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Sample GSM435063 Query DataSets for GSM435063
Status Public on Nov 04, 2009
Title Eset shRNA ES cells, biological replicate 2
Sample type RNA
 
Source name R1 mouse embryonic stem (ES) cells
Organism Mus musculus
Characteristics protocol: Eset depletion
cell type: R1 mouse embryonic stem cells
Treatment protocol n.a.
Growth protocol Mouse ES cells were cultured at 37C with 5% CO2. Mouse ES cells were maintained on mitomycin C-treated MEF feeders in Dulbecco's modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM Beta-mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol (Invitrogen) and purified with RNeasy minikit (Qiagen).
Label Biotin
Label protocol Biotinylated cRNA were prepared from 500 ng of total RNA according to the standard protocol (TotalPrep RNA Amplification Kit, Instruction Manual, Catalog #IL1791, Illumina).
 
Hybridization protocol 1.5 ug of cRNA were hybridized to Illumina Mouse Ref-6 V1 for 20 hr at 58oC on Ilumina Hybridization Oven.
Scan protocol Illumina Mouse Ref-6 V1 was washed and stained with streptavidin-Cy3 before scanning using the Illumina Bead Reader.
Description Gene expression data from mouse ES cells
Data processing The data were analyzed using Bead Array suite software. Rank invariant normalization method was chosen to obtain the signal intensity.
 
Submission date Jul 30, 2009
Last update date Mar 24, 2010
Contact name Ping Yuan
E-mail(s) yuanp@gis.a-star.edu.sg
Phone (65)64788144
Fax (65)64789004
Organization name Genome Institute of Singapore
Department Stem Cell
Lab Stem Cell 6
Street address 60 Biopolis Street #02-01
City Singapore
ZIP/Postal code 138672
Country Singapore
 
Platform ID GPL6333
Series (1)
GSE17439 Global gene-expression analyses of the Eset knock-down ES cells

Data table header descriptions
ID_REF Illumina probe ID
VALUE Signal intensity
DETECTION P-VALUE detection p-value

Data table
ID_REF VALUE DETECTION P-VALUE
10181072_239_rc-S 13.9 0.73886139
10181072_290-S 8.1 0.65779703
10181072_290_rc-S 10.4 0.68935644
10181072_311-S -8.4 0.41460396
10181072_311_rc-S -15.5 0.30507426
10181072_418-S -46 0.01237624
10181072_418_rc-S 12.5 0.72029703
10181072_486-S -4.6 0.47586634
10181072_486_rc-S 7 0.64294554
17974913_3385-S 17.9 0.77970297
17974913_3385_rc-S -10.6 0.3799505
17974913_3999_rc-S -18.1 0.26113861
17974913_4071-S -39 0.03527228
17974913_4071_rc-S -37.3 0.04517327
17974913_4426-S -8.9 0.40470297
17974913_4426_rc-S 2.7 0.58539604
17974913_4962-S -37.7 0.04331683
17974913_4962_rc-S -14.4 0.31930693
18S_rRNA_X00686_301-S 18560.2 1
18S_rRNA_X00686_523-S 5978.8 1

Total number of rows: 46120

Table truncated, full table size 1584 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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