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| Status |
Public on Dec 09, 2005 |
| Title |
JEACFU-Bi-III, chip RAE230B |
| Sample type |
RNA |
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| Source name |
Primary culture; single cell colonies, Calvaria
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| Organism |
Rattus norvegicus |
| Characteristics |
Strain: Wistar
Gender: Both male and female fetuses
Karyotype: Diploid
Defining markers: Gene expression of osteocalcin, adipcin, L32
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| Treatment protocol |
Assays to confirm viability: Colony type was categorized by osteoblast and adipocyte specific gene expression
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| Growth protocol |
Growth medium: a-MEM
Media supplements: Ascorbic Acid, BGP, Dex, fetal bovine serum
Culture conditions: 37C, 5% CO2, for 4 weeks
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| 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
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| Label |
Biotin
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| 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 ([email protected]; 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)
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| Data processing |
Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06
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| Submission date |
Dec 07, 2005 |
| Last update date |
Jan 19, 2006 |
| Organization |
Ottawa Hospital Research Institute |
| Phone |
(613) 737-8899 -73255
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| Department |
Cellular and Molecular Medicine
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| Lab |
Ottawa Bioinformatics Core Facility
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| Street address |
501 Smyth Rd.
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| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1H 8L6 |
| Country |
Canada |
| |
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| Platform ID |
GPL342 |
| Series (1) |
| GSE3775 |
Global Gene Expression Profiles of Single-Cell Derived Fetal Rat Calvaria Cell Colonies with Adipocyte and Bone Markers |
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| 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 |
22712.4 |
P |
0.00110197 |
| AFFX-BioB-M_at |
29971.3 |
P |
4.42873e-05 |
| AFFX-BioB-3_at |
11530.3 |
P |
0.000972149 |
| AFFX-BioC-5_at |
26649.6 |
P |
8.14279e-05 |
| AFFX-BioC-3_at |
12921.8 |
P |
0.000509415 |
| AFFX-BioDn-5_at |
21813.6 |
P |
0.00159257 |
| AFFX-BioDn-3_at |
231310 |
P |
5.16732e-05 |
| AFFX-CreX-5_at |
500726 |
P |
4.42873e-05 |
| AFFX-CreX-3_at |
722164 |
P |
4.42873e-05 |
| AFFX-DapX-5_at |
862.96 |
A |
0.340661 |
| AFFX-DapX-M_at |
1281.22 |
A |
0.275146 |
| AFFX-DapX-3_at |
1487.08 |
A |
0.275146 |
| AFFX-LysX-5_at |
487.487 |
A |
0.5 |
| AFFX-LysX-M_at |
215.381 |
A |
0.749204 |
| AFFX-LysX-3_at |
2517.6 |
P |
0.00255552 |
| AFFX-PheX-5_at |
225.374 |
A |
0.783476 |
| AFFX-PheX-M_at |
117.678 |
A |
0.973889 |
| AFFX-PheX-3_at |
613.585 |
A |
0.574038 |
| AFFX-ThrX-5_at |
253.356 |
A |
0.921998 |
| AFFX-ThrX-M_at |
898.31 |
A |
0.250796 |
Total number of rows: 15333
Table truncated, full table size 447 Kbytes.
| Supplementary file |
Size |
Download |
File type/resource |
| GSM86612.CEL.gz |
2.2 Mb |
(ftp)(http) |
CEL |
| GSM86612.EXP.gz |
507 b |
(ftp)(http) |
EXP |
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