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Sample GSM861543 Query DataSets for GSM861543
Status Public on Jul 30, 2014
Title WT1 Hypoxia 24h 4X10^5 cells/6cm plate
Sample type RNA
 
Source name TT2 Mouse ES cells WT1 Hypoxia 24h 4X10^5 cells/6cm plate
Organism Mus musculus
Characteristics gender: Male
strain: TT2 (c57BL/6xCBA)
cell type: ES cells
genotype: Wild-type
treatment: Hypoxia
time: 24h
cell density: 4X10^5 cells/6cm plate
Treatment protocol Cells were cultured under hypoxic conditions (1% O2, 5% CO2 at 37°C) in an Invivo2 Hypoxia Workstation 400 hypoxic chamber (Ruskinn Technology) for 4 or 24 hours. Control cells were cultured in normoxic conditions (21% O2, 5% CO2 at 37°C) in a Forma Steri-Cycle CO2 incubator (Thermo Scientific)
Growth protocol Mouse ES cells were maintained and expanded in DMEM supplemented with 10% fetal calf serum, LIF (500U/ml), 55uM 2-mercaptoethanol, 2mM GlutaMAX, 0.1mM non-essential amino acids, 100U/ml Penicillin and 100ug/ml Steptomycin (Invitrogen).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from wild-type, JMJD1a KO, G9a KO or reconstituted G9a KO ES cells subjected to 24 hours normoxia, 4 hours hypoxia or 24 hours hypoxia treatments using the RNeasy Mini kit (Qiagen) according to manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent) using the RNA 6000 Nano Chip kit (Agilent) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >8) for all samples.
Label Cy3
Label protocol 500ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion).
 
Hybridization protocol 750ng of each cRNA sample was hybridized to MouseRef-8 v2.0 Expression BeadChip microarrays (Illumina) as per manufacturer specifications.
Scan protocol Microarrays were scanned on the BeadArray Reader (Illumina, USA) at scan factor 1 as per manufacturer specifications.
Data processing Raw intensity values were subjected to background subtraction on the BeadStudio Data Analysis Software (Illumina) and normalized using the cross-correlation method (Chua et al., 2006). Differential gene expression was identified based on a fold change cutoff of >1.5 compared to the average of the wild-type normoxic controls.
Normalized values represent linear relative data that have not been log transformed. They were obtained from the original microarray raw data after background subtraction on the Illumina Beadstudio platform followed by normalization using the cross-correlation method (Chua et al., 2006) performed on MATLAB.
references: Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.
 
Submission date Jan 12, 2012
Last update date Jul 30, 2014
Contact name Kian Leong LEE
E-mail(s) kianleong.lee@duke-nus.edu.sg
Phone +(65) 6601 3685
Organization name National University of Singapore (NUS)
Department Duke-NUS Medical School
Lab Cancer & Stem Cell Biology Program (CSCB)
Street address #07-21, 8 College Road
City Singapore
State/province Singapore
ZIP/Postal code 169857
Country Singapore
 
Platform ID GPL6885
Series (1)
GSE35061 Role of the hypoxia-inducible histone H3K9 methylation regulating enzymes Jmjd1a and G9a in stem cell self-renewal and tumorigenesis

Data table header descriptions
ID_REF
VALUE Background subtracted cross-correlation method normalised intensity values generated using MATLAB scripts
5374706003_H.Detection Pval

Data table
ID_REF VALUE 5374706003_H.Detection Pval
ILMN_2896528 723.39409 0
ILMN_2721178 151.95848 0
ILMN_3033922 150.06109 0
ILMN_3092673 688.5503 0
ILMN_2816356 38.897195 0
ILMN_2808939 367.14491 0
ILMN_2634564 361.7451 0
ILMN_2737647 20 0.1854637
ILMN_2734484 701.72247 0
ILMN_2952292 51.065742 0
ILMN_2699078 20 0.7418546
ILMN_1213681 112.14655 0
ILMN_2735413 20 0.3233083
ILMN_2735415 20 0.07518797
ILMN_2891688 164.89013 0
ILMN_2637698 347.60757 0
ILMN_2674228 267.13184 0
ILMN_2601546 20 0.2807018
ILMN_1230831 20 0.1541353
ILMN_2848071 22.258093 0.003759399

Total number of rows: 25697

Table truncated, full table size 656 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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