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Sample GSM93593 Query DataSets for GSM93593
Status Public on Jan 24, 2006
Title D4-A3, chip MOE430B
Sample type RNA
 
Source name C57 BL/6 ES cells (D4), Blastocyst
Organism Mus musculus
Characteristics Strain: C57 BL/6
Gender: Male
Karyotype: Normal
Treatment protocol Assays to confirm viability: Production of chimeras
Growth protocol Growth medium: Thromb-XTX-WES
Media supplements: LIF, sodium pyruvate, non-essential amino acids, beta-mercaptoethanol, glutamine
Culture conditions: 5% CO2, 37 C
Extracted molecule total RNA
Extraction protocol RNA prep method: RNeasy
Contaminating cell type: Mouse primary embryonic fibroblasts (MEF)
Method for estimating purity: ES cells grown on MEFs were trypsinized lightly to keep feeders attached. Cell suspension plated on fresh plate at 37 C for 1 hour
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. Marina Gertsenstein ([email protected]; Mount Sinai Hospital, 600 University Avenue room 881) for analysis.
Stembase Experiment ID: E124
Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124
SCGP Sample ID: S167
SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=124#SAMPLE_127
Short description: Late passage, high chimerism, germline, attached.
Estimated purity: ~90%
RNA concentration: 11.0 ul
Num cells for RNA prep: 2.0 ug/ul
Sample volume: ~10X10e6
Data processing Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06
 
Submission date Jan 23, 2006
Last update date Jan 23, 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)
GSE4087 D4 and C2 assessed for chimerism and germline transmission

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 14486.1 P 0.000509415
AFFX-BioB-M_at 26430.9 P 5.16732e-05
AFFX-BioB-3_at 12908.6 P 0.00010954
AFFX-BioC-5_at 33824.1 P 6.02111e-05
AFFX-BioC-3_at 23590 P 4.42873e-05
AFFX-BioDn-5_at 26454.1 P 5.16732e-05
AFFX-BioDn-3_at 183018 P 7.00668e-05
AFFX-CreX-5_at 324637 P 4.42873e-05
AFFX-CreX-3_at 553793 P 4.42873e-05
AFFX-DapX-5_at 76100.4 P 4.42873e-05
AFFX-DapX-M_at 279365 P 5.16732e-05
AFFX-DapX-3_at 496818 P 4.42873e-05
AFFX-LysX-5_at 27155.3 P 4.42873e-05
AFFX-LysX-M_at 71098.7 P 4.42873e-05
AFFX-LysX-3_at 165970 P 4.42873e-05
AFFX-PheX-5_at 6589.3 P 0.000146581
AFFX-PheX-M_at 10625.3 P 0.00010954
AFFX-PheX-3_at 26731.1 P 5.16732e-05
AFFX-ThrX-5_at 2975.85 P 0.00844047
AFFX-ThrX-M_at 5727.98 P 0.00227496

Total number of rows: 22575

Table truncated, full table size 664 Kbytes.




Supplementary file Size Download File type/resource
GSM93593.CEL.gz 3.1 Mb (ftp)(http) CEL
GSM93593.EXP.gz 498 b (ftp)(http) EXP

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