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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 09, 2005 |
| Title |
U4, chip MOE430B |
| Sample type |
RNA |
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| Source name |
Mammosphere passage 3, Mammary gland
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| Organism |
Mus musculus |
| Characteristics |
Strain: FVB
Gender: Female
Defining markers: Sca-1, Thy-1, Ecadherin
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| Treatment protocol |
Assays to confirm viability: Transplant into cleared fat pad of mice: mammary gland development recapitulated in recipient.
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| Growth protocol |
Growth medium: 3:1 DMEM: F12
Media supplements: B-27 supplement, basic fibroblast growth factor, epidermal growth factor, heparin
Culture conditions: 37C, 5% CO2
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA prep method: TRIzol
Contaminating cell type: 10% myoepithelial cells
Method for estimating purity: Analysis of cellular markers
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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. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID: E199
Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=199
SCGP Sample ID: S255
SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=199#SAMPLE_206
Short description: Undifferentiated mouse mammosphere RNA. Mammospheres are believed to be comprised of stem/progenitor cells.
Estimated purity: 90%
RNA concentration: 2.0 ug/ul
Num cells for RNA prep: ~ 1.0x10e7
Sample volume: 5.0 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) |
| GSE3777 |
Gene Expression Profiles of Undifferentiated and Differentiated Mammospheres |
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| Data table header descriptions |
| ID_REF |
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| 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 |
6153.46 |
P |
0.00227496 |
| AFFX-BioB-M_at |
15518.7 |
P |
7.00668e-05 |
| AFFX-BioB-3_at |
6910.84 |
P |
0.000224668 |
| AFFX-BioC-5_at |
18731.3 |
P |
9.4506e-05 |
| AFFX-BioC-3_at |
12921.1 |
P |
5.16732e-05 |
| AFFX-BioDn-5_at |
20881.7 |
P |
8.14279e-05 |
| AFFX-BioDn-3_at |
117356 |
P |
9.4506e-05 |
| AFFX-CreX-5_at |
211864 |
P |
4.42873e-05 |
| AFFX-CreX-3_at |
292020 |
P |
4.42873e-05 |
| AFFX-DapX-5_at |
108382 |
P |
4.42873e-05 |
| AFFX-DapX-M_at |
185028 |
P |
4.42873e-05 |
| AFFX-DapX-3_at |
251259 |
P |
4.42873e-05 |
| AFFX-LysX-5_at |
30536.1 |
P |
4.42873e-05 |
| AFFX-LysX-M_at |
47848.2 |
P |
4.42873e-05 |
| AFFX-LysX-3_at |
72331.2 |
P |
4.42873e-05 |
| AFFX-PheX-5_at |
9676.36 |
P |
4.42873e-05 |
| AFFX-PheX-M_at |
11534.5 |
P |
4.42873e-05 |
| AFFX-PheX-3_at |
15515 |
P |
5.16732e-05 |
| AFFX-ThrX-5_at |
4119.93 |
P |
0.000258358 |
| AFFX-ThrX-M_at |
4826.28 |
P |
0.00010954 |
Total number of rows: 22575
Table truncated, full table size 668 Kbytes.
| Supplementary file |
Size |
Download |
File type/resource |
| GSM86636.CEL.gz |
3.3 Mb |
(ftp)(http) |
CEL |
| GSM86636.EXP.gz |
504 b |
(ftp)(http) |
EXP |
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