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Sample GSM400311 Query DataSets for GSM400311
Status Public on Nov 13, 2009
Title Wild type + NaClO3- (20mM) rep3
Sample type RNA
 
Source name Wild type + NaClO3- (20mM)
Organism Mus musculus
Characteristics cell line: Wild type ES cells
treatment: NaClO3- (20mM) 24 hours
Treatment protocol Cells were treated 24h with either heparan sulfation inhibitor (NaClO3-, 20mM) or FGFR inhibitor (SU5402, 5μM)
Growth protocol Cells were cultured on gelatin coated plates in Glascow MEM (Sigma-Aldrich) supplemented with 15% FBS (Hyclone), 1000 IU/ml LIF, 2-mercaptoethanol, and Non-Essential Amino Acids (Gibco). Medium was changed daily and cells passaged every second day.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from 3 biological replicates of wild-type and Ndst1/2 - /- ES cells subjected to NaCIO3-, SU5402 or control treatments using the RNeasy Mini kit (Qiagen, Germany) according to manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent, USA) using the RNA 6000 Nano Chip kit (Agilent, USA) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >9) for all samples.
Label Biotin
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, USA).
 
Hybridization protocol 750ng of each cRNA sample was hybridized to MouseRef-8 v2.0 Expression BeadChip microarrays (Illumina, USA) as per manufacturer specifications.
Scan protocol Microarrays were scanned on the BeadArray Reader (Illumina, USA) at scan factor 1 as per manufacturer specifications.
Description Biological replicate 3
Data processing The microarray data was subjected to background subtraction on the BeadStudio Data Analysis software (Illumina, USA) and normalized using the Cross-correlation method (Chua et al., 2006). Differentially expressed transcripts were identified based on the mean Log2 fold change in expression values compared to the wild type ES cell controls with a cutoff at 1.5-fold change. Reference: 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 May 06, 2009
Last update date Nov 13, 2009
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)
GSE15974 Heparan Sulfation Dependent FGF Signalling Maintains ES Cells Primed for Differentiation in a Heterogeneous State

Data table header descriptions
ID_REF
VALUE Background subtracted cross-correlation method normalized intensity values generated using MATLAB scripts

Data table
ID_REF VALUE
ILMN_2470646 90.727
ILMN_2972748 37.505
ILMN_1225176 1069.341
ILMN_2778111 74.543
ILMN_1246609 376.855
ILMN_2690839 51.270
ILMN_1260020 88.683
ILMN_1233172 176.409
ILMN_2813830 20.000
ILMN_2689731 87.338
ILMN_2825817 48.076
ILMN_2604835 55.865
ILMN_2611180 48.135
ILMN_2942011 34.989
ILMN_1240318 136.325
ILMN_1224110 30.576
ILMN_2633996 20.000
ILMN_1222824 31.182
ILMN_2723965 20.000
ILMN_2723826 136.408

Total number of rows: 25697

Table truncated, full table size 511 Kbytes.




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

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