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Sample GSM87238 Query DataSets for GSM87238
Status Public on Dec 09, 2005
Title Osteo25 VD3-3, chip MOE430B
Sample type RNA
 
Source name D3, Blastocyst
Organism Mus musculus
Characteristics Strain: 129 SV
Gender: Male
Karyotype: normal
Defining markers: n/a
Biomaterial provider Contact details for sample vendor: n/a
Vendor catalogue number: n/a
Treatment protocol Assays to confirm viability: RT-PCR analysis shows expression of osteocalcin (mature osteoblast marker) peaks at day 30. Cbfa1, a transcription factor implicated in osteoblast differentiation shows expression from days 16-25. Osteocalcin, osteopontin, osteonectin, and bone sia
Growth protocol Growth medium: DMEM
Media supplements: Vitamin D3 5 x 10e3 M, B-glycerophosphate, Ascorbic Acid
Culture conditions: 37 C
Extracted molecule total RNA
Extraction protocol RNA prep method: RNeasy
Amplification method: n/a
Cell purification method: clone
Contaminating cell type: Undetermined
Method for estimating purity: n/a
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. Derrick Rancourt (rancourt@ucalgary.ca; Room 2221 Health Sciences Centre; 3330 Hospital Drive NW) for analysis.
Stembase Experiment ID: E202
Stembase Experiment ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202
SCGP Sample ID: S194
SCGP Sample ID link: http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202#SAMPLE_239
Short description: D3 murine embryonic stem cells were allowed to undergo directed differentiation toward the osteoblast lineage by the addition of vitamin D3, B-glycerophosphate, and absorbic acid. Assessment of the gene expression patterns of differentiated cells at day 4, 5, 6, 8, 16, 25, and 30 and comparison to profiles of mES cells that have undergone non-directed differentiation will allow the elucidation of genes that are important to the early commitment of these cells to the osteoblast lineage.
Analysis requested: For SCGP, compare gene expression in samples ctrl vs. VD3 treated in Osteo_1 -- Osteo_4
Cell line clone ID: n/a
Estimated purity: pure clone
RNA concentration: 100 ng/ul
Num cells for RNA prep: 3 x 10^6
Sample volume: 12ul - 6ul for BA and 6 ul for exp
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)
GSE3792 Osteoblast differentiation time course

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 17536 P 0.000509415
AFFX-BioB-M_at 26750.6 P 4.42873e-05
AFFX-BioB-3_at 16103.8 P 5.16732e-05
AFFX-BioC-5_at 40981.2 P 5.16732e-05
AFFX-BioC-3_at 31334.2 P 4.42873e-05
AFFX-BioDn-5_at 36427.8 P 6.02111e-05
AFFX-BioDn-3_at 169482 P 5.16732e-05
AFFX-CreX-5_at 408460 P 4.42873e-05
AFFX-CreX-3_at 523122 P 4.42873e-05
AFFX-DapX-5_at 177328 P 4.42873e-05
AFFX-DapX-M_at 600550 P 4.42873e-05
AFFX-DapX-3_at 749487 P 4.42873e-05
AFFX-LysX-5_at 149305 P 4.42873e-05
AFFX-LysX-M_at 620468 P 4.42873e-05
AFFX-LysX-3_at 645936 P 4.42873e-05
AFFX-PheX-5_at 53496.2 P 4.42873e-05
AFFX-PheX-M_at 160420 P 4.42873e-05
AFFX-PheX-3_at 486989 P 4.42873e-05
AFFX-ThrX-5_at 4115.9 P 0.0020226
AFFX-ThrX-M_at 24417.6 P 4.42873e-05

Total number of rows: 22575

Table truncated, full table size 666 Kbytes.




Supplementary file Size Download File type/resource
GSM87238.CEL.gz 3.1 Mb (ftp)(http) CEL
GSM87238.EXP.gz 510 b (ftp)(http) EXP

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