Search results for the GEO ID: GSE15541  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM389324 | GPL1261 |
|
NUP98-HOXD13+MIY-ctrl_rep1
|
Cultured bone marrow, MIY-ctrl
|
cell type: cultured bone marrow cells transformed by NUP98-HOXD13
|
Retroviral vector coding for YFP (MIY) was introduced as negative control in cultured bone marrow cells transformed by NUP98-HOXD13
|
| Sample_geo_accession | GSM389324
| | Sample_status | Public on Apr 09 2009
| | Sample_submission_date | Apr 03 2009
| | Sample_last_update_date | Apr 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mice were bred and maintained at the British Columbia Cancer Research Center Animal Facility (Vancouver, BC). All experimental protocols were approved by the University of British Columbia Animal Care Committee. Establishment and characterization of pre-leukemic BM cell lines following transduction of BM cells with ND13 have been previously described (Pineault, Abramovich et al. 2005; Palmqvist, Argiropoulos et al. 2006). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained for a period of 4 weeks in liquid culture [Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/ml of human interleukin-6 (hIL-6), 6 ng/ml of murine interleukin-3 (mIL3), and 100 ng/ml of murine stem cell factor (mSCF)]. All culture media and growth factors were obtained from StemCell Technologies Inc. (Vancouver, BC, Canada). Cells were maintained at a cell density below 1 x 106/ml. Cells were counted with the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter Inc., Fullerton, California). To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 ug/ml of protamine sulfate (Sigma, Oakville, ON, Canada).
| | 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 | The labeling was done according to the manufacturer instructions and performed at the Swegene MARC, Department of Immunotechnology, Lund University, Sweden
| | Sample_hyb_protocol | Protocol EukGE-WS2v5
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 30
| | 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 6
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 35
| | Sample_hyb_protocol | First Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 30
| | 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) 300
| | Sample_hyb_protocol | Third Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 35
| | 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 1.56
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date Nov 01 2005 12:46PM
| | Sample_scan_protocol | Scanner ID 50206370
| | Sample_scan_protocol | Number of Scans 1
| | Sample_scan_protocol | Scanner Type M10
| | Sample_data_processing | GCOS 1.2
| | Sample_platform_id | GPL1261
| | 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/GSM389nnn/GSM389324/suppl/GSM389324.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389324/suppl/GSM389324.CHP.gz
| | Sample_series_id | GSE15541
| | Sample_data_row_count | 45101
| | |
|
GSM389334 | GPL1261 |
|
NUP98-HOXD13_MIY-ctrl_rep2
|
Cultured bone marrow, MIY-ctrl
|
cell type: cultured bone marrow cells transformed by NUP98-HOXD13
|
Retroviral vector coding for YFP (MIY) was introduced as negative control in cultured bone marrow cells transformed by NUP98-HOXD13
|
| Sample_geo_accession | GSM389334
| | Sample_status | Public on Apr 09 2009
| | Sample_submission_date | Apr 03 2009
| | Sample_last_update_date | Apr 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mice were bred and maintained at the British Columbia Cancer Research Center Animal Facility (Vancouver, BC). All experimental protocols were approved by the University of British Columbia Animal Care Committee. Establishment and characterization of pre-leukemic BM cell lines following transduction of BM cells with ND13 have been previously described (Pineault, Abramovich et al. 2005; Palmqvist, Argiropoulos et al. 2006). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained for a period of 4 weeks in liquid culture [Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/ml of human interleukin-6 (hIL-6), 6 ng/ml of murine interleukin-3 (mIL3), and 100 ng/ml of murine stem cell factor (mSCF)]. All culture media and growth factors were obtained from StemCell Technologies Inc. (Vancouver, BC, Canada). Cells were maintained at a cell density below 1 x 106/ml. Cells were counted with the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter Inc., Fullerton, California). To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 µg/ml of protamine sulfate (Sigma, Oakville, ON, Canada).
| | 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 | The labeling was done according to the manufacturer instructions and performed at the Swegene MARC, Department of Immunotechnology, Lund University
| | Sample_hyb_protocol | Protocol EukGE-WS2v5
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 30
| | 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 6
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 35
| | Sample_hyb_protocol | First Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 30
| | 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) 300
| | Sample_hyb_protocol | Third Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 35
| | 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 1.56
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date Nov 01 2005 12:46PM
| | Sample_scan_protocol | Scanner ID 50206370
| | Sample_scan_protocol | Number of Scans 1
| | Sample_scan_protocol | Scanner Type M10
| | Sample_data_processing | GCOS 1.2
| | Sample_platform_id | GPL1261
| | 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/GSM389nnn/GSM389334/suppl/GSM389334.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389334/suppl/GSM389334.CHP.gz
| | Sample_series_id | GSE15541
| | Sample_data_row_count | 45101
| | |
|
GSM389339 | GPL1261 |
|
NUP98-HOXD13+MIY-ctrl_rep3
|
Cultured bone marrow, MIY-ctrl
|
cell type: cultured bone marrow cells transformed by NUP98-HOXD13
|
Retroviral vector coding for YFP (MIY) was introduced as negative control in cultured bone marrow cells transformed by NUP98-HOXD13
|
| Sample_geo_accession | GSM389339
| | Sample_status | Public on Apr 09 2009
| | Sample_submission_date | Apr 03 2009
| | Sample_last_update_date | Apr 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mice were bred and maintained at the British Columbia Cancer Research Center Animal Facility (Vancouver, BC). All experimental protocols were approved by the University of British Columbia Animal Care Committee. Establishment and characterization of pre-leukemic BM cell lines following transduction of BM cells with ND13 have been previously described (Pineault, Abramovich et al. 2005; Palmqvist, Argiropoulos et al. 2006). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained for a period of 4 weeks in liquid culture [Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/ml of human interleukin-6 (hIL-6), 6 ng/ml of murine interleukin-3 (mIL3), and 100 ng/ml of murine stem cell factor (mSCF)]. All culture media and growth factors were obtained from StemCell Technologies Inc. (Vancouver, BC, Canada). Cells were maintained at a cell density below 1 x 106/ml. Cells were counted with the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter Inc., Fullerton, California). To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 µg/ml of protamine sulfate (Sigma, Oakville, ON, Canada).
| | 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 | The labeling was done according to the manufacturer instructions and performed at the Swegene MARC, Department of Immunotechnology, Lund University, Sweden
| | Sample_hyb_protocol | Protocol EukGE-WS2v5
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 30
| | 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 6
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 35
| | Sample_hyb_protocol | First Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 30
| | 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) 300
| | Sample_hyb_protocol | Third Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 35
| | 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 1.56
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date Nov 01 2005
| | Sample_scan_protocol | Scanner ID 50206370
| | Sample_scan_protocol | Number of Scans 1
| | Sample_scan_protocol | Scanner Type M10
| | Sample_data_processing | GCOS 1.2
| | Sample_platform_id | GPL1261
| | 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/GSM389nnn/GSM389339/suppl/GSM389339.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389339/suppl/GSM389339.CHP.gz
| | Sample_series_id | GSE15541
| | Sample_data_row_count | 45101
| | |
|
GSM389341 | GPL1261 |
|
NUP98-HOXD13+MEIS1-WT_rep1
|
Cultured bone marrow, MEIS1-WT
|
cell type: cultured bone marrow cells transformed by NUP98-HOXD13
|
Retroviral vector coding for wildtype MEIS1 was introduced in cultured bone marrow cells transformed by NUP98-HOXD13
|
| Sample_geo_accession | GSM389341
| | Sample_status | Public on Apr 09 2009
| | Sample_submission_date | Apr 03 2009
| | Sample_last_update_date | Apr 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mice were bred and maintained at the British Columbia Cancer Research Center Animal Facility (Vancouver, BC). All experimental protocols were approved by the University of British Columbia Animal Care Committee. Establishment and characterization of pre-leukemic BM cell lines following transduction of BM cells with ND13 have been previously described (Pineault, Abramovich et al. 2005; Palmqvist, Argiropoulos et al. 2006). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained for a period of 4 weeks in liquid culture [Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/ml of human interleukin-6 (hIL-6), 6 ng/ml of murine interleukin-3 (mIL3), and 100 ng/ml of murine stem cell factor (mSCF)]. All culture media and growth factors were obtained from StemCell Technologies Inc. (Vancouver, BC, Canada). Cells were maintained at a cell density below 1 x 106/ml. Cells were counted with the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter Inc., Fullerton, California). To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 µg/ml of protamine sulfate (Sigma, Oakville, ON, Canada).
| | 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 | The labeling was done according to the manufacturer instructions and performed at the Swegene MARC, Department of Immunotechnology, Lund University, Sweden
| | Sample_hyb_protocol | Chip Type Mouse430_2
| | Sample_hyb_protocol | Chip Lot AKE
| | Sample_hyb_protocol | Operator administrator
| | Sample_hyb_protocol | Sample Type total RNA
| | Sample_hyb_protocol | Project p0531
| | Sample_hyb_protocol | Protocol EukGE-WS2v5
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 30
| | 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 6
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 35
| | Sample_hyb_protocol | First Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 30
| | 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) 300
| | Sample_hyb_protocol | Third Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 35
| | 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 2
| | Sample_hyb_protocol | Module 3
| | Sample_hyb_protocol | Hybridize Date Oct 26 2005
| | Sample_scan_protocol | Pixel Size 1.56
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date Oct 26 2005
| | Sample_scan_protocol | Scanner ID 50206370
| | Sample_scan_protocol | Number of Scans 1
| | Sample_scan_protocol | Scanner Type M10
| | Sample_data_processing | GCOS 1.2
| | Sample_platform_id | GPL1261
| | 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/GSM389nnn/GSM389341/suppl/GSM389341.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389341/suppl/GSM389341.CHP.gz
| | Sample_series_id | GSE15541
| | Sample_data_row_count | 45101
| | |
|
GSM389342 | GPL1261 |
|
NUP98-HOXD13+MEIS1-WT_rep2
|
Cultured bone marrow, MEIS1-WT
|
cell type: cultured bone marrow cells transformed by NUP98-HOXD13
|
Retroviral vector coding for wildtype MEIS1 was introduced in cultured bone marrow cells transformed by NUP98-HOXD13
|
| Sample_geo_accession | GSM389342
| | Sample_status | Public on Apr 09 2009
| | Sample_submission_date | Apr 03 2009
| | Sample_last_update_date | Apr 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mice were bred and maintained at the British Columbia Cancer Research Center Animal Facility (Vancouver, BC). All experimental protocols were approved by the University of British Columbia Animal Care Committee. Establishment and characterization of pre-leukemic BM cell lines following transduction of BM cells with ND13 have been previously described (Pineault, Abramovich et al. 2005; Palmqvist, Argiropoulos et al. 2006). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained for a period of 4 weeks in liquid culture [Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/ml of human interleukin-6 (hIL-6), 6 ng/ml of murine interleukin-3 (mIL3), and 100 ng/ml of murine stem cell factor (mSCF)]. All culture media and growth factors were obtained from StemCell Technologies Inc. (Vancouver, BC, Canada). Cells were maintained at a cell density below 1 x 106/ml. Cells were counted with the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter Inc., Fullerton, California). To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 µg/ml of protamine sulfate (Sigma, Oakville, ON, Canada).
| | 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 | The labeling was done according to the manufacturer instructions and performed at the Swegene MARC, Department of Immunotechnology, Lund University, Sweden
| | Sample_hyb_protocol | Chip Type Mouse430_2
| | Sample_hyb_protocol | Chip Lot AKE
| | Sample_hyb_protocol | Operator administrator
| | Sample_hyb_protocol | Sample Type total RNA
| | Sample_hyb_protocol | Project p0531
| | Sample_hyb_protocol | Protocol EukGE-WS2v5
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 30
| | 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 6
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 35
| | Sample_hyb_protocol | First Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 30
| | 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) 300
| | Sample_hyb_protocol | Third Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 35
| | 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 2
| | Sample_hyb_protocol | Module 3
| | Sample_hyb_protocol | Hybridize Date Oct 26 2005
| | Sample_scan_protocol | Pixel Size 1.56
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date Oct 26 2005
| | Sample_scan_protocol | Scanner ID 50206370
| | Sample_scan_protocol | Number of Scans 1
| | Sample_scan_protocol | Scanner Type M10
| | Sample_data_processing | GCOS 1.2
| | Sample_platform_id | GPL1261
| | 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/GSM389nnn/GSM389342/suppl/GSM389342.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389342/suppl/GSM389342.CHP.gz
| | Sample_series_id | GSE15541
| | Sample_data_row_count | 45101
| | |
|
GSM389343 | GPL1261 |
|
NUP98-HOXD13+MEIS1-WT_rep3
|
Cultured bone marrow, MEIS1-WT
|
cell type: cultured bone marrow cells transformed by NUP98-HOXD13
|
Retroviral vector coding for wildtype MEIS1 was introduced in cultured bone marrow cells transformed by NUP98-HOXD13
|
| Sample_geo_accession | GSM389343
| | Sample_status | Public on Apr 09 2009
| | Sample_submission_date | Apr 03 2009
| | Sample_last_update_date | Apr 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mice were bred and maintained at the British Columbia Cancer Research Center Animal Facility (Vancouver, BC). All experimental protocols were approved by the University of British Columbia Animal Care Committee. Establishment and characterization of pre-leukemic BM cell lines following transduction of BM cells with ND13 have been previously described (Pineault, Abramovich et al. 2005; Palmqvist, Argiropoulos et al. 2006). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained for a period of 4 weeks in liquid culture [Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/ml of human interleukin-6 (hIL-6), 6 ng/ml of murine interleukin-3 (mIL3), and 100 ng/ml of murine stem cell factor (mSCF)]. All culture media and growth factors were obtained from StemCell Technologies Inc. (Vancouver, BC, Canada). Cells were maintained at a cell density below 1 x 106/ml. Cells were counted with the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter Inc., Fullerton, California). To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 µg/ml of protamine sulfate (Sigma, Oakville, ON, Canada).
| | 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 | The labeling was done according to the manufacturer instructions and performed at the Swegene MARC, Department of Immunotechnology, Lund University, Sweden
| | Sample_hyb_protocol | Chip Type Mouse430_2
| | Sample_hyb_protocol | Chip Lot AKE
| | Sample_hyb_protocol | Operator administrator
| | Sample_hyb_protocol | Sample Type total RNA
| | Sample_hyb_protocol | Project p0531
| | Sample_hyb_protocol | Protocol EukGE-WS2v5
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 30
| | 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 6
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 35
| | Sample_hyb_protocol | First Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 30
| | 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) 300
| | Sample_hyb_protocol | Third Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 35
| | 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 2
| | Sample_hyb_protocol | Module 3
| | Sample_hyb_protocol | Hybridize Date Nov 1 2005
| | Sample_scan_protocol | Pixel Size 1.56
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date Nov 1 2005
| | Sample_scan_protocol | Scanner ID 50206370
| | Sample_scan_protocol | Number of Scans 1
| | Sample_scan_protocol | Scanner Type M10
| | Sample_data_processing | GCOS 1.2
| | Sample_platform_id | GPL1261
| | 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/GSM389nnn/GSM389343/suppl/GSM389343.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389343/suppl/GSM389343.CHP.gz
| | Sample_series_id | GSE15541
| | Sample_data_row_count | 45101
| | |
|
GSM389344 | GPL1261 |
|
NUP98-HOXD13+MEIS1-deltaHD_rep1
|
Cultured bone marrow, MEIS1-deltaHD
|
cell type: cultured bone marrow cells transformed by NUP98-HOXD13
|
Retroviral vector coding for MEIS1, with deleted homeodomain, was introduced in cultured bone marrow cells transformed by NUP98-HOXD13
|
| Sample_geo_accession | GSM389344
| | Sample_status | Public on Apr 09 2009
| | Sample_submission_date | Apr 03 2009
| | Sample_last_update_date | Apr 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mice were bred and maintained at the British Columbia Cancer Research Center Animal Facility (Vancouver, BC). All experimental protocols were approved by the University of British Columbia Animal Care Committee. Establishment and characterization of pre-leukemic BM cell lines following transduction of BM cells with ND13 have been previously described (Pineault, Abramovich et al. 2005; Palmqvist, Argiropoulos et al. 2006). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained for a period of 4 weeks in liquid culture [Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/ml of human interleukin-6 (hIL-6), 6 ng/ml of murine interleukin-3 (mIL3), and 100 ng/ml of murine stem cell factor (mSCF)]. All culture media and growth factors were obtained from StemCell Technologies Inc. (Vancouver, BC, Canada). Cells were maintained at a cell density below 1 x 106/ml. Cells were counted with the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter Inc., Fullerton, California). To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 µg/ml of protamine sulfate (Sigma, Oakville, ON, Canada).
| | 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 | The labeling was done according to the manufacturer instructions and performed at the Swegene MARC, Department of Immunotechnology, Lund University, Sweden
| | Sample_hyb_protocol | Chip Type Mouse430_2
| | Sample_hyb_protocol | Chip Lot AKE
| | Sample_hyb_protocol | Operator administrator
| | Sample_hyb_protocol | Sample Type total RNA
| | Sample_hyb_protocol | Project p0531
| | Sample_hyb_protocol | Protocol EukGE-WS2v5
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 30
| | 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 6
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 35
| | Sample_hyb_protocol | First Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 30
| | 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) 300
| | Sample_hyb_protocol | Third Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 35
| | 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 2
| | Sample_hyb_protocol | Module 3
| | Sample_hyb_protocol | Hybridize Date Oct 26 2005
| | Sample_scan_protocol | Pixel Size 1.56
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date Oct 26 2005
| | Sample_scan_protocol | Scanner ID 50206370
| | Sample_scan_protocol | Number of Scans 1
| | Sample_scan_protocol | Scanner Type M10
| | Sample_data_processing | GCOS 1.2
| | Sample_platform_id | GPL1261
| | 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/GSM389nnn/GSM389344/suppl/GSM389344.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389344/suppl/GSM389344.CHP.gz
| | Sample_series_id | GSE15541
| | Sample_data_row_count | 45101
| | |
|
GSM389345 | GPL1261 |
|
NUP98-HOXD13+MEIS1-deltaHD_rep2
|
Cultured bone marrow, MEIS1-deltaHD
|
cell type: cultured bone marrow cells transformed by NUP98-HOXD13
|
Retroviral vector coding for MEIS1, with deleted homeodomain, was introduced in cultured bone marrow cells transformed by NUP98-HOXD13
|
| Sample_geo_accession | GSM389345
| | Sample_status | Public on Apr 09 2009
| | Sample_submission_date | Apr 03 2009
| | Sample_last_update_date | Apr 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mice were bred and maintained at the British Columbia Cancer Research Center Animal Facility (Vancouver, BC). All experimental protocols were approved by the University of British Columbia Animal Care Committee. Establishment and characterization of pre-leukemic BM cell lines following transduction of BM cells with ND13 have been previously described (Pineault, Abramovich et al. 2005; Palmqvist, Argiropoulos et al. 2006). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained for a period of 4 weeks in liquid culture [Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/ml of human interleukin-6 (hIL-6), 6 ng/ml of murine interleukin-3 (mIL3), and 100 ng/ml of murine stem cell factor (mSCF)]. All culture media and growth factors were obtained from StemCell Technologies Inc. (Vancouver, BC, Canada). Cells were maintained at a cell density below 1 x 106/ml. Cells were counted with the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter Inc., Fullerton, California). To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 µg/ml of protamine sulfate (Sigma, Oakville, ON, Canada).
| | 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 | The labeling was done according to the manufacturer instructions and performed at the Swegene MARC, Department of Immunotechnology, Lund University, Sweden
| | Sample_hyb_protocol | Chip Type Mouse430_2
| | Sample_hyb_protocol | Chip Lot AKE
| | Sample_hyb_protocol | Operator administrator
| | Sample_hyb_protocol | Sample Type total RNA
| | Sample_hyb_protocol | Project p0531
| | Sample_hyb_protocol | Protocol EukGE-WS2v5
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 30
| | 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 6
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 35
| | Sample_hyb_protocol | First Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 30
| | 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) 300
| | Sample_hyb_protocol | Third Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 35
| | 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 2
| | Sample_hyb_protocol | Module 3
| | Sample_hyb_protocol | Hybridize Date Oct 26 2005
| | Sample_scan_protocol | Pixel Size 1.56
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date Oct 26 2005
| | Sample_scan_protocol | Scanner ID 50206370
| | Sample_scan_protocol | Number of Scans 1
| | Sample_scan_protocol | Scanner Type M10
| | Sample_data_processing | GCOS 1.2
| | Sample_platform_id | GPL1261
| | 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/GSM389nnn/GSM389345/suppl/GSM389345.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389345/suppl/GSM389345.CHP.gz
| | Sample_series_id | GSE15541
| | Sample_data_row_count | 45101
| | |
|
GSM389346 | GPL1261 |
|
NUP98-HOXD13+MEIS1-deltaHD_rep3
|
Cultured bone marrow, MEIS1-deltaHD
|
cell type: cultured bone marrow cells transformed by NUP98-HOXD13
|
Retroviral vector coding for MEIS1, with deleted homeodomain, was introduced in cultured bone marrow cells transformed by NUP98-HOXD13
|
| Sample_geo_accession | GSM389346
| | Sample_status | Public on Apr 09 2009
| | Sample_submission_date | Apr 03 2009
| | Sample_last_update_date | Apr 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mice were bred and maintained at the British Columbia Cancer Research Center Animal Facility (Vancouver, BC). All experimental protocols were approved by the University of British Columbia Animal Care Committee. Establishment and characterization of pre-leukemic BM cell lines following transduction of BM cells with ND13 have been previously described (Pineault, Abramovich et al. 2005; Palmqvist, Argiropoulos et al. 2006). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained for a period of 4 weeks in liquid culture [Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/ml of human interleukin-6 (hIL-6), 6 ng/ml of murine interleukin-3 (mIL3), and 100 ng/ml of murine stem cell factor (mSCF)]. All culture media and growth factors were obtained from StemCell Technologies Inc. (Vancouver, BC, Canada). Cells were maintained at a cell density below 1 x 106/ml. Cells were counted with the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter Inc., Fullerton, California). To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 µg/ml of protamine sulfate (Sigma, Oakville, ON, Canada).
| | 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 | The labeling was done according to the manufacturer instructions and performed at the Swegene MARC, Department of Immunotechnology, Lund University, Sweden
| | Sample_hyb_protocol | Chip Type Mouse430_2
| | Sample_hyb_protocol | Chip Lot AKE
| | Sample_hyb_protocol | Operator administrator
| | Sample_hyb_protocol | Sample Type total RNA
| | Sample_hyb_protocol | Project p0531
| | Sample_hyb_protocol | Protocol EukGE-WS2v5
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 30
| | 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 6
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 35
| | Sample_hyb_protocol | First Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 30
| | 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) 300
| | Sample_hyb_protocol | Third Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 35
| | 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 2
| | Sample_hyb_protocol | Module 3
| | Sample_hyb_protocol | Hybridize Date Oct 26 2005
| | Sample_scan_protocol | Pixel Size 1.56
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date Oct 26 2005
| | Sample_scan_protocol | Scanner ID 50206370
| | Sample_scan_protocol | Number of Scans 1
| | Sample_scan_protocol | Scanner Type M10
| | Sample_data_processing | GCOS 1.2
| | Sample_platform_id | GPL1261
| | 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/GSM389nnn/GSM389346/suppl/GSM389346.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389346/suppl/GSM389346.CHP.gz
| | Sample_series_id | GSE15541
| | Sample_data_row_count | 45101
| | |
|
GSM389347 | GPL1261 |
|
NUP98-HOXD13+M33-MEIS1_rep1
|
Cultured bone marrow, M33-MEIS1
|
cell type: cultured bone marrow cells transformed by NUP98-HOXD13
|
Retroviral vector coding for M33-MEIS1 was introduced in cultured bone marrow cells transformed by NUP98-HOXD13
|
| Sample_geo_accession | GSM389347
| | Sample_status | Public on Apr 09 2009
| | Sample_submission_date | Apr 03 2009
| | Sample_last_update_date | Apr 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mice were bred and maintained at the British Columbia Cancer Research Center Animal Facility (Vancouver, BC). All experimental protocols were approved by the University of British Columbia Animal Care Committee. Establishment and characterization of pre-leukemic BM cell lines following transduction of BM cells with ND13 have been previously described (Pineault, Abramovich et al. 2005; Palmqvist, Argiropoulos et al. 2006). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained for a period of 4 weeks in liquid culture [Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/ml of human interleukin-6 (hIL-6), 6 ng/ml of murine interleukin-3 (mIL3), and 100 ng/ml of murine stem cell factor (mSCF)]. All culture media and growth factors were obtained from StemCell Technologies Inc. (Vancouver, BC, Canada). Cells were maintained at a cell density below 1 x 106/ml. Cells were counted with the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter Inc., Fullerton, California). To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 µg/ml of protamine sulfate (Sigma, Oakville, ON, Canada).
| | 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 | The labeling was done according to the manufacturer instructions and performed at the Swegene MARC, Department of Immunotechnology, Lund University, Sweden
| | Sample_hyb_protocol | Chip Type Mouse430_2
| | Sample_hyb_protocol | Chip Lot AKE
| | Sample_hyb_protocol | Operator administrator
| | Sample_hyb_protocol | Sample Type total RNA
| | Sample_hyb_protocol | Project p0531
| | Sample_hyb_protocol | Protocol EukGE-WS2v5
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 30
| | 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 6
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 35
| | Sample_hyb_protocol | First Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 30
| | 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) 300
| | Sample_hyb_protocol | Third Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 35
| | 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 2
| | Sample_hyb_protocol | Module 3
| | Sample_hyb_protocol | Hybridize Date Nov 1 2005
| | Sample_scan_protocol | Pixel Size 1.56
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date Nov 1 2005
| | Sample_scan_protocol | Scanner ID 50206370
| | Sample_scan_protocol | Number of Scans 1
| | Sample_scan_protocol | Scanner Type M10
| | Sample_data_processing | GCOS 1.2
| | Sample_platform_id | GPL1261
| | 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/GSM389nnn/GSM389347/suppl/GSM389347.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389347/suppl/GSM389347.CHP.gz
| | Sample_series_id | GSE15541
| | Sample_data_row_count | 45101
| | |
|
GSM389348 | GPL1261 |
|
NUP98-HOXD13+M33-MEIS1_rep2
|
Cultured bone marrow, M33-MEIS1
|
cell type: cultured bone marrow cells transformed by NUP98-HOXD13
|
Retroviral vector coding for M33-MEIS1 was introduced in cultured bone marrow cells transformed by NUP98-HOXD13
|
| Sample_geo_accession | GSM389348
| | Sample_status | Public on Apr 09 2009
| | Sample_submission_date | Apr 03 2009
| | Sample_last_update_date | Apr 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mice were bred and maintained at the British Columbia Cancer Research Center Animal Facility (Vancouver, BC). All experimental protocols were approved by the University of British Columbia Animal Care Committee. Establishment and characterization of pre-leukemic BM cell lines following transduction of BM cells with ND13 have been previously described (Pineault, Abramovich et al. 2005; Palmqvist, Argiropoulos et al. 2006). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained for a period of 4 weeks in liquid culture [Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/ml of human interleukin-6 (hIL-6), 6 ng/ml of murine interleukin-3 (mIL3), and 100 ng/ml of murine stem cell factor (mSCF)]. All culture media and growth factors were obtained from StemCell Technologies Inc. (Vancouver, BC, Canada). Cells were maintained at a cell density below 1 x 106/ml. Cells were counted with the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter Inc., Fullerton, California). To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 µg/ml of protamine sulfate (Sigma, Oakville, ON, Canada).
| | 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 | The labeling was done according to the manufacturer instructions and performed at the Swegene MARC, Department of Immunotechnology, Lund University, Sweden
| | Sample_hyb_protocol | Chip Type Mouse430_2
| | Sample_hyb_protocol | Chip Lot AKE
| | Sample_hyb_protocol | Operator administrator
| | Sample_hyb_protocol | Sample Type total RNA
| | Sample_hyb_protocol | Project p0531
| | Sample_hyb_protocol | Protocol EukGE-WS2v5
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 30
| | 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 6
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 35
| | Sample_hyb_protocol | First Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 30
| | 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) 300
| | Sample_hyb_protocol | Third Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 35
| | 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 2
| | Sample_hyb_protocol | Module 3
| | Sample_hyb_protocol | Hybridize Date Nov 1 2005
| | Sample_scan_protocol | Pixel Size 1.56
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date Nov 1 2005
| | Sample_scan_protocol | Scanner ID 50206370
| | Sample_scan_protocol | Number of Scans 1
| | Sample_scan_protocol | Scanner Type M10
| | Sample_data_processing | GCOS 1.2
| | Sample_platform_id | GPL1261
| | 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/GSM389nnn/GSM389348/suppl/GSM389348.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389348/suppl/GSM389348.CHP.gz
| | Sample_series_id | GSE15541
| | Sample_data_row_count | 45101
| | |
|
GSM389349 | GPL1261 |
|
NUP98-HOXD13+M33-MEIS1_rep3
|
Cultured bone marrow, M33-MEIS1
|
cell type: cultured bone marrow cells transformed by NUP98-HOXD13
|
Retroviral vector coding for M33-MEIS1 was introduced in cultured bone marrow cells transformed by NUP98-HOXD13
|
| Sample_geo_accession | GSM389349
| | Sample_status | Public on Apr 09 2009
| | Sample_submission_date | Apr 03 2009
| | Sample_last_update_date | Apr 08 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mice were bred and maintained at the British Columbia Cancer Research Center Animal Facility (Vancouver, BC). All experimental protocols were approved by the University of British Columbia Animal Care Committee. Establishment and characterization of pre-leukemic BM cell lines following transduction of BM cells with ND13 have been previously described (Pineault, Abramovich et al. 2005; Palmqvist, Argiropoulos et al. 2006). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained for a period of 4 weeks in liquid culture [Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/ml of human interleukin-6 (hIL-6), 6 ng/ml of murine interleukin-3 (mIL3), and 100 ng/ml of murine stem cell factor (mSCF)]. All culture media and growth factors were obtained from StemCell Technologies Inc. (Vancouver, BC, Canada). Cells were maintained at a cell density below 1 x 106/ml. Cells were counted with the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter Inc., Fullerton, California). To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 µg/ml of protamine sulfate (Sigma, Oakville, ON, Canada).
| | 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 | The labeling was done according to the manufacturer instructions and performed at the Swegene MARC, Department of Immunotechnology, Lund University, Sweden
| | Sample_hyb_protocol | Chip Type Mouse430_2
| | Sample_hyb_protocol | Chip Lot AKE
| | Sample_hyb_protocol | Operator administrator
| | Sample_hyb_protocol | Sample Type total RNA
| | Sample_hyb_protocol | Project p0531
| | Sample_hyb_protocol | Protocol EukGE-WS2v5
| | Sample_hyb_protocol | Wash A1 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A1 Temperature (C) 30
| | 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 6
| | Sample_hyb_protocol | Mixes per Wash B Cycle 15
| | Sample_hyb_protocol | Stain Temperature (C) 35
| | Sample_hyb_protocol | First Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A2 Temperature (C) 30
| | 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) 300
| | Sample_hyb_protocol | Third Stain Time (seconds) 300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes 0
| | Sample_hyb_protocol | Wash A3 Temperature (C) 35
| | 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 2
| | Sample_hyb_protocol | Module 3
| | Sample_hyb_protocol | Hybridize Date Nov 29 2005
| | Sample_scan_protocol | Pixel Size 1.56
| | Sample_scan_protocol | Filter 570
| | Sample_scan_protocol | Scan Temperature
| | Sample_scan_protocol | Scan Date Nov 29 2005
| | Sample_scan_protocol | Scanner ID 50206370
| | Sample_scan_protocol | Number of Scans 1
| | Sample_scan_protocol | Scanner Type M10
| | Sample_data_processing | GCOS 1.2
| | Sample_platform_id | GPL1261
| | 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/GSM389nnn/GSM389349/suppl/GSM389349.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM389nnn/GSM389349/suppl/GSM389349.CHP.gz
| | Sample_series_id | GSE15541
| | Sample_data_row_count | 45101
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