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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 09, 2005 |
| Title |
6999A, chip MOE430B |
| Sample type |
RNA |
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| Source name |
R1 embryonic stem cell line (Oct-4 GFP), Blastocyst
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| Organism |
Mus musculus |
| Characteristics |
Strain:
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| Treatment protocol |
Assays to confirm viability: Trypan blue exclusion, embryoid body and colony forming assays
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| Growth protocol |
Growth medium: DMEM, 15% FBS
Media supplements: LIF, glutamine, non-essential amino acids, penicillin/streptomycin
Culture conditions: 5% CO2, 37C, grown on gelatin
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA prep method: RNeasy
Contaminating cell type: None
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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. James Piret (jpiret@chml.ubc.ca; 315-6174 University Boulevard) for analysis.
Stembase Experiment ID: E177
Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=177
SCGP Sample ID: S219
SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=177#SAMPLE_177
Short description: RNA samples generated from 3 days growth in serum lot 6999.
Estimated purity: 100%
RNA concentration: 100 ug/ul
Num cells for RNA prep: 3.1x10e6
Sample volume: 10.0 ul
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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 |
GPL340 |
| Series (1) |
| GSE3774 |
Gene Expression in Embryonic Stem Cells Grown in a Maintenance Serum vs. a Non-maintenance Serum |
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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 |
6843.45 |
P |
0.0044838 |
| AFFX-BioB-M_at |
11926.4 |
P |
4.42873e-05 |
| AFFX-BioB-3_at |
7415.76 |
P |
0.00010954 |
| AFFX-BioC-5_at |
22563.8 |
P |
0.00010954 |
| AFFX-BioC-3_at |
17347.7 |
P |
7.00668e-05 |
| AFFX-BioDn-5_at |
16156.9 |
P |
0.000169227 |
| AFFX-BioDn-3_at |
100328 |
P |
6.02111e-05 |
| AFFX-CreX-5_at |
190291 |
P |
4.42873e-05 |
| AFFX-CreX-3_at |
356670 |
P |
4.42873e-05 |
| AFFX-DapX-5_at |
271858 |
P |
4.42873e-05 |
| AFFX-DapX-M_at |
423257 |
P |
4.42873e-05 |
| AFFX-DapX-3_at |
405136 |
P |
4.42873e-05 |
| AFFX-LysX-5_at |
172980 |
P |
4.42873e-05 |
| AFFX-LysX-M_at |
406777 |
P |
4.42873e-05 |
| AFFX-LysX-3_at |
389032 |
P |
4.42873e-05 |
| AFFX-PheX-5_at |
130632 |
P |
4.42873e-05 |
| AFFX-PheX-M_at |
245353 |
P |
4.42873e-05 |
| AFFX-PheX-3_at |
352585 |
P |
4.42873e-05 |
| AFFX-ThrX-5_at |
19668 |
P |
0.00010954 |
| AFFX-ThrX-M_at |
61881.7 |
P |
4.42873e-05 |
Total number of rows: 22575
Table truncated, full table size 666 Kbytes.
| Supplementary file |
Size |
Download |
File type/resource |
| GSM86590.CEL.gz |
3.3 Mb |
(ftp)(http) |
CEL |
| GSM86590.EXP.gz |
499 b |
(ftp)(http) |
EXP |
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