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Sample GSM64939 Query DataSets for GSM64939
Status Public on Jul 22, 2005
Title R1 EB 12h 3, chip MOE430B
Sample type RNA
 
Source name R1, Fetal cells
Organism Mus musculus
Characteristics Strain: 129/Sv x 129/Sv-CP
Gender: Male
Biomaterial provider Contact details for sample vendor: R1 sample obtained from Andras Nagy's lab
Growth protocol Growth medium: ES Cell Medium - DMEM (high glucose)
Media supplements: Hyclone FCS (heat inactivated), non-essential amino acids, Glutamax, Penicillin/Streptomycin, sodium pyruvate, beta-mercaptoethanol
Culture conditions: 37 C, 5% CO2
Extracted molecule total RNA
Extraction protocol RNA prep method: RNeasy
Cell purification method: Culturing
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: E165
Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID: S208
SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_167
Short description: 12 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies. All samples investigated in triplicate. The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity: 100%
RNA concentration: 2.0 ug/uL
Num cells for RNA prep: Unable to break up embryoid bodies to do a cell count.
Sample volume: 15 uL
Data processing Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06
 
Submission date Jul 21, 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)
GSE2972 R1 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 12540.2 P 0.000753643
AFFX-BioB-M_at 18124.9 P 0.000126798
AFFX-BioB-3_at 8180.35 P 0.000581214
AFFX-BioC-5_at 28329.3 P 9.4506e-05
AFFX-BioC-3_at 20429.4 P 5.16732e-05
AFFX-BioDn-5_at 18619.2 P 6.02111e-05
AFFX-BioDn-3_at 145403 P 9.4506e-05
AFFX-CreX-5_at 249298 P 4.42873e-05
AFFX-CreX-3_at 359023 P 4.42873e-05
AFFX-DapX-5_at 99410.4 P 4.42873e-05
AFFX-DapX-M_at 262561 P 5.16732e-05
AFFX-DapX-3_at 343818 P 4.42873e-05
AFFX-LysX-5_at 27104.6 P 4.42873e-05
AFFX-LysX-M_at 53545.6 P 4.42873e-05
AFFX-LysX-3_at 99646.7 P 4.42873e-05
AFFX-PheX-5_at 11929.6 P 8.14279e-05
AFFX-PheX-M_at 14368.5 P 8.14279e-05
AFFX-PheX-3_at 21943.3 P 4.42873e-05
AFFX-ThrX-5_at 3249.94 P 0.002867
AFFX-ThrX-M_at 5887.43 P 0.0044838

Total number of rows: 22575

Table truncated, full table size 664 Kbytes.




Supplementary file Size Download File type/resource
GSM64939.CEL.gz 3.2 Mb (ftp)(http) CEL
GSM64939.EXP.gz 490 b (ftp)(http) EXP

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