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Sample GSM86514 Query DataSets for GSM86514
Status Public on Dec 09, 2005
Title 1D1, chip MG_U74Bv2
Sample type RNA
 
Source name Mesenchymal cells, Limb bud
Organism Mus musculus
Characteristics Strain: CD-1
Defining markers: Sox9, type II collagen
Treatment protocol Assays to confirm viability: Cells were allowed to differentiate <i>in vitro</i> into chondrocytes
Extracted molecule total RNA
Extraction protocol RNA prep method: RNeasy
Cell purification method: Cells were isolated from the subridge region of the developing limb
Contaminating cell type: Fibroblasts
Method for estimating purity: Morphology of cultures 3 days post harvest
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. T. Michael Underhill (tunderhi@uwo.ca; 1400 Western Road) for analysis.
Stembase Experiment ID: E30
Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30
SCGP Sample ID: S33
SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30#SAMPLE_31
Short description: Chondroprogenitors harvested at 1 day.
Estimated purity: 90-95%
Num cells for RNA prep: 6x10e6
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)
GSE3770 Temporal Analysis of Differentiating Limb Bud Mesenchymal Cell Gene Expression

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 161.237 A 0.868639
AFFX-MurIL10_at 213.745 A 0.659339
AFFX-MurIL4_at 178.878 A 0.699394
AFFX-MurFAS_at 866.762 M 0.050229
AFFX-BioB-5_at 5127.65 P 0.0020226
AFFX-BioB-M_at 11235.6 P 7.00668e-05
AFFX-BioB-3_at 6811.51 P 0.000169227
AFFX-BioC-5_at 16553.2 P 0.000126798
AFFX-BioC-3_at 14706.5 P 5.16732e-05
AFFX-BioDn-5_at 17920.6 P 6.02111e-05
AFFX-BioDn-3_at 83609.1 P 6.02111e-05
AFFX-CreX-5_at 156416 P 4.42873e-05
AFFX-CreX-3_at 215884 P 4.42873e-05
AFFX-BioB-5_st 471.606 A 0.250796
AFFX-BioB-M_st 508.96 A 0.382599
AFFX-BioB-3_st 428.468 A 0.617401
AFFX-BioC-5_st 180.343 A 0.891021
AFFX-BioC-3_st 607.402 A 0.51489
AFFX-BioDn-5_st 1386.28 A 0.108979
AFFX-BioDn-3_st 2259.47 P 0.0284573

Total number of rows: 12477

Table truncated, full table size 363 Kbytes.




Supplementary file Size Download File type/resource
GSM86514.CEL.gz 2.8 Mb (ftp)(http) CEL
GSM86514.EXP.gz 513 b (ftp)(http) EXP

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