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Sample GSM86676 Query DataSets for GSM86676
Status Public on Dec 09, 2005
Title 9447-4 -/-, chip MOE430B
Sample type RNA
 
Source name neurospheres, brain germinal zone
Organism Mus musculus
Characteristics Strain: SV129
Defining markers: Nestin Expression
Treatment protocol Assays to confirm viability: Nestin Positive Neurospheres, Cell culture
Growth protocol Growth medium: stem cell medium
Media supplements: bFGF
Culture conditions: Serum Free Stem Cell Medium, 37C, 5%CO2
Extracted molecule total RNA
Extraction protocol RNA prep method: RNeasy, EtOH pptn.
Amplification method: Replication in growth factor supplement
Cell purification method: Specialized growth conditions to select cells
Contaminating cell type: progenitor cells
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. Ruth Slack (rslack@uottawa.ca; ) for analysis.
Stembase Experiment ID: E206
Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=206
SCGP Sample ID: S272
SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=206#SAMPLE_261
Short description: The ganglionic eminence was dissected and neurospheres were cultured from the brain of E13.5 embroys. RNA was isolated from neurospheres cultured from p107-/- embryos and their wildtype littermates. P107 knockout mice have previously been shown to have an increased number of stem cells and enhanced stem cell self renewal. With the microarray experiment we are hoping to discover the genes involved in stem cell number and self renewal along with p107
Analysis requested: compare against wildtype littermates
Estimated purity: minimal non-neural contamination
RNA concentration: 2 ug/uL
Num cells for RNA prep: 15 x 10^6
Sample volume: 10 uL
Data processing Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06
 
Submission date Dec 08, 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)
GSE3779 p107 knockout vs. wild type neurospheres

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 14988.8 P 0.000296708
AFFX-BioB-M_at 22956.8 P 0.000258358
AFFX-BioB-3_at 12603.8 P 0.000509415
AFFX-BioC-5_at 31619.5 P 8.14279e-05
AFFX-BioC-3_at 24210.2 P 5.16732e-05
AFFX-BioDn-5_at 19687.9 P 9.4506e-05
AFFX-BioDn-3_at 144567 P 0.00010954
AFFX-CreX-5_at 272137 P 4.42873e-05
AFFX-CreX-3_at 370056 P 4.42873e-05
AFFX-DapX-5_at 37460.1 P 4.42873e-05
AFFX-DapX-M_at 101602 P 6.02111e-05
AFFX-DapX-3_at 154473 P 4.42873e-05
AFFX-LysX-5_at 8835.24 P 4.42873e-05
AFFX-LysX-M_at 18924.4 P 6.02111e-05
AFFX-LysX-3_at 29843.8 P 4.42873e-05
AFFX-PheX-5_at 2928.9 P 0.000856509
AFFX-PheX-M_at 3721.42 P 0.0239288
AFFX-PheX-3_at 6458.03 P 0.000389797
AFFX-ThrX-5_at 1073.33 A 0.185131
AFFX-ThrX-M_at 1984.98 A 0.102165

Total number of rows: 22575

Table truncated, full table size 665 Kbytes.




Supplementary file Size Download File type/resource
GSM86676.CEL.gz 3.2 Mb (ftp)(http) CEL
GSM86676.EXP.gz 505 b (ftp)(http) EXP

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