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Sample GSM86610 Query DataSets for GSM86610
Status Public on Dec 09, 2005
Title JEACFU-Bi-II, chip RAE230B
Sample type RNA
 
Source name Primary culture; single cell colonies, Calvaria
Organism Rattus norvegicus
Characteristics Strain: Wistar
Gender: Both male and female fetuses
Karyotype: Diploid
Defining markers: Gene expression of osteocalcin, adipcin, L32
Treatment protocol Assays to confirm viability: Colony type was categorized by osteoblast and adipocyte specific gene expression
Growth protocol Growth medium: a-MEM
Media supplements: Ascorbic Acid, BGP, Dex, fetal bovine serum
Culture conditions: 37C, 5% CO2, for 4 weeks
Extracted molecule total RNA
Extraction protocol RNA prep method: RNeasy
Amplification method: Affymetrix small sample target labelling (V. I)
Cell purification method: Single cell sorting by flow cytometry
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. Jane Aubin (jane.aubin@utoronto.ca; 6230 Medical Building; 1 King's College Circle) for analysis.
Stembase Experiment ID: E179
Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=179
SCGP Sample ID: S222
SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=179#SAMPLE_180
Short description: RNA was isolated from colonies expressing both the osteocalcin and the adipsin markers.
Num cells for RNA prep: 100-300 (single colonies)
Sample volume: 17 ul (first strand cDNA)
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 GPL342
Series (1)
GSE3775 Global Gene Expression Profiles of Single-Cell Derived Fetal Rat Calvaria Cell Colonies with Adipocyte and Bone Markers

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 6284.35 P 0.00227496
AFFX-BioB-M_at 10376.1 P 8.14279e-05
AFFX-BioB-3_at 7305.47 P 0.000445901
AFFX-BioC-5_at 19168.3 P 7.00668e-05
AFFX-BioC-3_at 11356.4 P 7.00668e-05
AFFX-BioDn-5_at 16746.9 P 0.000169227
AFFX-BioDn-3_at 97401.6 P 5.16732e-05
AFFX-CreX-5_at 169480 P 4.42873e-05
AFFX-CreX-3_at 277575 P 4.42873e-05
AFFX-DapX-5_at 488.587 A 0.262827
AFFX-DapX-M_at 781.103 M 0.0629293
AFFX-DapX-3_at 487.992 A 0.737173
AFFX-LysX-5_at 81.3136 A 0.737173
AFFX-LysX-M_at 105.223 A 0.904333
AFFX-LysX-3_at 928.556 P 0.0200219
AFFX-PheX-5_at 37.3738 A 0.979978
AFFX-PheX-M_at 54.4354 A 0.843268
AFFX-PheX-3_at 328.654 A 0.631562
AFFX-ThrX-5_at 129.559 A 0.686277
AFFX-ThrX-M_at 241.635 A 0.617401

Total number of rows: 15333

Table truncated, full table size 452 Kbytes.




Supplementary file Size Download File type/resource
GSM86610.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM86610.EXP.gz 505 b (ftp)(http) EXP

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