZO) as label was performed with the MEGAscript kit from Ambion according to the manufacturer's instructions.
| | Sample_label_protocol_ch1 | Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 _l MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 _g of labeled cRNA in 200 _l MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Affymetrix-HP GeneArray scanner. Scanned arrays were processed with Affymetrix MicroArray Suite 5.0. This includes automatic background and noise subtraction and calculation of “Average Difference” number values and ‘P’ (present, expressed) or ‘A’ (absent, not expressed) calls. Please refer to www.affymetrix.com for detailed information. Default Affymetrix settings and global scaling to 300 was used.
| | Sample_data_processing | Data were normalized using MAS5 algorithm (scaled to 300) and further analysed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductur. Control probe sets were removed from global gene lists before normalization.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180047/suppl/GSM180047.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180047/suppl/GSM180047.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180047/suppl/GSM180047.EXP.gz
| | Sample_series_id | GSE7579
| | Sample_data_row_count | 12625
| | |
|
GSM180048 | GPL8300 |
|
Erythroid progenitor cells. Epo+insulin cells 24hr 2.
|
Cord blood derived erythroid progenitors. differentiation for 24 hrs in Epo+insulin
|
Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) for 24 hrs
|
Drug treatment of human red blood precursor cells. Human red blood precursor cells (SCF/Epo cells), differentiated SCF/Epo cells and differentiated SCF/Epo cells in the presence of thyroid hormone (T3/T4), 9-cis retinoic acid (9cRA) or T3 plus 9cRA.
|
| Sample_geo_accession | GSM180048
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Apr 03 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l _-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M. Growth factors were added every 2 days and cells were maintained at 2 million cells/ml cell density.
| | Sample_growth_protocol_ch1 | After 8 days of culture progenitor cells were induced to fully differentiate into erythrocytes in modified S13 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO Invitrogen Corporation, Paisley, UK) and 1U/ml Epo and 10 ng/ml insulin for 4 days (1 million cells/ml). Those cytokine/hormone were added every day and cells were maintained at 1 million cells/ml cell density.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the maufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 _g total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription employing double stranded cDNA as template and biotinylated UTP and CTP (Perkin Elmer/ENZO) as label was performed with the MEGAscript kit from Ambion according to the manufacturer's instructions.
| | Sample_label_protocol_ch1 | Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 _l MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 _g of labeled cRNA in 200 _l MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Affymetrix-HP GeneArray scanner. Scanned arrays were processed with Affymetrix MicroArray Suite 5.0. This includes automatic background and noise subtraction and calculation of “Average Difference” number values and ‘P’ (present, expressed) or ‘A’ (absent, not expressed) calls. Please refer to www.affymetrix.com for detailed information. Default Affymetrix settings and global scaling to 300 was used.
| | Sample_data_processing | Data were normalized using MAS5 algorithm (scaled to 300) and further analyzed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductor. Control probe sets were removed from global gene lists before normalization.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180048/suppl/GSM180048.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180048/suppl/GSM180048.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180048/suppl/GSM180048.EXP.gz
| | Sample_series_id | GSE7579
| | Sample_data_row_count | 12625
| | |
|
GSM180049 | GPL8300 |
|
Erythroid progenitor cells. Epo+insulin cells 48hr 1.
|
Cord blood derived erythroid progenitors. differentiation for 48 hrs in Epo+insulin
|
Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) for 48 hrs
|
Drug treatment of human red blood precursor cells. Human red blood precursor cells (SCF/Epo cells), differentiated SCF/Epo cells and differentiated SCF/Epo cells in the presence of thyroid hormone (T3/T4), 9-cis retinoic acid (9cRA) or T3 plus 9cRA.
|
| Sample_geo_accession | GSM180049
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Apr 03 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l _-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M. Growth factors were added every 2 days and cells were maintained at 2 million cells/ml cell density.
| | Sample_growth_protocol_ch1 | After 8 days of culture progenitor cells were induced to fully differentiate into erythrocytes in modified S13 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO Invitrogen Corporation, Paisley, UK) and 1U/ml Epo and 10 ng/ml insulin for 4 days (1 million cells/ml). Those cytokine/hormone were added every day and cells were maintained at 1 million cells/ml cell density.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the maufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 _g total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription employing double stranded cDNA as template and biotinylated UTP and CTP (Perkin Elmer/ENZO) as label was performed with the MEGAscript kit from Ambion according to the manufacturer's instructions.
| | Sample_label_protocol_ch1 | Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 _l MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 _g of labeled cRNA in 200 _l MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Affymetrix-HP GeneArray scanner. Scanned arrays were processed with Affymetrix MicroArray Suite 5.0. This includes automatic background and noise subtraction and calculation of “Average Difference” number values and ‘P’ (present, expressed) or ‘A’ (absent, not expressed) calls. Please refer to www.affymetrix.com for detailed information. Default Affymetrix settings and global scaling to 300 was used.
| | Sample_data_processing | Data were normalized using MAS5 algorithm (scaled to 300) and further analyzed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductor. Control probe sets were removed from global gene lists before normalization.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180049/suppl/GSM180049.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180049/suppl/GSM180049.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180049/suppl/GSM180049.EXP.gz
| | Sample_series_id | GSE7579
| | Sample_data_row_count | 12625
| | |
|
GSM180050 | GPL8300 |
|
Erythroid progenitor cells. Epo+insulin cells 48hr 2.
|
Cord blood derived erythroid progenitors. differentiation for 48 hrs in Epo+insulin
|
Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) for 48 hrs
|
Drug treatment of human red blood precursor cells. Human red blood precursor cells (SCF/Epo cells), differentiated SCF/Epo cells and differentiated SCF/Epo cells in the presence of thyroid hormone (T3/T4), 9-cis retinoic acid (9cRA) or T3 plus 9cRA.
|
| Sample_geo_accession | GSM180050
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Apr 03 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l _-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M. Growth factors were added every 2 days and cells were maintained at 2 million cells/ml cell density.
| | Sample_growth_protocol_ch1 | After 8 days of culture progenitor cells were induced to fully differentiate into erythrocytes in modified S13 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO Invitrogen Corporation, Paisley, UK) and 1U/ml Epo and 10 ng/ml insulin for 4 days (1 million cells/ml). Those cytokine/hormone were added every day and cells were maintained at 1 million cells/ml cell density.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the maufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 _g total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription employing double stranded cDNA as template and biotinylated UTP and CTP (Perkin Elmer/ENZO) as label was performed with the MEGAscript kit from Ambion according to the manufacturer's instructions.
| | Sample_label_protocol_ch1 | Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 _l MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 _g of labeled cRNA in 200 _l MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Affymetrix-HP GeneArray scanner. Scanned arrays were processed with Affymetrix MicroArray Suite 5.0. This includes automatic background and noise subtraction and calculation of “Average Difference” number values and ‘P’ (present, expressed) or ‘A’ (absent, not expressed) calls. Please refer to www.affymetrix.com for detailed information. Default Affymetrix settings and global scaling to 300 was used.
| | Sample_data_processing | Data were normalized using MAS5 algorithm (scaled to 300) and further analyzed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductor. Control probe sets were removed from global gene lists before normalization.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180050/suppl/GSM180050.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180050/suppl/GSM180050.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180050/suppl/GSM180050.EXP.gz
| | Sample_series_id | GSE7579
| | Sample_data_row_count | 12625
| | |
|
GSM180051 | GPL8300 |
|
Erythroid progenitor cells. Epo+insulin cells 8hr +T3 +9cRA 2.
|
Cord blood derived erythroid progenitors. differentiation for 8hrs in Epo+insulin +T3 +9cRA
|
Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) and T3, 9cRA or T3+9cRA
|
Drug treatment of human red blood precursor cells. Human red blood precursor cells (SCF/Epo cells), differentiated SCF/Epo cells and differentiated SCF/Epo cells in the presence of thyroid hormone (T3/T4), 9-cis retinoic acid (9cRA) or T3 plus 9cRA.
|
| Sample_geo_accession | GSM180051
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Apr 03 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Erythroid progenitors were differentiated with Epo and insulin and simultaneously treated with thyroid hormone T3 (1x10-7 M, Sigma) and retonic acid 9cRA (1x10-6M, Sigma) for 8 hrs
| | Sample_growth_protocol_ch1 | Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l _-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M. Growth factors were added every 2 days and cells were maintained at 2 million cells/ml cell density.
| | Sample_growth_protocol_ch1 | After 8 days of culture progenitor cells were induced to fully differentiate into erythrocytes in modified S13 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO Invitrogen Corporation, Paisley, UK) and 1U/ml Epo and 10 ng/ml insulin for 4 days (1 million cells/ml). Those cytokine/hormone were added every day and cells were maintained at 1 million cells/ml cell density.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the manufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 _g total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription employing double stranded cDNA as template and biotinylated UTP and CTP (Perkin Elmer/ENZO) as label was performed with the MEGAscript kit from Ambion according to the manufacturer's instructions.
| | Sample_label_protocol_ch1 | Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 _l MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 _g of labeled cRNA in 200 _l MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Affymetrix-HP GeneArray scanner. Scanned arrays were processed with Affymetrix MicroArray Suite 5.0. This includes automatic background and noise subtraction and calculation of “Average Difference” number values and ‘P’ (present, expressed) or ‘A’ (absent, not expressed) calls. Please refer to www.affymetrix.com for detailed information. Default Affymetrix settings and global scaling to 300 was used.
| | Sample_data_processing | Data were normalized using MAS5 algorithm (scaled to 300) and further analyzed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductor. Control probe sets were removed from global gene lists before normalization.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180051/suppl/GSM180051.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180051/suppl/GSM180051.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180051/suppl/GSM180051.EXP.gz
| | Sample_series_id | GSE7579
| | Sample_data_row_count | 12625
| | |
|
GSM180052 | GPL8300 |
|
Erythroid progenitor cells. Epo+insulin cells 24hr +T3 +9cRA 2.
|
Cord blood derived erythroid progenitors. differentiation for 24hrs in Epo+insulin +T3 +9cRA
|
Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) and T3, 9cRA or T3+9cRA for 24 hrs.
|
Drug treatment of human red blood precursor cells. Human red blood precursor cells (SCF/Epo cells), differentiated SCF/Epo cells and differentiated SCF/Epo cells in the presence of thyroid hormone (T3/T4), 9-cis retinoic acid (9cRA) or T3 plus 9cRA.
|
| Sample_geo_accession | GSM180052
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Apr 03 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Erythroid progenitors were differentiated with Epo and insulin and simultaneously treated with thyroid hormone T3 (1x10-7 M, Sigma) and retonic acid 9cRA (1x10-6M, Sigma) for 24 hrs
| | Sample_growth_protocol_ch1 | Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l _-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M. Growth factors were added every 2 days and cells were maintained at 2 million cells/ml cell density.
| | Sample_growth_protocol_ch1 | After 8 days of culture progenitor cells were induced to fully differentiate into erythrocytes in modified S13 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO Invitrogen Corporation, Paisley, UK) and 1U/ml Epo and 10 ng/ml insulin for 4 days (1 million cells/ml). Those cytokine/hormone were added every day and cells were maintained at 1 million cells/ml cell density.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the manufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 _g total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription employing double stranded cDNA as template and biotinylated UTP and CTP (Perkin Elmer/ENZO) as label was performed with the MEGAscript kit from Ambion according to the manufacturer's instructions.
| | Sample_label_protocol_ch1 | Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 _l MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 _g of labeled cRNA in 200 _l MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Affymetrix-HP GeneArray scanner. Scanned arrays were processed with Affymetrix MicroArray Suite 5.0. This includes automatic background and noise subtraction and calculation of “Average Difference” number values and ‘P’ (present, expressed) or ‘A’ (absent, not expressed) calls. Please refer to www.affymetrix.com for detailed information. Default Affymetrix settings and global scaling to 300 was used.
| | Sample_data_processing | Data were normalized using MAS5 algorithm (scaled to 300) and further analyzed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductor. Control probe sets were removed from global gene lists before normalization.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180052/suppl/GSM180052.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180052/suppl/GSM180052.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180052/suppl/GSM180052.EXP.gz
| | Sample_series_id | GSE7579
| | Sample_data_row_count | 12625
| | |
|
GSM180053 | GPL8300 |
|
Erythroid progenitor cells. Epo+insulin cells 48hr +T3 +9cRA 2.
|
Cord blood derived erythroid progenitors. differentiation for 48hrs in Epo+insulin +T3 +9cRA
|
Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) and T3, 9cRA or T3+9cRA for 48 hrs.
|
Drug treatment of human red blood precursor cells. Human red blood precursor cells (SCF/Epo cells), differentiated SCF/Epo cells and differentiated SCF/Epo cells in the presence of thyroid hormone (T3/T4), 9-cis retinoic acid (9cRA) or T3 plus 9cRA.
|
| Sample_geo_accession | GSM180053
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Apr 03 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Erythroid progenitors were differentiated with Epo and insulin and simultaneously treated with thyroid hormone T3 (1x10-7 M, Sigma) and retonic acid 9cRA (1x10-6M, Sigma) for 48 hrs
| | Sample_growth_protocol_ch1 | Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l _-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M. Growth factors were added every 2 days and cells were maintained at 2 million cells/ml cell density.
| | Sample_growth_protocol_ch1 | After 8 days of culture progenitor cells were induced to fully differentiate into erythrocytes in modified S13 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO Invitrogen Corporation, Paisley, UK) and 1U/ml Epo and 10 ng/ml insulin for 4 days (1 million cells/ml). Those cytokine/hormone were added every day and cells were maintained at 1 million cells/ml cell density.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the manufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 _g total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription employing double stranded cDNA as template and biotinylated UTP and CTP (Perkin Elmer/ENZO) as label was performed with the MEGAscript kit from Ambion according to the manufacturer's instructions.
| | Sample_label_protocol_ch1 | Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 _l MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 _g of labeled cRNA in 200 _l MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Affymetrix-HP GeneArray scanner. Scanned arrays were processed with Affymetrix MicroArray Suite 5.0. This includes automatic background and noise subtraction and calculation of “Average Difference” number values and ‘P’ (present, expressed) or ‘A’ (absent, not expressed) calls. Please refer to www.affymetrix.com for detailed information. Default Affymetrix settings and global scaling to 300 was used.
| | Sample_data_processing | Data were normalized using MAS5 algorithm (scaled to 300) and further analyzed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductor. Control probe sets were removed from global gene lists before normalization.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180053/suppl/GSM180053.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180053/suppl/GSM180053.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180053/suppl/GSM180053.EXP.gz
| | Sample_series_id | GSE7579
| | Sample_data_row_count | 12625
| | |
|
GSM180054 | GPL8300 |
|
Erythroid progenitor cells. Epo+insulin cells 8hr +9cRA 2.
|
Cord blood derived erythroid progenitors. differentiation for 8hrs in Epo+insulin +9cRA
|
Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) and T3, 9cRA or T3+9cRA for 8 hrs
|
Drug treatment of human red blood precursor cells. Human red blood precursor cells (SCF/Epo cells), differentiated SCF/Epo cells and differentiated SCF/Epo cells in the presence of thyroid hormone (T3/T4), 9-cis retinoic acid (9cRA) or T3 plus 9cRA.
|
| Sample_geo_accession | GSM180054
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Apr 03 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Erythroid progenitors were differentiated with Epo and insulin and simultaneously treated with retonic acid 9cRA (1x10-6M, Sigma) for 8 hrs
| | Sample_growth_protocol_ch1 | Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l _-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M. Growth factors were added every 2 days and cells were maintained at 2 million cells/ml cell density.
| | Sample_growth_protocol_ch1 | After 8 days of culture progenitor cells were induced to fully differentiate into erythrocytes in modified S13 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO Invitrogen Corporation, Paisley, UK) and 1U/ml Epo and 10 ng/ml insulin for 4 days (1 million cells/ml). Those cytokine/hormone were added every day and cells were maintained at 1 million cells/ml cell density.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the manufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 _g total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription employing double stranded cDNA as template and biotinylated UTP and CTP (Perkin Elmer/ENZO) as label was performed with the MEGAscript kit from Ambion according to the manufacturer's instructions.
| | Sample_label_protocol_ch1 | Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 _l MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 _g of labeled cRNA in 200 _l MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Affymetrix-HP GeneArray scanner. Scanned arrays were processed with Affymetrix MicroArray Suite 5.0. This includes automatic background and noise subtraction and calculation of “Average Difference” number values and ‘P’ (present, expressed) or ‘A’ (absent, not expressed) calls. Please refer to www.affymetrix.com for detailed information. Default Affymetrix settings and global scaling to 300 was used.
| | Sample_data_processing | Data were normalized using MAS5 algorithm (scaled to 300) and further analyzed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductor. Control probe sets were removed from global gene lists before normalization.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180054/suppl/GSM180054.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180054/suppl/GSM180054.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180054/suppl/GSM180054.EXP.gz
| | Sample_series_id | GSE7579
| | Sample_data_row_count | 12625
| | |
|
GSM180056 | GPL8300 |
|
Erythroid progenitor cells. Epo+insulin cells 8hr +T3 2.
|
Cord blood derived erythroid progenitors. differentiation for 8hrs in Epo+insulin +T3
|
Human umbilical cord blood was collected according to institutional guidelines after full term pregnancies. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation and MNC (2-3 million cells/ml) were cultured with SCF, Epo and dexamethasone (SCF/Epo cells) and differentiated into red blood cells with Epo and insulin (Epo/insulin cells) and T3, 9cRA or T3+9cRA for 8 hrs
|
Drug treatment of human red blood precursor cells. Human red blood precursor cells (SCF/Epo cells), differentiated SCF/Epo cells and differentiated SCF/Epo cells in the presence of thyroid hormone (T3/T4), 9-cis retinoic acid (9cRA) or T3 plus 9cRA.
|
| Sample_geo_accession | GSM180056
| | Sample_status | Public on Jul 31 2008
| | Sample_submission_date | Apr 03 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Erythroid progenitors were differentiated with Epo and insulin and simultaneously treated with thyroid hormone T3 (1x10-7 M, Sigma) for 8 hrs
| | Sample_growth_protocol_ch1 | Erythroid progenitor cells were obtained from mononuclear cells of human cord blood by employing a two-step amplification/differentiation protocol. Mononuclear cells (MNC) were recovered by Ficoll-Hypaque gradient centrifugation. MNC (2-3 million cells/ml) were cultured in culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) with 15% fetal calf serum (FCS; Roche Diagnostics, Mannheim, Germany), 1% deionized, delipidated, dialyzed bovine serum albumin (BSA, fraction V; Sigma, St Louis, MO), 15% distilled water, 1.9 mmol/l sodium bicarbonate, 0.1 mmol/l _-mercaptoethanol (Sigma), 0.128 mg/ml iron-saturated human transferrin (Sigma) and 100 U/ml penicillin and streptomycin (Invitrogen) with 100 ng/ml stem cell factor (SCF), 1U/ml Erythropoietin (Epo), 10-6M. Growth factors were added every 2 days and cells were maintained at 2 million cells/ml cell density.
| | Sample_growth_protocol_ch1 | After 8 days of culture progenitor cells were induced to fully differentiate into erythrocytes in modified S13 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO Invitrogen Corporation, Paisley, UK) and 1U/ml Epo and 10 ng/ml insulin for 4 days (1 million cells/ml). Those cytokine/hormone were added every day and cells were maintained at 1 million cells/ml cell density.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) using the manufacturer's buffers and protocols. An additional DNAse digestion with RNAse free DNAse (Qiagen) was performed. First and second strand cDNA synthesis were done from 7 _g total RNA with the SuperScript Choice system (Gibco BRL) and a T7-(dT)24 Primer (Biotez, Berlin, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription employing double stranded cDNA as template and biotinylated UTP and CTP (Perkin Elmer/ENZO) as label was performed with the MEGAscript kit from Ambion according to the manufacturer's instructions.
| | Sample_label_protocol_ch1 | Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 _l MES hybridization buffer for 10 minutes at 45˚C with rotation (60U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 _g of labeled cRNA in 200 _l MES hybridization buffer were applied to the array thereby leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Affymetrix-HP GeneArray scanner. Scanned arrays were processed with Affymetrix MicroArray Suite 5.0. This includes automatic background and noise subtraction and calculation of “Average Difference” number values and ‘P’ (present, expressed) or ‘A’ (absent, not expressed) calls. Please refer to www.affymetrix.com for detailed information. Default Affymetrix settings and global scaling to 300 was used.
| | Sample_data_processing | Data were normalized using MAS5 algorithm (scaled to 300) and further analyzed using GeneSpring (Agilent Technologies, Palo Alto, CA, USA) and BioConductor. Control probe sets were removed from global gene lists before normalization.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180056/suppl/GSM180056.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180056/suppl/GSM180056.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM180nnn/GSM180056/suppl/GSM180056.EXP.gz
| | Sample_series_id | GSE7579
| | Sample_data_row_count | 12625
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