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Sample GSM37110 Query DataSets for GSM37110
Status Public on May 01, 2008
Title S1_d3SB
Sample type RNA
Source name Embryonic stem cell line
Organism Mus musculus
Extracted molecule total RNA
Extraction protocol Total RNAs from adherent ES cells were prepared with the Qiagen column kit and treated with Dnase, 5u/100 microgrames (Sigma).
Label Biotin
Label protocol Biotinylated cRNAs were prepared according to the standard Affymetrix protocole (Expression Analysis Technical manual, 1999).
Hybridization protocol Detailed procedure in Duval et al, 2006. Cell Death and Differentiation, 13,564-575.
Scan protocol Detailed procedure in Duval et al, 2006. Cell Death and Differentiation, 13,564-575.
Description S1 ES cell line, feeder free, derived as described (Hogan BL et al. 1994. Manipulating the mouse embryo. A laboratory manual, second edition. Cold Spring Harbor Laboratory Press, pp255-272), was grown in DMEM, high glucose supplemented with 0.1 mM beta mercaptoethanol, 10% FCS, 400 ug/ml gentamycin and 500 pM Leukaemia Inhibitory Factor (LIF). For microarray experiments, ES cells were diluted at
10 000 cells/ml in ES cell medium without LIF in the presence of 10 uM SB203580. Cell medium was changed every day and cells were lysed after 3 days. Total RNA from adherent cells were extracted using Qiagen RNeasy kit and treated with DNAse. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 1999, Affymetrix). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on murine MG_U74A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and further scanned using the Hewlett-Packard GeneArray Scanner G2500A. The image data were analysed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of the array was arbitrarily set to 300.
Submission date Dec 06, 2004
Last update date Sep 28, 2007
Contact name Helene BOEUF
Phone 05 57 57 46 33
Organization name UMR-CNRS-5164-CIRID
Street address
ZIP/Postal code 33076
Country France
Platform ID GPL32
Series (1)
GSE2042 Apoptosis and differentiation commitment:novel insights revealed by gene profiling studies in mouse Embryonic Stem cells

Data table header descriptions
VALUE MAS 5.0 signal intensity, a measure of transcript abundance
ABS_CALL MAS 5.0 detection call, a flag that indicates if the transcript was present (P), absent (A), marginal (M) or no call (NC)
DETECTION P-VALUE p-value that indicates the significance level of the MAS 5.0 detection call

Data table
100000_at 0 NC -1
100001_at 4.4 A 0.992457
100002_at 12.1 A 0.837065
100003_at 9.9 A 0.715253
100004_at 162.8 P 0.002617
100005_at 805.1 P 0.000219
100006_at 1.3 A 0.781017
100007_at 385.6 P 0.000562
100008_at 0 NC -1
100009_r_at 2900.3 P 0.000219
100010_at 154.1 P 0.001602
100011_at 53.7 P 0.002228
100012_at 35.4 A 0.35869
100013_at 46.4 A 0.67917
100014_at 162.7 P 0.001602
100015_at 148.9 A 0.138765
100016_at 60.8 P 0.019304
100017_at 69.6 A 0.204022
100018_at 64.6 A 0.541184
100019_at 192 P 0.031336

Total number of rows: 12654

Table truncated, full table size 300 Kbytes.

Supplementary file Size Download File type/resource
GSM37110.cel.gz 3.0 Mb (ftp)(http) CEL
GSM37110.exp.gz 489 b (ftp)(http) EXP

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