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| Status |
Public on Sep 01, 2005 |
| Title |
CPGSC#20, chip MOE430B |
| Sample type |
RNA |
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| Source name |
V6.5 (P18), Embryonic
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| Organism |
Mus musculus |
| Characteristics |
Strain: 129SV x C57Bl/6
Gender: Male
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| Biomaterial provider |
Contact details for sample vendor: V6.5 cell line originally obtained from Dr. R. Jaenesch's lab in Boston
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| Treatment protocol |
Assays to confirm viability: Stratagene mycoplasma PCR test
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| Growth protocol |
Growth medium: ES Cell Medium - DMEM (high glucose)
Media supplements: Hyclone FCS (heat inactivated), non-essential amino acids, Glutamax, Penicillin/Streptomycin, sodium pyruvate, beta-mercaptoethanol, LIF
Culture conditions: 37 C, 5% CO2
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA prep method: RNeasy
Cell purification method: Cultured
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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID: E113
Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID: S153
SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_113
Short description: 0 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies. All samples investigated in triplicate.
Estimated purity: 100%
RNA concentration: 3.8 ug/ul
Num cells for RNA prep: 2X10e6
Sample volume: 30 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 |
Aug 30, 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) |
| GSE3231 |
V6.5 Embryonic Stem Cell and Embryoid Body Time Course |
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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 |
12928.5 |
P |
0.000662269 |
| AFFX-BioB-M_at |
25134.1 |
P |
4.42873e-05 |
| AFFX-BioB-3_at |
12168.5 |
P |
0.000224668 |
| AFFX-BioC-5_at |
31129.5 |
P |
9.4506e-05 |
| AFFX-BioC-3_at |
29293.5 |
P |
7.00668e-05 |
| AFFX-BioDn-5_at |
32883.5 |
P |
4.42873e-05 |
| AFFX-BioDn-3_at |
178757 |
P |
7.00668e-05 |
| AFFX-CreX-5_at |
372213 |
P |
4.42873e-05 |
| AFFX-CreX-3_at |
623145 |
P |
4.42873e-05 |
| AFFX-DapX-5_at |
85009.7 |
P |
4.42873e-05 |
| AFFX-DapX-M_at |
204080 |
P |
5.16732e-05 |
| AFFX-DapX-3_at |
301092 |
P |
4.42873e-05 |
| AFFX-LysX-5_at |
23534.9 |
P |
4.42873e-05 |
| AFFX-LysX-M_at |
33384.9 |
P |
4.42873e-05 |
| AFFX-LysX-3_at |
81454.7 |
P |
6.02111e-05 |
| AFFX-PheX-5_at |
7607.22 |
P |
8.14279e-05 |
| AFFX-PheX-M_at |
9217.08 |
P |
0.000126798 |
| AFFX-PheX-3_at |
15875.7 |
P |
7.00668e-05 |
| AFFX-ThrX-5_at |
2894.83 |
P |
0.026111 |
| AFFX-ThrX-M_at |
5012.51 |
M |
0.0542134 |
Total number of rows: 22575
Table truncated, full table size 663 Kbytes.
| Supplementary file |
Size |
Download |
File type/resource |
| GSM72803.CEL.gz |
2.9 Mb |
(ftp)(http) |
CEL |
| GSM72803.EXP.gz |
512 b |
(ftp)(http) |
EXP |
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