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Sample GSM64940 Query DataSets for GSM64940
Status Public on Jul 22, 2005
Title R1 EB 18h 1, chip MOE430A
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: S209
SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_168
Short description: 18 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: 15.0 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 Apr 01, 2011
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 GPL339
Series (1)
GSE2972 R1 Embryonic Stem Cell and Embryoid Body Time Course
Relations
Reanalyzed by GSE26498

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 1572.42 P 0.0012475
AFFX-BioB-M_at 2924.11 P 6.02111e-05
AFFX-BioB-3_at 1308.7 P 0.000258358
AFFX-BioC-5_at 4599.34 P 9.4506e-05
AFFX-BioC-3_at 3378.32 P 6.02111e-05
AFFX-BioDn-5_at 3393.81 P 4.42873e-05
AFFX-BioDn-3_at 26826.3 P 9.4506e-05
AFFX-CreX-5_at 49365 P 4.42873e-05
AFFX-CreX-3_at 77002.8 P 4.42873e-05
AFFX-DapX-5_at 29895.6 P 4.42873e-05
AFFX-DapX-M_at 53929.1 P 5.16732e-05
AFFX-DapX-3_at 68003.5 P 4.42873e-05
AFFX-LysX-5_at 8216.95 P 4.42873e-05
AFFX-LysX-M_at 12506.9 P 4.42873e-05
AFFX-LysX-3_at 20982 P 4.42873e-05
AFFX-PheX-5_at 2977.36 P 4.42873e-05
AFFX-PheX-M_at 2943.66 P 8.14279e-05
AFFX-PheX-3_at 4286.18 P 4.42873e-05
AFFX-ThrX-5_at 891.144 P 0.000389797
AFFX-ThrX-M_at 1353.5 P 0.000340305

Total number of rows: 22690

Table truncated, full table size 697 Kbytes.




Supplementary file Size Download File type/resource
GSM64940.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM64940.EXP.gz 498 b (ftp)(http) EXP

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