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Sample GSM72825 Query DataSets for GSM72825
Status Public on Sep 01, 2005
Title CPGSC#31, chip MOE430B
Sample type RNA
 
Source name V6.5 (P18), Embryonic
Organism Mus musculus
Characteristics Strain: 129SV x C57Bl/6
Biomaterial provider Contact details for sample vendor: V6.5 cell line originally obtained from Dr. R. Jaenesch's lab in Boston
Treatment protocol Assays to confirm viability: Stratagene mycoplasma PCR test
Growth protocol Growth medium: ES Cell Medium - DMEM (high glucose)
Media supplements: Hyclone FCS (heat inactivated), non-essential amino acids, Glutamax, Penicillin/Streptomycin, beta-mercaptoethanol
Culture conditions: 37 C, 5% CO2
Extracted molecule total RNA
Extraction protocol RNA prep method: RNeasy
Cell purification method: Cultured
Contaminating cell type: none
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: E113
Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID: S156
SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_116
Short description: 18 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies. All samples investigated in triplicate.
Estimated purity: 100%
RNA concentration: 3.1 ug/ul
Num cells for RNA prep: Unable to break up embryoid bodies to do a cell count.
Sample volume: 30 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)
GSE3231 V6.5 Embryonic Stem Cell and Embryoid Body Time Course

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 10686.4 P 0.000856509
AFFX-BioB-M_at 21038.8 P 5.16732e-05
AFFX-BioB-3_at 9508.82 P 0.000169227
AFFX-BioC-5_at 23253.5 P 9.4506e-05
AFFX-BioC-3_at 16882.3 P 4.42873e-05
AFFX-BioDn-5_at 18118 P 5.16732e-05
AFFX-BioDn-3_at 127876 P 7.00668e-05
AFFX-CreX-5_at 218465 P 4.42873e-05
AFFX-CreX-3_at 316945 P 4.42873e-05
AFFX-DapX-5_at 90009.2 P 4.42873e-05
AFFX-DapX-M_at 212336 P 5.16732e-05
AFFX-DapX-3_at 308975 P 4.42873e-05
AFFX-LysX-5_at 22306.5 P 4.42873e-05
AFFX-LysX-M_at 45373.1 P 4.42873e-05
AFFX-LysX-3_at 57139.3 P 5.16732e-05
AFFX-PheX-5_at 8769.12 P 6.02111e-05
AFFX-PheX-M_at 9393.6 P 0.000146581
AFFX-PheX-3_at 15609.4 P 0.00010954
AFFX-ThrX-5_at 3763.08 P 0.00401721
AFFX-ThrX-M_at 4485.49 P 0.0044838

Total number of rows: 22575

Table truncated, full table size 665 Kbytes.




Supplementary file Size Download File type/resource
GSM72825.CEL.gz 3.2 Mb (ftp)(http) CEL
GSM72825.EXP.gz 507 b (ftp)(http) EXP

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