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Sample GSM86480 Query DataSets for GSM86480
Status Public on Dec 09, 2005
Title R1ES n+2, chip MG_U74Bv2
Sample type RNA
 
Source name ES cell line, Blastocyst
Organism Mus musculus
Characteristics Strain: 129/SV
Defining markers: Oct4
Treatment protocol Assays to confirm viability: None, grown in normal stem cell conditions
Growth protocol Growth medium: 0.1% gelatin
Media supplements: high glucose, +15% HyClone FBS, Lif, NaPyruvate, nonessential aa, L-glutamine, B-mercaptoethanol, !Sample_extract_protocol = RNA prep method: RNeasy
Extracted molecule total RNA
Extraction protocol Cell purification method: None
Contaminating cell type: differentiated ES cells may be present
Method for estimating purity: Visual inspection
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. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID: E11
Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID: S13
SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_11
Short description: R1ES: Embryonic stem cells (WT)
Estimated purity: 95-99%
RNA concentration: 5.10 ug/ul
Sample volume: 40.0 ul
Data processing Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06
 
Submission date Dec 07, 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 GPL82
Series (1)
GSE3766 Trophoblast stem cells

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-MurIL2_at 192.978 A 0.9273
AFFX-MurIL10_at 1087.16 A 0.425962
AFFX-MurIL4_at 141.064 A 0.814869
AFFX-MurFAS_at 663.237 A 0.574038
AFFX-BioB-5_at 22571.1 P 0.000258358
AFFX-BioB-M_at 52420.8 P 4.42873e-05
AFFX-BioB-3_at 31854.3 P 4.42873e-05
AFFX-BioC-5_at 61001 P 6.02111e-05
AFFX-BioC-3_at 56422.8 P 4.42873e-05
AFFX-BioDn-5_at 61524 P 5.16732e-05
AFFX-BioDn-3_at 291755 P 4.42873e-05
AFFX-CreX-5_at 597384 P 4.42873e-05
AFFX-CreX-3_at 787237 P 4.42873e-05
AFFX-BioB-5_st 2620.88 A 0.216524
AFFX-BioB-M_st 3194.28 A 0.0956669
AFFX-BioB-3_st 1314.71 A 0.52976
AFFX-BioC-5_st 1375.74 A 0.368438
AFFX-BioC-3_st 1576 A 0.195266
AFFX-BioDn-5_st 4978.44 M 0.0584438
AFFX-BioDn-3_st 10855.4 P 0.00618711

Total number of rows: 12477

Table truncated, full table size 358 Kbytes.




Supplementary file Size Download File type/resource
GSM86480.CEL.gz 2.6 Mb (ftp)(http) CEL
GSM86480.EXP.gz 518 b (ftp)(http) EXP

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