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Status
Public on Sep 01, 2005
Title
J1-D1, chip MOE430B
Sample type
RNA
Source name
J1 ES Cells, embryonic
Organism
Mus musculus
Characteristics
Strain: 129/Sv Gender: Male
Growth protocol
Growth medium: D-MEM Media supplements: 10% fetal bovine serum, glutamax, non-essential amino-acids, penicillin, streptomycin Culture conditions: Bacterial Petri dishes at 37C, 5% CO2 for 5 days
Extracted molecule
total RNA
Extraction protocol
RNA prep method: RNeasy
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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis. Stembase Experiment ID: E95 Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=95 SCGP Sample ID: S127 SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=95#SAMPLE_95 Short description: Total RNA was extracted from J1 embryoid bodies following 5 days of culture. RNA concentration: 2 ug/ul Num cells for RNA prep: 8-10x10E6 Sample volume: 20 ul
Data processing
Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06
Submission date
Aug 30, 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
GPL340
Series (1)
GSE3223
Comparison of Gene Expression Profiles of J1 ES and J1 EB Cells.
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
9381.02
P
0.002867
AFFX-BioB-M_at
12158.8
P
0.000126798
AFFX-BioB-3_at
5271.89
P
0.0239288
AFFX-BioC-5_at
16984.3
P
0.000169227
AFFX-BioC-3_at
14926.4
P
5.16732e-05
AFFX-BioDn-5_at
21137.7
P
4.42873e-05
AFFX-BioDn-3_at
130745
P
8.14279e-05
AFFX-CreX-5_at
251055
P
4.42873e-05
AFFX-CreX-3_at
343840
P
4.42873e-05
AFFX-DapX-5_at
88395.4
P
5.16732e-05
AFFX-DapX-M_at
172833
P
5.16732e-05
AFFX-DapX-3_at
231765
P
4.42873e-05
AFFX-LysX-5_at
23659.9
P
5.16732e-05
AFFX-LysX-M_at
28410.3
P
4.42873e-05
AFFX-LysX-3_at
62064.2
P
4.42873e-05
AFFX-PheX-5_at
8004.99
P
0.000340305
AFFX-PheX-M_at
8866.59
P
0.000340305
AFFX-PheX-3_at
10313.9
P
5.16732e-05
AFFX-ThrX-5_at
3301.82
P
0.00255552
AFFX-ThrX-M_at
4939.34
P
0.00618711
Total number of rows: 22575 Table truncated, full table size 665 Kbytes .Supplementary file
Size
Download
File type/resource
GSM72617.CEL.gz
3.4 Mb
(ftp) (http)
CEL
GSM72617.EXP.gz
500 b
(ftp) (http)
EXP