Search results for the GEO ID: GSE9079  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM230132 | GPL339 |
|
Sca+Lin-PBM_MIG_rep1
|
Primary bone marrow
|
Donors of primary bone marrow cells were male mice (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) older than 12-weeks.
|
Retroviral vector only coding for GFP (MIG) were introduced as negative control in primary bone marrow cells.
|
| Sample_geo_accession | GSM230132
| | Sample_status | Public on Oct 01 2007
| | Sample_submission_date | Sep 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | British Columbia Cancer Research Centre animal facility
| | Sample_treatment_protocol_ch1 | Mice were treated with 5-fluorouracil 4 days prior to bone marrow collection.
| | Sample_growth_protocol_ch1 | Bone marrow cells were harvested from mice treated 4 days previously with 150 mg/kg 5-fluorouracil (Faulding, Underdaler, Australia) and prestimulated for 48 hours in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (IL-3), and 100 ng/mL murine stem cell factor (mSF) (StemCell Technologies, Vancouver, BC, Canada). Cells were infected by co-cultivation with irradiated (4000 cGy x-ray) GP+E86 viral producer cells with the addition of 5 µg/mL protamine sulfate (Sigma, Oakville, ON, Canada). Loosely adherent and nonadherent cells were harvested from the co-cultures after 2 days and were cultured for 24 hours in the same medium without protamine sulfate.
| | Sample_growth_protocol_ch1 | The single cell suspensions collected were blocked for 10 min on ice with 5 μg/ml anti mouse CD16/CD32 (Fc Block, BD Pharmingen) in Phosphate Buffered Saline (STI) + 2% Fetal Bovine Serum (PF). Cells were washed once with PF and then incubated on ice for 20 min with the primary mAb. Cells were then washed once, incubated with the secondary antibody if needed, washed again, and then analysed by flow cytometry using a FACSCalibur™ flow cytometer and CELLQuest™ software (BD Pharmingen). GFP+ Sca-1+Lin- cells were sorted using a FACSVantage™ (BD Pharmingen). Purity > 90% were confirmed by re-analysis of sorted cells. The forward versus side scatter profile was used to gate on viable cells and an unstained sample was used to determine appropriate gating for expression. Monoclonal antibodies (mAbs) were all purchased from PharMingen (San Diego, CA) (phycoerythrin [PE]–labeled Gr-1, B220, Ter-119, CD4, CD5 and CD8).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Sorted cells were lyzed in Trizol™ (Invitrogen) and total RNA was extracted according to the manufacturer instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA from each sample were double linear amplified with the ENZO BioArray High Yield RNA Transcript Labeling kit and the GeneChip Eukaryotic Small Sample Target Labeling Assay, Version II protocol (Affymetrix, Santa Clara, CA) to produce target for hybridization to Affymetrix MOE430 according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Protocol EukGE-WS2v4
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A1 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle 2
| | Sample_hyb_protocol | Wash B Recovery Mixes 0
| | Sample_hyb_protocol | Wash B Temperature (C) 50
| | Sample_hyb_protocol | Number of Wash B Cycles 4
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 25
| | Sample_hyb_protocol | First Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A2 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle 4
| | Sample_hyb_protocol | Second Stain Time (seconds) 600
| | Sample_hyb_protocol | Third Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 30
| | Sample_hyb_protocol | Number of Wash A3 Cycles 15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle 4
| | Sample_hyb_protocol | Holding Temperature (C) 25
| | Sample_hyb_protocol | Station 1
| | Sample_hyb_protocol | Module 1
| | Sample_scan_protocol | Pixel Size 3
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date
| | Sample_scan_protocol | Scanner ID
| | Sample_scan_protocol | Number of Scans 2
| | Sample_scan_protocol | Scanner Type HP
| | Sample_data_processing | MAS 5.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lars,,Palmqvist
| | Sample_contact_email | lars.palmqvist@clinchem.gu.se
| | Sample_contact_department | Clinical Chemistry and Transfusion Medicine
| | Sample_contact_institute | Institute of Biomedicine
| | Sample_contact_address | Sahlgrenska University Hospital
| | Sample_contact_city | Gothenburg
| | Sample_contact_zip/postal_code | 41345
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230132/suppl/GSM230132.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230132/suppl/GSM230132.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230132/suppl/GSM230132.EXP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230132/suppl/GSM230132.RPT.gz
| | Sample_series_id | GSE9079
| | Sample_data_row_count | 22690
| | |
|
GSM230133 | GPL339 |
|
Sca+Lin-PBM_NA10_rep1
|
Primary bone marrow
|
Donors of primary bone marrow cells were male mice (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) older than 12-weeks.
|
Retroviral vector coding for NUP98-HOXA10 (NA10) were introduced in primary bone marrow cells.
|
| Sample_geo_accession | GSM230133
| | Sample_status | Public on Oct 01 2007
| | Sample_submission_date | Sep 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | British Columbia Cancer Research Centre animal facility
| | Sample_treatment_protocol_ch1 | Mice were treated with 5-fluorouracil 4 days prior to bone marrow collection.
| | Sample_growth_protocol_ch1 | Bone marrow cells were harvested from mice treated 4 days previously with 150 mg/kg 5-fluorouracil (Faulding, Underdaler, Australia) and prestimulated for 48 hours in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (IL-3), and 100 ng/mL murine stem cell factor (mSF) (StemCell Technologies, Vancouver, BC, Canada). Cells were infected by co-cultivation with irradiated (4000 cGy x-ray) GP+E86 viral producer cells with the addition of 5 µg/mL protamine sulfate (Sigma, Oakville, ON, Canada). Loosely adherent and nonadherent cells were harvested from the co-cultures after 2 days and were cultured for 24 hours in the same medium without protamine sulfate.
| | Sample_growth_protocol_ch1 | The single cell suspensions collected were blocked for 10 min on ice with 5 μg/ml anti mouse CD16/CD32 (Fc Block, BD Pharmingen) in Phosphate Buffered Saline (STI) + 2% Fetal Bovine Serum (PF). Cells were washed once with PF and then incubated on ice for 20 min with the primary mAb. Cells were then washed once, incubated with the secondary antibody if needed, washed again, and then analysed by flow cytometry using a FACSCalibur™ flow cytometer and CELLQuest™ software (BD Pharmingen). GFP+ Sca-1+Lin- cells were sorted using a FACSVantage™ (BD Pharmingen). Purity > 90% were confirmed by re-analysis of sorted cells. The forward versus side scatter profile was used to gate on viable cells and an unstained sample was used to determine appropriate gating for expression. Monoclonal antibodies (mAbs) were all purchased from PharMingen (San Diego, CA) (phycoerythrin [PE]–labeled Gr-1, B220, Ter-119, CD4, CD5 and CD8).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Sorted cells were lyzed in Trizol™ (Invitrogen) and total RNA was extracted according to the manufacturer instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA from each sample were double linear amplified with the ENZO BioArray High Yield RNA Transcript Labeling kit and the GeneChip Eukaryotic Small Sample Target Labeling Assay, Version II protocol (Affymetrix, Santa Clara, CA) to produce target for hybridization to Affymetrix MOE430 according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Protocol EukGE-WS2v4
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A1 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle 2
| | Sample_hyb_protocol | Wash B Recovery Mixes 0
| | Sample_hyb_protocol | Wash B Temperature (C) 50
| | Sample_hyb_protocol | Number of Wash B Cycles 4
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 25
| | Sample_hyb_protocol | First Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A2 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle 4
| | Sample_hyb_protocol | Second Stain Time (seconds) 600
| | Sample_hyb_protocol | Third Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 30
| | Sample_hyb_protocol | Number of Wash A3 Cycles 15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle 4
| | Sample_hyb_protocol | Holding Temperature (C) 25
| | Sample_hyb_protocol | Station 1
| | Sample_hyb_protocol | Module 1
| | Sample_scan_protocol | Pixel Size 3
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date
| | Sample_scan_protocol | Scanner ID
| | Sample_scan_protocol | Number of Scans 2
| | Sample_scan_protocol | Scanner Type HP
| | Sample_data_processing | MAS 5.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lars,,Palmqvist
| | Sample_contact_email | lars.palmqvist@clinchem.gu.se
| | Sample_contact_department | Clinical Chemistry and Transfusion Medicine
| | Sample_contact_institute | Institute of Biomedicine
| | Sample_contact_address | Sahlgrenska University Hospital
| | Sample_contact_city | Gothenburg
| | Sample_contact_zip/postal_code | 41345
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230133/suppl/GSM230133.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230133/suppl/GSM230133.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230133/suppl/GSM230133.EXP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230133/suppl/GSM230133.RPT.gz
| | Sample_series_id | GSE9079
| | Sample_data_row_count | 22690
| | |
|
GSM230134 | GPL339 |
|
Sca+Lin-PBM_ND13_rep1
|
Primary bone marrow
|
Donors of primary bone marrow cells were male mice (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) older than 12-weeks.
|
Retroviral vector coding for NUP98-HOXD13 (ND13) were introduced in primary bone marrow cells.
|
| Sample_geo_accession | GSM230134
| | Sample_status | Public on Oct 01 2007
| | Sample_submission_date | Sep 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | British Columbia Cancer Research Centre animal facility
| | Sample_treatment_protocol_ch1 | Mice were treated with 5-fluorouracil 4 days prior to bone marrow collection.
| | Sample_growth_protocol_ch1 | Bone marrow cells were harvested from mice treated 4 days previously with 150 mg/kg 5-fluorouracil (Faulding, Underdaler, Australia) and prestimulated for 48 hours in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (IL-3), and 100 ng/mL murine stem cell factor (mSF) (StemCell Technologies, Vancouver, BC, Canada). Cells were infected by co-cultivation with irradiated (4000 cGy x-ray) GP+E86 viral producer cells with the addition of 5 µg/mL protamine sulfate (Sigma, Oakville, ON, Canada). Loosely adherent and nonadherent cells were harvested from the co-cultures after 2 days and were cultured for 24 hours in the same medium without protamine sulfate.
| | Sample_growth_protocol_ch1 | The single cell suspensions collected were blocked for 10 min on ice with 5 μg/ml anti mouse CD16/CD32 (Fc Block, BD Pharmingen) in Phosphate Buffered Saline (STI) + 2% Fetal Bovine Serum (PF). Cells were washed once with PF and then incubated on ice for 20 min with the primary mAb. Cells were then washed once, incubated with the secondary antibody if needed, washed again, and then analysed by flow cytometry using a FACSCalibur™ flow cytometer and CELLQuest™ software (BD Pharmingen). GFP+ Sca-1+Lin- cells were sorted using a FACSVantage™ (BD Pharmingen). Purity > 90% were confirmed by re-analysis of sorted cells. The forward versus side scatter profile was used to gate on viable cells and an unstained sample was used to determine appropriate gating for expression. Monoclonal antibodies (mAbs) were all purchased from PharMingen (San Diego, CA) (phycoerythrin [PE]–labeled Gr-1, B220, Ter-119, CD4, CD5 and CD8).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Sorted cells were lyzed in Trizol™ (Invitrogen) and total RNA was extracted according to the manufacturer instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA from each sample were double linear amplified with the ENZO BioArray High Yield RNA Transcript Labeling kit and the GeneChip Eukaryotic Small Sample Target Labeling Assay, Version II protocol (Affymetrix, Santa Clara, CA) to produce target for hybridization to Affymetrix MOE430 according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Protocol EukGE-WS2v4
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A1 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle 2
| | Sample_hyb_protocol | Wash B Recovery Mixes 0
| | Sample_hyb_protocol | Wash B Temperature (C) 50
| | Sample_hyb_protocol | Number of Wash B Cycles 4
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 25
| | Sample_hyb_protocol | First Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A2 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle 4
| | Sample_hyb_protocol | Second Stain Time (seconds) 600
| | Sample_hyb_protocol | Third Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 30
| | Sample_hyb_protocol | Number of Wash A3 Cycles 15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle 4
| | Sample_hyb_protocol | Holding Temperature (C) 25
| | Sample_hyb_protocol | Station 1
| | Sample_hyb_protocol | Module 1
| | Sample_scan_protocol | Pixel Size 3
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date
| | Sample_scan_protocol | Scanner ID
| | Sample_scan_protocol | Number of Scans 2
| | Sample_scan_protocol | Scanner Type HP
| | Sample_data_processing | MAS 5.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lars,,Palmqvist
| | Sample_contact_email | lars.palmqvist@clinchem.gu.se
| | Sample_contact_department | Clinical Chemistry and Transfusion Medicine
| | Sample_contact_institute | Institute of Biomedicine
| | Sample_contact_address | Sahlgrenska University Hospital
| | Sample_contact_city | Gothenburg
| | Sample_contact_zip/postal_code | 41345
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230134/suppl/GSM230134.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230134/suppl/GSM230134.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230134/suppl/GSM230134.RPT.gz
| | Sample_series_id | GSE9079
| | Sample_data_row_count | 22690
| | |
|
GSM230135 | GPL339 |
|
Sca+Lin-PBM_ND13N51S_rep1
|
Primary bone marrow
|
Donors of primary bone marrow cells were male mice (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) older than 12-weeks.
|
Retroviral vector coding for NUP98-HOXD13 with a mutation (N51S) were introduced in primary bone marrow cells.
|
| Sample_geo_accession | GSM230135
| | Sample_status | Public on Oct 01 2007
| | Sample_submission_date | Sep 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | British Columbia Cancer Research Centre animal facility
| | Sample_treatment_protocol_ch1 | Mice were treated with 5-fluorouracil 4 days prior to bone marrow collection.
| | Sample_growth_protocol_ch1 | Bone marrow cells were harvested from mice treated 4 days previously with 150 mg/kg 5-fluorouracil (Faulding, Underdaler, Australia) and prestimulated for 48 hours in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (IL-3), and 100 ng/mL murine stem cell factor (mSF) (StemCell Technologies, Vancouver, BC, Canada). Cells were infected by co-cultivation with irradiated (4000 cGy x-ray) GP+E86 viral producer cells with the addition of 5 µg/mL protamine sulfate (Sigma, Oakville, ON, Canada). Loosely adherent and nonadherent cells were harvested from the co-cultures after 2 days and were cultured for 24 hours in the same medium without protamine sulfate.
| | Sample_growth_protocol_ch1 | The single cell suspensions collected were blocked for 10 min on ice with 5 μg/ml anti mouse CD16/CD32 (Fc Block, BD Pharmingen) in Phosphate Buffered Saline (STI) + 2% Fetal Bovine Serum (PF). Cells were washed once with PF and then incubated on ice for 20 min with the primary mAb. Cells were then washed once, incubated with the secondary antibody if needed, washed again, and then analysed by flow cytometry using a FACSCalibur™ flow cytometer and CELLQuest™ software (BD Pharmingen). GFP+ Sca-1+Lin- cells were sorted using a FACSVantage™ (BD Pharmingen). Purity > 90% were confirmed by re-analysis of sorted cells. The forward versus side scatter profile was used to gate on viable cells and an unstained sample was used to determine appropriate gating for expression. Monoclonal antibodies (mAbs) were all purchased from PharMingen (San Diego, CA) (phycoerythrin [PE]–labeled Gr-1, B220, Ter-119, CD4, CD5 and CD8).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Sorted cells were lyzed in Trizol™ (Invitrogen) and total RNA was extracted according to the manufacturer instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA from each sample were double linear amplified with the ENZO BioArray High Yield RNA Transcript Labeling kit and the GeneChip Eukaryotic Small Sample Target Labeling Assay, Version II protocol (Affymetrix, Santa Clara, CA) to produce target for hybridization to Affymetrix MOE430 according to the manufacturer’s instructions and performed at the Genome Science Centre, BC Cancer Agency, Vancouver, Canada.
| | Sample_hyb_protocol | Protocol EukGE-WS2v4
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A1 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle 2
| | Sample_hyb_protocol | Wash B Recovery Mixes 0
| | Sample_hyb_protocol | Wash B Temperature (C) 50
| | Sample_hyb_protocol | Number of Wash B Cycles 4
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 25
| | Sample_hyb_protocol | First Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A2 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle 4
| | Sample_hyb_protocol | Second Stain Time (seconds) 600
| | Sample_hyb_protocol | Third Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 30
| | Sample_hyb_protocol | Number of Wash A3 Cycles 15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle 4
| | Sample_hyb_protocol | Holding Temperature (C) 25
| | Sample_hyb_protocol | Station 1
| | Sample_hyb_protocol | Module 1
| | Sample_scan_protocol | Pixel Size 3
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date
| | Sample_scan_protocol | Scanner ID
| | Sample_scan_protocol | Number of Scans 2
| | Sample_scan_protocol | Scanner Type HP
| | Sample_data_processing | MAS 5.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lars,,Palmqvist
| | Sample_contact_email | lars.palmqvist@clinchem.gu.se
| | Sample_contact_department | Clinical Chemistry and Transfusion Medicine
| | Sample_contact_institute | Institute of Biomedicine
| | Sample_contact_address | Sahlgrenska University Hospital
| | Sample_contact_city | Gothenburg
| | Sample_contact_zip/postal_code | 41345
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230135/suppl/GSM230135.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230135/suppl/GSM230135.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230135/suppl/GSM230135.RPT.gz
| | Sample_series_id | GSE9079
| | Sample_data_row_count | 22690
| | |
|
GSM230136 | GPL339 |
|
Sca+Lin-PBM_MIG_rep2
|
Primary bone marrow
|
Donors of primary bone marrow cells were male mice (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) older than 12-weeks.
|
Retroviral vector only coding for GFP (MIG) were introduced as negative control in primary bone marrow cells.
|
| Sample_geo_accession | GSM230136
| | Sample_status | Public on Oct 01 2007
| | Sample_submission_date | Sep 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | British Columbia Cancer Research Centre animal facility
| | Sample_treatment_protocol_ch1 | Mice were treated with 5-fluorouracil 4 days prior to bone marrow collection.
| | Sample_growth_protocol_ch1 | Bone marrow cells were harvested from mice treated 4 days previously with 150 mg/kg 5-fluorouracil (Faulding, Underdaler, Australia) and prestimulated for 48 hours in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (IL-3), and 100 ng/mL murine stem cell factor (mSF) (StemCell Technologies, Vancouver, BC, Canada). Cells were infected by co-cultivation with irradiated (4000 cGy x-ray) GP+E86 viral producer cells with the addition of 5 µg/mL protamine sulfate (Sigma, Oakville, ON, Canada). Loosely adherent and nonadherent cells were harvested from the co-cultures after 2 days and were cultured for 24 hours in the same medium without protamine sulfate.
| | Sample_growth_protocol_ch1 | The single cell suspensions collected were blocked for 10 min on ice with 5 μg/ml anti mouse CD16/CD32 (Fc Block, BD Pharmingen) in Phosphate Buffered Saline (STI) + 2% Fetal Bovine Serum (PF). Cells were washed once with PF and then incubated on ice for 20 min with the primary mAb. Cells were then washed once, incubated with the secondary antibody if needed, washed again, and then analysed by flow cytometry using a FACSCalibur™ flow cytometer and CELLQuest™ software (BD Pharmingen). GFP+ Sca-1+Lin- cells were sorted using a FACSVantage™ (BD Pharmingen). Purity > 90% were confirmed by re-analysis of sorted cells. The forward versus side scatter profile was used to gate on viable cells and an unstained sample was used to determine appropriate gating for expression. Monoclonal antibodies (mAbs) were all purchased from PharMingen (San Diego, CA) (phycoerythrin [PE]–labeled Gr-1, B220, Ter-119, CD4, CD5 and CD8).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Sorted cells were lyzed in Trizol™ (Invitrogen) and total RNA was extracted according to the manufacturer instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA from each sample were double linear amplified with the ENZO BioArray High Yield RNA Transcript Labeling kit and the GeneChip Eukaryotic Small Sample Target Labeling Assay, Version II protocol (Affymetrix, Santa Clara, CA) to produce target for hybridization to Affymetrix MOE430 according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Protocol EukGE-WS2v4
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A1 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle 2
| | Sample_hyb_protocol | Wash B Recovery Mixes 0
| | Sample_hyb_protocol | Wash B Temperature (C) 50
| | Sample_hyb_protocol | Number of Wash B Cycles 4
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 25
| | Sample_hyb_protocol | First Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A2 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle 4
| | Sample_hyb_protocol | Second Stain Time (seconds) 600
| | Sample_hyb_protocol | Third Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 30
| | Sample_hyb_protocol | Number of Wash A3 Cycles 15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle 4
| | Sample_hyb_protocol | Holding Temperature (C) 25
| | Sample_hyb_protocol | Station 1
| | Sample_hyb_protocol | Module 1
| | Sample_scan_protocol | Pixel Size 3
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date
| | Sample_scan_protocol | Scanner ID
| | Sample_scan_protocol | Number of Scans 2
| | Sample_scan_protocol | Scanner Type HP
| | Sample_data_processing | MAS 5.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lars,,Palmqvist
| | Sample_contact_email | lars.palmqvist@clinchem.gu.se
| | Sample_contact_department | Clinical Chemistry and Transfusion Medicine
| | Sample_contact_institute | Institute of Biomedicine
| | Sample_contact_address | Sahlgrenska University Hospital
| | Sample_contact_city | Gothenburg
| | Sample_contact_zip/postal_code | 41345
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230136/suppl/GSM230136.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230136/suppl/GSM230136.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230136/suppl/GSM230136.RPT.gz
| | Sample_series_id | GSE9079
| | Sample_data_row_count | 22690
| | |
|
GSM230137 | GPL339 |
|
Sca+Lin-PBM_NA10_rep2
|
Primary bone marrow
|
Donors of primary bone marrow cells were male mice (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) older than 12-weeks.
|
Retroviral vector coding for NUP98-HOXA10 (NA10) were introduced in primary bone marrow cells.
|
| Sample_geo_accession | GSM230137
| | Sample_status | Public on Oct 01 2007
| | Sample_submission_date | Sep 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | British Columbia Cancer Research Centre animal facility
| | Sample_treatment_protocol_ch1 | Mice were treated with 5-fluorouracil 4 days prior to bone marrow collection.
| | Sample_growth_protocol_ch1 | Bone marrow cells were harvested from mice treated 4 days previously with 150 mg/kg 5-fluorouracil (Faulding, Underdaler, Australia) and prestimulated for 48 hours in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (IL-3), and 100 ng/mL murine stem cell factor (mSF) (StemCell Technologies, Vancouver, BC, Canada). Cells were infected by co-cultivation with irradiated (4000 cGy x-ray) GP+E86 viral producer cells with the addition of 5 µg/mL protamine sulfate (Sigma, Oakville, ON, Canada). Loosely adherent and nonadherent cells were harvested from the co-cultures after 2 days and were cultured for 24 hours in the same medium without protamine sulfate.
| | Sample_growth_protocol_ch1 | The single cell suspensions collected were blocked for 10 min on ice with 5 μg/ml anti mouse CD16/CD32 (Fc Block, BD Pharmingen) in Phosphate Buffered Saline (STI) + 2% Fetal Bovine Serum (PF). Cells were washed once with PF and then incubated on ice for 20 min with the primary mAb. Cells were then washed once, incubated with the secondary antibody if needed, washed again, and then analysed by flow cytometry using a FACSCalibur™ flow cytometer and CELLQuest™ software (BD Pharmingen). GFP+ Sca-1+Lin- cells were sorted using a FACSVantage™ (BD Pharmingen). Purity > 90% were confirmed by re-analysis of sorted cells. The forward versus side scatter profile was used to gate on viable cells and an unstained sample was used to determine appropriate gating for expression. Monoclonal antibodies (mAbs) were all purchased from PharMingen (San Diego, CA) (phycoerythrin [PE]–labeled Gr-1, B220, Ter-119, CD4, CD5 and CD8).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Sorted cells were lyzed in Trizol™ (Invitrogen) and total RNA was extracted according to the manufacturer instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA from each sample were double linear amplified with the ENZO BioArray High Yield RNA Transcript Labeling kit and the GeneChip Eukaryotic Small Sample Target Labeling Assay, Version II protocol (Affymetrix, Santa Clara, CA) to produce target for hybridization to Affymetrix MOE430 according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Protocol EukGE-WS2v4
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A1 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle 2
| | Sample_hyb_protocol | Wash B Recovery Mixes 0
| | Sample_hyb_protocol | Wash B Temperature (C) 50
| | Sample_hyb_protocol | Number of Wash B Cycles 4
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 25
| | Sample_hyb_protocol | First Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A2 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle 4
| | Sample_hyb_protocol | Second Stain Time (seconds) 600
| | Sample_hyb_protocol | Third Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 30
| | Sample_hyb_protocol | Number of Wash A3 Cycles 15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle 4
| | Sample_hyb_protocol | Holding Temperature (C) 25
| | Sample_hyb_protocol | Station 1
| | Sample_hyb_protocol | Module 1
| | Sample_scan_protocol | Pixel Size 3
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date
| | Sample_scan_protocol | Scanner ID
| | Sample_scan_protocol | Number of Scans 2
| | Sample_scan_protocol | Scanner Type HP
| | Sample_data_processing | MAS 5.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lars,,Palmqvist
| | Sample_contact_email | lars.palmqvist@clinchem.gu.se
| | Sample_contact_department | Clinical Chemistry and Transfusion Medicine
| | Sample_contact_institute | Institute of Biomedicine
| | Sample_contact_address | Sahlgrenska University Hospital
| | Sample_contact_city | Gothenburg
| | Sample_contact_zip/postal_code | 41345
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230137/suppl/GSM230137.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230137/suppl/GSM230137.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230137/suppl/GSM230137.RPT.gz
| | Sample_series_id | GSE9079
| | Sample_data_row_count | 22690
| | |
|
GSM230138 | GPL339 |
|
Sca+Lin-PBM_ND13_rep2
|
Primary bone marrow
|
Donors of primary bone marrow cells were male mice (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) older than 12-weeks.
|
Retroviral vector coding for NUP98-HOXD13 (ND13) were introduced in primary bone marrow cells.
|
| Sample_geo_accession | GSM230138
| | Sample_status | Public on Oct 01 2007
| | Sample_submission_date | Sep 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | British Columbia Cancer Research Centre animal facility
| | Sample_treatment_protocol_ch1 | Mice were treated with 5-fluorouracil 4 days prior to bone marrow collection.
| | Sample_growth_protocol_ch1 | Bone marrow cells were harvested from mice treated 4 days previously with 150 mg/kg 5-fluorouracil (Faulding, Underdaler, Australia) and prestimulated for 48 hours in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (IL-3), and 100 ng/mL murine stem cell factor (mSF) (StemCell Technologies, Vancouver, BC, Canada). Cells were infected by co-cultivation with irradiated (4000 cGy x-ray) GP+E86 viral producer cells with the addition of 5 µg/mL protamine sulfate (Sigma, Oakville, ON, Canada). Loosely adherent and nonadherent cells were harvested from the co-cultures after 2 days and were cultured for 24 hours in the same medium without protamine sulfate.
| | Sample_growth_protocol_ch1 | The single cell suspensions collected were blocked for 10 min on ice with 5 μg/ml anti mouse CD16/CD32 (Fc Block, BD Pharmingen) in Phosphate Buffered Saline (STI) + 2% Fetal Bovine Serum (PF). Cells were washed once with PF and then incubated on ice for 20 min with the primary mAb. Cells were then washed once, incubated with the secondary antibody if needed, washed again, and then analysed by flow cytometry using a FACSCalibur™ flow cytometer and CELLQuest™ software (BD Pharmingen). GFP+ Sca-1+Lin- cells were sorted using a FACSVantage™ (BD Pharmingen). Purity > 90% were confirmed by re-analysis of sorted cells. The forward versus side scatter profile was used to gate on viable cells and an unstained sample was used to determine appropriate gating for expression. Monoclonal antibodies (mAbs) were all purchased from PharMingen (San Diego, CA) (phycoerythrin [PE]–labeled Gr-1, B220, Ter-119, CD4, CD5 and CD8).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Sorted cells were lyzed in Trizol™ (Invitrogen) and total RNA was extracted according to the manufacturer instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA from each sample were double linear amplified with the ENZO BioArray High Yield RNA Transcript Labeling kit and the GeneChip Eukaryotic Small Sample Target Labeling Assay, Version II protocol (Affymetrix, Santa Clara, CA) to produce target for hybridization to Affymetrix MOE430 according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Protocol EukGE-WS2v4
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A1 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle 2
| | Sample_hyb_protocol | Wash B Recovery Mixes 0
| | Sample_hyb_protocol | Wash B Temperature (C) 50
| | Sample_hyb_protocol | Number of Wash B Cycles 4
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 25
| | Sample_hyb_protocol | First Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A2 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle 4
| | Sample_hyb_protocol | Second Stain Time (seconds) 600
| | Sample_hyb_protocol | Third Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 30
| | Sample_hyb_protocol | Number of Wash A3 Cycles 15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle 4
| | Sample_hyb_protocol | Holding Temperature (C) 25
| | Sample_hyb_protocol | Station 1
| | Sample_hyb_protocol | Module 1
| | Sample_scan_protocol | Pixel Size 3
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date
| | Sample_scan_protocol | Scanner ID
| | Sample_scan_protocol | Number of Scans 2
| | Sample_scan_protocol | Scanner Type HP
| | Sample_data_processing | MAS 5.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lars,,Palmqvist
| | Sample_contact_email | lars.palmqvist@clinchem.gu.se
| | Sample_contact_department | Clinical Chemistry and Transfusion Medicine
| | Sample_contact_institute | Institute of Biomedicine
| | Sample_contact_address | Sahlgrenska University Hospital
| | Sample_contact_city | Gothenburg
| | Sample_contact_zip/postal_code | 41345
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230138/suppl/GSM230138.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230138/suppl/GSM230138.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230138/suppl/GSM230138.RPT.gz
| | Sample_series_id | GSE9079
| | Sample_data_row_count | 22690
| | |
|
GSM230139 | GPL339 |
|
Sca+Lin-PBM_ND13N51S_rep2
|
Primary bone marrow
|
Donors of primary bone marrow cells were male mice (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) older than 12-weeks.
|
Retroviral vector coding for NUP98-HOXD13 with a mutation (N51S) were introduced in primary bone marrow cells.
|
| Sample_geo_accession | GSM230139
| | Sample_status | Public on Oct 01 2007
| | Sample_submission_date | Sep 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | British Columbia Cancer Research Centre animal facility
| | Sample_treatment_protocol_ch1 | Mice were treated with 5-fluorouracil 4 days prior to bone marrow collection.
| | Sample_growth_protocol_ch1 | Bone marrow cells were harvested from mice treated 4 days previously with 150 mg/kg 5-fluorouracil (Faulding, Underdaler, Australia) and prestimulated for 48 hours in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (IL-3), and 100 ng/mL murine stem cell factor (mSF) (StemCell Technologies, Vancouver, BC, Canada). Cells were infected by co-cultivation with irradiated (4000 cGy x-ray) GP+E86 viral producer cells with the addition of 5 µg/mL protamine sulfate (Sigma, Oakville, ON, Canada). Loosely adherent and nonadherent cells were harvested from the co-cultures after 2 days and were cultured for 24 hours in the same medium without protamine sulfate.
| | Sample_growth_protocol_ch1 | The single cell suspensions collected were blocked for 10 min on ice with 5 μg/ml anti mouse CD16/CD32 (Fc Block, BD Pharmingen) in Phosphate Buffered Saline (STI) + 2% Fetal Bovine Serum (PF). Cells were washed once with PF and then incubated on ice for 20 min with the primary mAb. Cells were then washed once, incubated with the secondary antibody if needed, washed again, and then analysed by flow cytometry using a FACSCalibur™ flow cytometer and CELLQuest™ software (BD Pharmingen). GFP+ Sca-1+Lin- cells were sorted using a FACSVantage™ (BD Pharmingen). Purity > 90% were confirmed by re-analysis of sorted cells. The forward versus side scatter profile was used to gate on viable cells and an unstained sample was used to determine appropriate gating for expression. Monoclonal antibodies (mAbs) were all purchased from PharMingen (San Diego, CA) (phycoerythrin [PE]–labeled Gr-1, B220, Ter-119, CD4, CD5 and CD8).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Sorted cells were lyzed in Trizol™ (Invitrogen) and total RNA was extracted according to the manufacturer instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA from each sample were double linear amplified with the ENZO BioArray High Yield RNA Transcript Labeling kit and the GeneChip Eukaryotic Small Sample Target Labeling Assay, Version II protocol (Affymetrix, Santa Clara, CA) to produce target for hybridization to Affymetrix MOE430 according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Protocol EukGE-WS2v4
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A1 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle 2
| | Sample_hyb_protocol | Wash B Recovery Mixes 0
| | Sample_hyb_protocol | Wash B Temperature (C) 50
| | Sample_hyb_protocol | Number of Wash B Cycles 4
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 25
| | Sample_hyb_protocol | First Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A2 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle 4
| | Sample_hyb_protocol | Second Stain Time (seconds) 600
| | Sample_hyb_protocol | Third Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 30
| | Sample_hyb_protocol | Number of Wash A3 Cycles 15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle 4
| | Sample_hyb_protocol | Holding Temperature (C) 25
| | Sample_hyb_protocol | Station 1
| | Sample_hyb_protocol | Module 1
| | Sample_scan_protocol | Pixel Size 3
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date
| | Sample_scan_protocol | Scanner ID
| | Sample_scan_protocol | Number of Scans 2
| | Sample_scan_protocol | Scanner Type HP
| | Sample_data_processing | MAS 5.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lars,,Palmqvist
| | Sample_contact_email | lars.palmqvist@clinchem.gu.se
| | Sample_contact_department | Clinical Chemistry and Transfusion Medicine
| | Sample_contact_institute | Institute of Biomedicine
| | Sample_contact_address | Sahlgrenska University Hospital
| | Sample_contact_city | Gothenburg
| | Sample_contact_zip/postal_code | 41345
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230139/suppl/GSM230139.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230139/suppl/GSM230139.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230139/suppl/GSM230139.RPT.gz
| | Sample_series_id | GSE9079
| | Sample_data_row_count | 22690
| | |
|
GSM230140 | GPL339 |
|
Sca+Lin-PBM_MIG_rep3
|
Primary bone marrow
|
Donors of primary bone marrow cells were male mice (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) older than 12-weeks.
|
Retroviral vector only coding for GFP (MIG) were introduced as negative control in primary bone marrow cells.
|
| Sample_geo_accession | GSM230140
| | Sample_status | Public on Oct 01 2007
| | Sample_submission_date | Sep 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | British Columbia Cancer Research Centre animal facility
| | Sample_treatment_protocol_ch1 | Mice were treated with 5-fluorouracil 4 days prior to bone marrow collection.
| | Sample_growth_protocol_ch1 | Bone marrow cells were harvested from mice treated 4 days previously with 150 mg/kg 5-fluorouracil (Faulding, Underdaler, Australia) and prestimulated for 48 hours in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (IL-3), and 100 ng/mL murine stem cell factor (mSF) (StemCell Technologies, Vancouver, BC, Canada). Cells were infected by co-cultivation with irradiated (4000 cGy x-ray) GP+E86 viral producer cells with the addition of 5 µg/mL protamine sulfate (Sigma, Oakville, ON, Canada). Loosely adherent and nonadherent cells were harvested from the co-cultures after 2 days and were cultured for 24 hours in the same medium without protamine sulfate.
| | Sample_growth_protocol_ch1 | The single cell suspensions collected were blocked for 10 min on ice with 5 μg/ml anti mouse CD16/CD32 (Fc Block, BD Pharmingen) in Phosphate Buffered Saline (STI) + 2% Fetal Bovine Serum (PF). Cells were washed once with PF and then incubated on ice for 20 min with the primary mAb. Cells were then washed once, incubated with the secondary antibody if needed, washed again, and then analysed by flow cytometry using a FACSCalibur™ flow cytometer and CELLQuest™ software (BD Pharmingen). GFP+ Sca-1+Lin- cells were sorted using a FACSVantage™ (BD Pharmingen). Purity > 90% were confirmed by re-analysis of sorted cells. The forward versus side scatter profile was used to gate on viable cells and an unstained sample was used to determine appropriate gating for expression. Monoclonal antibodies (mAbs) were all purchased from PharMingen (San Diego, CA) (phycoerythrin [PE]–labeled Gr-1, B220, Ter-119, CD4, CD5 and CD8).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Sorted cells were lyzed in Trizol™ (Invitrogen) and total RNA was extracted according to the manufacturer instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA from each sample were double linear amplified with the ENZO BioArray High Yield RNA Transcript Labeling kit and the GeneChip Eukaryotic Small Sample Target Labeling Assay, Version II protocol (Affymetrix, Santa Clara, CA) to produce target for hybridization to Affymetrix MOE430 according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Protocol EukGE-WS2v4
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A1 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle 2
| | Sample_hyb_protocol | Wash B Recovery Mixes 0
| | Sample_hyb_protocol | Wash B Temperature (C) 50
| | Sample_hyb_protocol | Number of Wash B Cycles 4
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 25
| | Sample_hyb_protocol | First Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A2 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle 4
| | Sample_hyb_protocol | Second Stain Time (seconds) 600
| | Sample_hyb_protocol | Third Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 30
| | Sample_hyb_protocol | Number of Wash A3 Cycles 15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle 4
| | Sample_hyb_protocol | Holding Temperature (C) 25
| | Sample_hyb_protocol | Station 1
| | Sample_hyb_protocol | Module 1
| | Sample_scan_protocol | Pixel Size 3
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date
| | Sample_scan_protocol | Scanner ID
| | Sample_scan_protocol | Number of Scans 2
| | Sample_scan_protocol | Scanner Type HP
| | Sample_data_processing | MAS 5.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lars,,Palmqvist
| | Sample_contact_email | lars.palmqvist@clinchem.gu.se
| | Sample_contact_department | Clinical Chemistry and Transfusion Medicine
| | Sample_contact_institute | Institute of Biomedicine
| | Sample_contact_address | Sahlgrenska University Hospital
| | Sample_contact_city | Gothenburg
| | Sample_contact_zip/postal_code | 41345
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230140/suppl/GSM230140.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230140/suppl/GSM230140.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230140/suppl/GSM230140.RPT.gz
| | Sample_series_id | GSE9079
| | Sample_data_row_count | 22690
| | |
|
GSM230141 | GPL339 |
|
Sca+Lin-PBM_NA10_rep3
|
Primary bone marrow
|
Donors of primary bone marrow cells were male mice (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) older than 12-weeks.
|
Retroviral vector coding for NUP98-HOXA10 (NA10) were introduced in primary bone marrow cells.
|
| Sample_geo_accession | GSM230141
| | Sample_status | Public on Oct 01 2007
| | Sample_submission_date | Sep 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | British Columbia Cancer Research Centre animal facility
| | Sample_treatment_protocol_ch1 | Mice were treated with 5-fluorouracil 4 days prior to bone marrow collection.
| | Sample_growth_protocol_ch1 | Bone marrow cells were harvested from mice treated 4 days previously with 150 mg/kg 5-fluorouracil (Faulding, Underdaler, Australia) and prestimulated for 48 hours in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (IL-3), and 100 ng/mL murine stem cell factor (mSF) (StemCell Technologies, Vancouver, BC, Canada). Cells were infected by co-cultivation with irradiated (4000 cGy x-ray) GP+E86 viral producer cells with the addition of 5 µg/mL protamine sulfate (Sigma, Oakville, ON, Canada). Loosely adherent and nonadherent cells were harvested from the co-cultures after 2 days and were cultured for 24 hours in the same medium without protamine sulfate.
| | Sample_growth_protocol_ch1 | The single cell suspensions collected were blocked for 10 min on ice with 5 μg/ml anti mouse CD16/CD32 (Fc Block, BD Pharmingen) in Phosphate Buffered Saline (STI) + 2% Fetal Bovine Serum (PF). Cells were washed once with PF and then incubated on ice for 20 min with the primary mAb. Cells were then washed once, incubated with the secondary antibody if needed, washed again, and then analysed by flow cytometry using a FACSCalibur™ flow cytometer and CELLQuest™ software (BD Pharmingen). GFP+ Sca-1+Lin- cells were sorted using a FACSVantage™ (BD Pharmingen). Purity > 90% were confirmed by re-analysis of sorted cells. The forward versus side scatter profile was used to gate on viable cells and an unstained sample was used to determine appropriate gating for expression. Monoclonal antibodies (mAbs) were all purchased from PharMingen (San Diego, CA) (phycoerythrin [PE]–labeled Gr-1, B220, Ter-119, CD4, CD5 and CD8).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Sorted cells were lyzed in Trizol™ (Invitrogen) and total RNA was extracted according to the manufacturer instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA from each sample were double linear amplified with the ENZO BioArray High Yield RNA Transcript Labeling kit and the GeneChip Eukaryotic Small Sample Target Labeling Assay, Version II protocol (Affymetrix, Santa Clara, CA) to produce target for hybridization to Affymetrix MOE430 according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Protocol EukGE-WS2v4
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A1 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle 2
| | Sample_hyb_protocol | Wash B Recovery Mixes 0
| | Sample_hyb_protocol | Wash B Temperature (C) 50
| | Sample_hyb_protocol | Number of Wash B Cycles 4
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 25
| | Sample_hyb_protocol | First Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A2 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle 4
| | Sample_hyb_protocol | Second Stain Time (seconds) 600
| | Sample_hyb_protocol | Third Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 30
| | Sample_hyb_protocol | Number of Wash A3 Cycles 15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle 4
| | Sample_hyb_protocol | Holding Temperature (C) 25
| | Sample_hyb_protocol | Station 1
| | Sample_hyb_protocol | Module 1
| | Sample_scan_protocol | Pixel Size 3
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date
| | Sample_scan_protocol | Scanner ID
| | Sample_scan_protocol | Number of Scans 2
| | Sample_scan_protocol | Scanner Type HP
| | Sample_data_processing | MAS 5.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lars,,Palmqvist
| | Sample_contact_email | lars.palmqvist@clinchem.gu.se
| | Sample_contact_department | Clinical Chemistry and Transfusion Medicine
| | Sample_contact_institute | Institute of Biomedicine
| | Sample_contact_address | Sahlgrenska University Hospital
| | Sample_contact_city | Gothenburg
| | Sample_contact_zip/postal_code | 41345
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230141/suppl/GSM230141.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230141/suppl/GSM230141.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230141/suppl/GSM230141.RPT.gz
| | Sample_series_id | GSE9079
| | Sample_data_row_count | 22690
| | |
|
GSM230142 | GPL339 |
|
Sca+Lin-PBM_ND13_rep3
|
Primary bone marrow
|
Donors of primary bone marrow cells were male mice (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) older than 12-weeks.
|
Retroviral vector coding for NUP98-HOXD13 (ND13) were introduced in primary bone marrow cells.
|
| Sample_geo_accession | GSM230142
| | Sample_status | Public on Oct 01 2007
| | Sample_submission_date | Sep 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | British Columbia Cancer Research Centre animal facility
| | Sample_treatment_protocol_ch1 | Mice were treated with 5-fluorouracil 4 days prior to bone marrow collection.
| | Sample_growth_protocol_ch1 | Bone marrow cells were harvested from mice treated 4 days previously with 150 mg/kg 5-fluorouracil (Faulding, Underdaler, Australia) and prestimulated for 48 hours in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (IL-3), and 100 ng/mL murine stem cell factor (mSF) (StemCell Technologies, Vancouver, BC, Canada). Cells were infected by co-cultivation with irradiated (4000 cGy x-ray) GP+E86 viral producer cells with the addition of 5 µg/mL protamine sulfate (Sigma, Oakville, ON, Canada). Loosely adherent and nonadherent cells were harvested from the co-cultures after 2 days and were cultured for 24 hours in the same medium without protamine sulfate.
| | Sample_growth_protocol_ch1 | The single cell suspensions collected were blocked for 10 min on ice with 5 μg/ml anti mouse CD16/CD32 (Fc Block, BD Pharmingen) in Phosphate Buffered Saline (STI) + 2% Fetal Bovine Serum (PF). Cells were washed once with PF and then incubated on ice for 20 min with the primary mAb. Cells were then washed once, incubated with the secondary antibody if needed, washed again, and then analysed by flow cytometry using a FACSCalibur™ flow cytometer and CELLQuest™ software (BD Pharmingen). GFP+ Sca-1+Lin- cells were sorted using a FACSVantage™ (BD Pharmingen). Purity > 90% were confirmed by re-analysis of sorted cells. The forward versus side scatter profile was used to gate on viable cells and an unstained sample was used to determine appropriate gating for expression. Monoclonal antibodies (mAbs) were all purchased from PharMingen (San Diego, CA) (phycoerythrin [PE]–labeled Gr-1, B220, Ter-119, CD4, CD5 and CD8).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Sorted cells were lyzed in Trizol™ (Invitrogen) and total RNA was extracted according to the manufacturer instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA from each sample were double linear amplified with the ENZO BioArray High Yield RNA Transcript Labeling kit and the GeneChip Eukaryotic Small Sample Target Labeling Assay, Version II protocol (Affymetrix, Santa Clara, CA) to produce target for hybridization to Affymetrix MOE430 according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Protocol EukGE-WS2v4
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A1 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle 2
| | Sample_hyb_protocol | Wash B Recovery Mixes 0
| | Sample_hyb_protocol | Wash B Temperature (C) 50
| | Sample_hyb_protocol | Number of Wash B Cycles 4
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 25
| | Sample_hyb_protocol | First Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A2 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle 4
| | Sample_hyb_protocol | Second Stain Time (seconds) 600
| | Sample_hyb_protocol | Third Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 30
| | Sample_hyb_protocol | Number of Wash A3 Cycles 15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle 4
| | Sample_hyb_protocol | Holding Temperature (C) 25
| | Sample_hyb_protocol | Station 1
| | Sample_hyb_protocol | Module 1
| | Sample_scan_protocol | Pixel Size 3
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date
| | Sample_scan_protocol | Scanner ID
| | Sample_scan_protocol | Number of Scans 2
| | Sample_scan_protocol | Scanner Type HP
| | Sample_data_processing | MAS 5.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lars,,Palmqvist
| | Sample_contact_email | lars.palmqvist@clinchem.gu.se
| | Sample_contact_department | Clinical Chemistry and Transfusion Medicine
| | Sample_contact_institute | Institute of Biomedicine
| | Sample_contact_address | Sahlgrenska University Hospital
| | Sample_contact_city | Gothenburg
| | Sample_contact_zip/postal_code | 41345
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230142/suppl/GSM230142.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230142/suppl/GSM230142.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230142/suppl/GSM230142.RPT.gz
| | Sample_series_id | GSE9079
| | Sample_data_row_count | 22690
| | |
|
GSM230143 | GPL339 |
|
Sca+Lin-PBM_ND13N51S_rep3
|
Primary bone marrow
|
Donors of primary bone marrow cells were male mice (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) older than 12-weeks.
|
Retroviral vector coding for NUP98-HOXD13 with a mutation (N51S) were introduced in primary bone marrow cells.
|
| Sample_geo_accession | GSM230143
| | Sample_status | Public on Oct 01 2007
| | Sample_submission_date | Sep 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | British Columbia Cancer Research Centre animal facility
| | Sample_treatment_protocol_ch1 | Mice were treated with 5-fluorouracil 4 days prior to bone marrow collection.
| | Sample_growth_protocol_ch1 | Bone marrow cells were harvested from mice treated 4 days previously with 150 mg/kg 5-fluorouracil (Faulding, Underdaler, Australia) and prestimulated for 48 hours in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (IL-3), and 100 ng/mL murine stem cell factor (mSF) (StemCell Technologies, Vancouver, BC, Canada). Cells were infected by co-cultivation with irradiated (4000 cGy x-ray) GP+E86 viral producer cells with the addition of 5 µg/mL protamine sulfate (Sigma, Oakville, ON, Canada). Loosely adherent and nonadherent cells were harvested from the co-cultures after 2 days and were cultured for 24 hours in the same medium without protamine sulfate.
| | Sample_growth_protocol_ch1 | The single cell suspensions collected were blocked for 10 min on ice with 5 μg/ml anti mouse CD16/CD32 (Fc Block, BD Pharmingen) in Phosphate Buffered Saline (STI) + 2% Fetal Bovine Serum (PF). Cells were washed once with PF and then incubated on ice for 20 min with the primary mAb. Cells were then washed once, incubated with the secondary antibody if needed, washed again, and then analysed by flow cytometry using a FACSCalibur™ flow cytometer and CELLQuest™ software (BD Pharmingen). GFP+ Sca-1+Lin- cells were sorted using a FACSVantage™ (BD Pharmingen). Purity > 90% were confirmed by re-analysis of sorted cells. The forward versus side scatter profile was used to gate on viable cells and an unstained sample was used to determine appropriate gating for expression. Monoclonal antibodies (mAbs) were all purchased from PharMingen (San Diego, CA) (phycoerythrin [PE]–labeled Gr-1, B220, Ter-119, CD4, CD5 and CD8).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Sorted cells were lyzed in Trizol™ (Invitrogen) and total RNA was extracted according to the manufacturer instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA from each sample were double linear amplified with the ENZO BioArray High Yield RNA Transcript Labeling kit and the GeneChip Eukaryotic Small Sample Target Labeling Assay, Version II protocol (Affymetrix, Santa Clara, CA) to produce target for hybridization to Affymetrix MOE430 according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Protocol EukGE-WS2v4
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A1 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle 2
| | Sample_hyb_protocol | Wash B Recovery Mixes 0
| | Sample_hyb_protocol | Wash B Temperature (C) 50
| | Sample_hyb_protocol | Number of Wash B Cycles 4
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 25
| | Sample_hyb_protocol | First Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 25
| | Sample_hyb_protocol | Number of Wash A2 Cycles 10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle 4
| | Sample_hyb_protocol | Second Stain Time (seconds) 600
| | Sample_hyb_protocol | Third Stain Time (seconds) 600
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 30
| | Sample_hyb_protocol | Number of Wash A3 Cycles 15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle 4
| | Sample_hyb_protocol | Holding Temperature (C) 25
| | Sample_hyb_protocol | Station 1
| | Sample_hyb_protocol | Module 1
| | Sample_scan_protocol | Pixel Size 3
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date
| | Sample_scan_protocol | Scanner ID
| | Sample_scan_protocol | Number of Scans 2
| | Sample_scan_protocol | Scanner Type HP
| | Sample_data_processing | MAS 5.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Lars,,Palmqvist
| | Sample_contact_email | lars.palmqvist@clinchem.gu.se
| | Sample_contact_department | Clinical Chemistry and Transfusion Medicine
| | Sample_contact_institute | Institute of Biomedicine
| | Sample_contact_address | Sahlgrenska University Hospital
| | Sample_contact_city | Gothenburg
| | Sample_contact_zip/postal_code | 41345
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230143/suppl/GSM230143.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230143/suppl/GSM230143.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM230nnn/GSM230143/suppl/GSM230143.RPT.gz
| | Sample_series_id | GSE9079
| | Sample_data_row_count | 22690
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
