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Sample GSM1250622 Query DataSets for GSM1250622
Status Public on Mar 25, 2014
Title Primary calvarial osteoblast,Transfected with BICC1_3,RNA extracted 48 hours post-transfection,rep1
Sample type RNA
Source name Primary calvarial osteoblast,Transfected with BICC1_3,RNA extracted 48 hours post-transfection,rep1
Organism Mus musculus
Characteristics gender: Mixed Gender
strain: C57BL6/J
cell type: primary calvarial osteoblasts
Treatment protocol siRNA transfection experiments cells were handled as outlined above except they were plated at 150,000 cells/well, transfected ~24h after plating using Lipofectamine 2000 Reagent (Invitrogen) according to manufacturer’s directions
Growth protocol Primary calvarial osteoblasts were isolated from 3-9 day old neonates using sequential Collagenase P digestions. Cells were plated into 6 well plates at 300,000 cells/2ml sterile plating media (DMEM, 10% heat-inactivated FBS, 100 U/ml penicillin, 100 μg/ml streptomycin) per well.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Qiagen Rneasy Mini Kit.
Label Biotin
Label protocol Biotin-labeled cRNA was synthesized by the total prep RNA amplification kit from Ambion (Austin, TX).
Hybridization protocol cRNA was quantified and normalized to 77 ng/μl, and then 850 ng was hybridized to Beadchips.
Scan protocol The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner. cRNA synthesis, hybridization and scanning was performed by the Genome Sciences Laboratory in the Center for Public Health Genomics at the University of Virginia.
Data processing Illumina GenomeStudio generated raw intensity values. The expression values were transformed using the Variance Stabilizing Transformation (VST), and quantile normalized using the LumiR R package.
Submission date Oct 25, 2013
Last update date Mar 25, 2014
Contact name Charles R Farber
Organization name University of Virginia
Department Center for Public Health Genomics
Street address P.O. Box 800717
City Charlottesville
State/province VA
ZIP/Postal code 22908
Country USA
Platform ID GPL6885
Series (1)
GSE51693 Osteoblast Gene Expression in Response to Bicc1 Knockdown

Data table header descriptions
VALUE lumiR transformed and quantile normalized values
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 10.54701223 1
ILMN_2721178 8.682727483 1
ILMN_3033922 9.949190154 1
ILMN_3092673 11.48089811 1
ILMN_2816356 8.010540529 1
ILMN_2808939 10.12422956 1
ILMN_2634564 8.586184274 1
ILMN_2737647 7.488103987 0.64912
ILMN_2734484 8.717314542 1
ILMN_2952292 7.71591176 0.98622
ILMN_2699078 7.412764066 0.16291
ILMN_1213681 8.711611816 1
ILMN_2735413 7.479783194 0.61028
ILMN_2735415 7.505734729 0.7193
ILMN_2891688 9.216988295 1
ILMN_2637698 11.49155634 1
ILMN_2674228 8.496022621 1
ILMN_2601546 7.572845203 0.87218
ILMN_1230831 7.447365037 0.42607
ILMN_2848071 7.669804547 0.97619

Total number of rows: 25697

Table truncated, full table size 763 Kbytes.

Supplementary data files not provided
Processed data included within Sample table
Raw data are available on Series record

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