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Sample GSM72871 Query DataSets for GSM72871
Status Public on Sep 01, 2005
Title DR4-1, chip MOE430B
Sample type RNA
 
Source name Embryonic fibroblasts, Embryos (day15)
Organism Mus musculus
Characteristics Strain: 129/SV x OlaHsd x Balb/C x C57BL/6
Growth protocol Growth medium: D-MEM
Media supplements: 15% Hyclone FBS (heat inactivated), Glutamax, sodium pyruvate, non-essential amino acids, Penicillin/Streptomycin, beta-mercaptoethanol, LIF
Culture conditions: Gelatin (0.1%), 37 C, 5% CO2
Extracted molecule total RNA
Extraction protocol RNA prep method: RNeasy
Label Biotin
 
Description This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID: E140
Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=140
SCGP Sample ID: S180
SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=140#SAMPLE_140
Short description: This sample, investigated in triplicate, is a control for the J1, R1 and V6.5 ES samples. The DR4 cell type acts as a feeder cell for stem cells and as such is a small contaminant of the embryonic stem cell growth environment.
RNA concentration: 2.4 ug/ul
Num cells for RNA prep: 12x10e6
Sample volume: 13 ul
Data processing Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06
 
Submission date Aug 30, 2005
Last update date Jan 19, 2006
Organization Ottawa Hospital Research Institute
Phone (613) 737-8899 -73255
Department Cellular and Molecular Medicine
Lab Ottawa Bioinformatics Core Facility
Street address 501 Smyth Rd.
City Ottawa
State/province ON
ZIP/Postal code K1H 8L6
Country Canada
 
Platform ID GPL340
Series (1)
GSE3232 DR4 Control for J1, R1 and V6.5 ES

Data table header descriptions
ID_REF
VALUE 'signal' a measure of the abundance of a transcript. Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06.
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 12160.2 P 0.000856509
AFFX-BioB-M_at 29239 P 5.16732e-05
AFFX-BioB-3_at 14963.9 P 6.02111e-05
AFFX-BioC-5_at 36527.9 P 8.14279e-05
AFFX-BioC-3_at 29973.7 P 5.16732e-05
AFFX-BioDn-5_at 29238.4 P 4.42873e-05
AFFX-BioDn-3_at 188186 P 6.02111e-05
AFFX-CreX-5_at 387804 P 4.42873e-05
AFFX-CreX-3_at 609411 P 4.42873e-05
AFFX-DapX-5_at 67351 P 4.42873e-05
AFFX-DapX-M_at 175018 P 5.16732e-05
AFFX-DapX-3_at 267904 P 4.42873e-05
AFFX-LysX-5_at 15521.8 P 4.42873e-05
AFFX-LysX-M_at 33687.4 P 4.42873e-05
AFFX-LysX-3_at 66501.9 P 5.16732e-05
AFFX-PheX-5_at 6176.7 P 0.00010954
AFFX-PheX-M_at 7362.67 P 0.000581214
AFFX-PheX-3_at 12547.9 P 8.14279e-05
AFFX-ThrX-5_at 1898.27 P 0.036569
AFFX-ThrX-M_at 4187.66 P 0.00401721

Total number of rows: 22575

Table truncated, full table size 664 Kbytes.




Supplementary file Size Download File type/resource
GSM72871.CEL.gz 3.2 Mb (ftp)(http) CEL
GSM72871.EXP.gz 495 b (ftp)(http) EXP

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