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Sample GSM844864 Query DataSets for GSM844864
Status Public on Dec 31, 2012
Title WT Control replicate 3
Sample type RNA
 
Source name Primary culture of c-Kit enriched bone marrow
Organism Mus musculus
Characteristics strain: C57Bl/6
genotype/variation: wildtype
retrovirus transduction: Control
tissue: Bone marrow
Growth protocol Bone marrow cells were isolated from 4 8-week old Booreana and age matched C57Bl6 mice and enriched for c-Kit expressing cells using MACS CD117 microbeads (Miltenyi). Cells were transduced with retroviral supernatants prepared from MSCV-I-GFP and MSCV-AML1-ETO9a-I-GFP. Cells were transduced by retroviral supernatants by spinoculation using fibronectin (Sigma, F-1141) or Retronectin (Takara) using manufacturer’s guidelines. Cells were cultured in IMDM with 20% fetal calf serum and a cocktail of IL-3, IL-6 and SCF cytokines produced in-house. 48 hours post-transduction, cells were sorted for GFP-positive, c-Kit positive cells on a MoFlo (Beckman Coulter) using an anti-c-Kit PECy7 antibody (eBioscience).
Extracted molecule total RNA
Extraction protocol RNA was extracted with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Label biotin
Label protocol Illumina TotalPrep RNA Amplification Kit (Ambion) was used to make cRNA
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description WTV3
replicate 3
Data processing Variance stabilisation and quantile normalisation using lumi package (R/Bioconductor)
 
Submission date Dec 07, 2011
Last update date Dec 31, 2012
Contact name Konstantin Shakhbazov
Organization name UQDI
Street address Ipswich Road
City Brisbane
ZIP/Postal code 4102
Country Australia
 
Platform ID GPL6885
Series (1)
GSE34224 Interaction of c-Myb with p300 is required for the induction of acute myeloid leukemia (AML) by human AML oncogenes

Data table header descriptions
ID_REF
VALUE quantile normalized signal
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 8.385006111 0.05639098
ILMN_1212612 8.281611963 0.2969925
ILMN_1212619 8.330162665 0.1441103
ILMN_1212628 8.323216804 0.1641604
ILMN_1212632 8.298062938 0.2318296
ILMN_1212636 12.25923268 0
ILMN_1212637 9.727195034 0
ILMN_1212645 11.27695351 0
ILMN_1212648 9.240118783 0
ILMN_1212653 8.321377669 0.1666667
ILMN_1212672 9.707370478 0
ILMN_1212682 8.570760885 0.002506266
ILMN_1212683 8.097493504 0.9874687
ILMN_1212685 8.24937405 0.4849624
ILMN_1212692 10.98017431 0
ILMN_1212693 8.337188704 0.1190476
ILMN_1212695 11.8870222 0
ILMN_1212698 8.118061866 0.9736842
ILMN_1212702 8.67930042 0
ILMN_1212703 8.525029621 0.003759399

Total number of rows: 25697

Table truncated, full table size 811 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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