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Sample GSM566154 Query DataSets for GSM566154
Status Public on May 19, 2011
Title Gr1/Mac1_rep2
Sample type RNA
 
Source name Bone marrow
Organism Mus musculus
Characteristics cell type: Gr1/Mac1
tissue: Bone marrow
strain: C57BL/6J
location: bred and maintained in the animal research center of the British Columbia Cancer Agency, Vancouver, BC, Canada
Treatment protocol Bone marrow cells were harvested from mice treated with 150 mg of 5-fluorouracil/kg 4 days before harvest and stimulated for 48 hours in 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 (mIL-3), and 20 ng/mL of murine stem cell factor (mSCF; all from StemCell Technologies Inc., Vancouver, Canada). MN1 was introduced into bone marrow cells by cocultivation with irradiated (4,000 cGy) GP+ E86 viral producer cells in the presence of 5 µg/mL protamine sulfate (Sigma-Aldrich, Oakville, Canada). Cells were then sorted for GFP expression and maintained in 6 ng/ml mIL-3, 10 ng/ml hIL-6, and 20 ng/ml mSCF. The transduced bone marrow cells from C57BL/6J mice were then injected into the tail vein of lethally irradiated syngeneic recipient mice that were exposed to a single dose of 750 cGy total-body irradiation accompanied by a life-sparing dose of 1 x 105 freshly isolated bone marrow cells from syngeneic mice. Donor chimerism was monitored by tail vein bleeds and FACS analysis of GFP expressing cells every four weeks. We have showed at the single cell level that CMPs, but not GMPs, are susceptible to MN1-induced transformation. To identify transcriptional differences between CMPs and GMPs that may explain this difference in susceptibilities to MN1 transformation we produced gene expression profiles of bone marrow cells from MN1 leukemic mice and mature myeloid bone marrow cells (Gr1+/CD11b+) from healthy mice and compared those to already published gene expression profiles of CMPs and GMPs (Krivtsov, A.V., et al. (2006). Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9. Nature 442, 818-822).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol reagent (Invitrogen), and RNA quality was assessed using the Bioanalyzer 2100 (Agilent Technologies, Mississauga, ON).
Label Biotin
Label protocol The labeling was done according to the manufacturer instructions.
 
Hybridization protocol Hybridization was done on the Affymetrix GeneChip Mouse430 2.0 microarray according to manufacturer’s instructions.
Protocol EukGE-WS2v5
Wash A1 Recovery Mixes 0
Wash A1 Temperature (C) 30
Number of Wash A1 Cycles 10
Mixes per Wash A1 Cycle 2
Wash B Recovery Mixes 0
Wash B Temperature (C) 50
Number of Wash B Cycles 6
Mixes per Wash B Cycle 15
Stain Temperature (C) 35
First Stain Time (seconds) 300
Wash A2 Recovery Mixes 0
Wash A2 Temperature (C) 30
Number of Wash A2 Cycles 10
Mixes per Wash A2 Cycle 4
Second Stain Time (seconds) 300
Third Stain Time (seconds) 300
Wash A3 Recovery Mixes 0
Wash A3 Temperature (C) 35
Number of Wash A3 Cycles 15
Mixes per Wash A3 Cycle 4
Holding Temperature (C) 25
Scan protocol Pixel Size 1.56
Filter 570
Scan Temperature
Scanner ID 50206370
Number of Scans 1
Scanner Type M10
Description All arrays were performed at British Columbia Genome Sciences Centre, Vancouver, BC, Canada.
Data processing Data were processed using MAS5 with default setting with GCOS 1.3.0.
 
Submission date Jul 13, 2010
Last update date May 19, 2011
Contact name Lars Palmqvist
E-mail(s) lars.palmqvist@clinchem.gu.se
Organization name University of Gothenburg
Department Institute of Biomedicine
Lab Department of Laboratory Medicine
Street address Sahlgrenska University Hospital
City Gothenburg
ZIP/Postal code 41345
Country Sweden
 
Platform ID GPL1261
Series (1)
GSE22923 Cell of origin in AML: Susceptibility to MN1-induced transformation is regulated by the MEIS1/abdB-like HOX protein complex

Data table header descriptions
ID_REF
VALUE VALUE
ABS_CALL ABS_CALL
DETECTION P-VALUE DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 728.898 P 0.0012475
AFFX-BioB-M_at 1078.52 P 4.42873e-05
AFFX-BioB-3_at 637.359 P 7.00668e-05
AFFX-BioC-5_at 2344.63 P 5.16732e-05
AFFX-BioC-3_at 2551.61 P 4.42873e-05
AFFX-BioDn-5_at 4942.2 P 4.42873e-05
AFFX-BioDn-3_at 8482.07 P 7.00668e-05
AFFX-CreX-5_at 21851.1 P 6.02111e-05
AFFX-CreX-3_at 27715.9 P 4.42873e-05
AFFX-DapX-5_at 1.94613 A 0.949771
AFFX-DapX-M_at 5.01653 A 0.824672
AFFX-DapX-3_at 4.07357 A 0.984817
AFFX-LysX-5_at 1.0652 A 0.953518
AFFX-LysX-M_at 12.2734 A 0.760937
AFFX-LysX-3_at 27.8364 M 0.050229
AFFX-PheX-5_at 4.83589 A 0.9273
AFFX-PheX-M_at 1.83471 A 0.92207
AFFX-PheX-3_at 10.7219 A 0.672921
AFFX-ThrX-5_at 31.8536 A 0.250796
AFFX-ThrX-M_at 6.77472 A 0.686292

Total number of rows: 45101

Table truncated, full table size 1369 Kbytes.




Supplementary file Size Download File type/resource
GSM566154.CEL.gz 3.9 Mb (ftp)(http) CEL
GSM566154.CHP.gz 246.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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