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Sample GSM844854 Query DataSets for GSM844854
Status Public on Dec 31, 2012
Title Boo Control replicate 1
Sample type RNA
Source name Primary culture of c-Kit enriched bone marrow
Organism Mus musculus
Characteristics genotype/variation: Booreana
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 BooV1
replicate 1
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
VALUE quantile normalized signal
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 8.310582543 0.1954887
ILMN_1212612 8.219607523 0.6541353
ILMN_1212619 8.337040194 0.1203008
ILMN_1212628 8.192427909 0.7982456
ILMN_1212632 8.205057464 0.735589
ILMN_1212636 12.01122319 0
ILMN_1212637 9.65786651 0
ILMN_1212645 10.60351938 0
ILMN_1212648 9.490217443 0
ILMN_1212653 8.336940932 0.1203008
ILMN_1212672 9.946058516 0
ILMN_1212682 8.605813554 0
ILMN_1212683 8.202774239 0.7418546
ILMN_1212685 8.233758759 0.556391
ILMN_1212692 9.899660593 0
ILMN_1212693 8.243266967 0.5062656
ILMN_1212695 10.84126707 0
ILMN_1212698 8.212612679 0.7030075
ILMN_1212702 12.26487464 0
ILMN_1212703 8.46651102 0.0112782

Total number of rows: 25697

Table truncated, full table size 805 Kbytes.

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

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