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Sample GSM844857 Query DataSets for GSM844857
Status Public on Dec 31, 2012
Title Boo Control replicate 4
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 BooV4
replicate 4
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 8.263382512 0.4323308
ILMN_1212612 8.280730841 0.3233083
ILMN_1212619 8.227632628 0.6516291
ILMN_1212628 8.29180091 0.2694235
ILMN_1212632 8.28689971 0.2919799
ILMN_1212636 11.56016682 0
ILMN_1212637 8.933575518 0
ILMN_1212645 11.13914283 0
ILMN_1212648 9.785397869 0
ILMN_1212653 8.241715815 0.5601504
ILMN_1212672 9.317345168 0
ILMN_1212682 8.976694703 0
ILMN_1212683 8.163218018 0.8847118
ILMN_1212685 8.253110248 0.5062656
ILMN_1212692 9.572620837 0
ILMN_1212693 8.488773434 0.01503759
ILMN_1212695 10.80708459 0
ILMN_1212698 8.06848101 0.991228
ILMN_1212702 12.98184624 0
ILMN_1212703 8.406490451 0.04010025

Total number of rows: 25697

Table truncated, full table size 817 Kbytes.




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

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