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Sample GSM770006 Query DataSets for GSM770006
Status Public on Aug 02, 2011
Title aTC1_d5_gw8510_3.3uM_bio rep2
Sample type RNA
 
Source name aTC1 cells, 5-day treatment, 3.3 uM GW8511
Organism Mus musculus
Characteristics cell line: aTC1
compound: GW8510
Treatment protocol 0.5 ul GW8510, dissolved at 1000-fold desired assay concentration (3.3 uM) in DMSO, was added to begin treatment. For 5-day treatment, media was changed and new compound added on day 3. All compound treatments were performed in 0.1% final DMSO concentration. DMSO treatment was used as a vehicle control
Growth protocol aTC1 cells were cultured in low-glucose DMEM supplemented by 10% FBS, 10 U/ml penicillin and 50 ug/ml streptomycin. 24 h prior to compound treatment, 200,000 cells were plated per well in a 12-well plate in 500 ul medium.
Extracted molecule total RNA
Extraction protocol Following 5-day compound treatment, cells were lysed and RNA isolated using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s protocol.
Label biotin
Label protocol 500 ng of total RNA was used to prepare complementary RNA (cRNA) target with the Genechip® HT One-Cycle cDNA synthesis Kit (Affymetrix 900687) and the GeneChip® HT IVT Labeling Kit (Affymetrix 900688).
 
Hybridization protocol Biotinlyated cRNA targets were normalized, fragmented and hybridized to Affymetrix Mouse 430A 2.0 arrays (GPL8321) using Affymetrix GeneChip® Array Station (GCAS) automation platform.
Scan protocol The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332)
Description Gene expression data from alpha cells (aTC1) treated with 3.3 uM GW8510 in 0.1% DMSO for 5 days, biological replicate 2
Data processing The data were analyzed with GenePattern (modules ExpressionFileCreator, PreProcessDataset, and GSEA) using robust multi-array (RMA) analysis for background correction, thresholding and normalization.
 
Submission date Aug 01, 2011
Last update date Aug 02, 2011
Contact name Dina A. Fomina-Yadlin
E-mail(s) dinafominayadlin@gmail.com
Organization name Broad Institute
Street address 7 Cambridge Center, 3112-D
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL8321
Series (1)
GSE31102 Expression data from GW8510 treatment of pancreatic cells

Data table header descriptions
ID_REF
VALUE Normalized Affymetrix count

Data table
ID_REF VALUE
1415670_at 1360.58442
1415671_at 6162.047402
1415672_at 4359.019338
1415673_at 1034.071491
1415674_a_at 855.7483224
1415675_at 768.2034277
1415676_a_at 3381.871501
1415677_at 382.2011269
1415678_at 1857.934771
1415679_at 2987.550455
1415680_at 916.0996196
1415681_at 2370.564846
1415682_at 215.9530247
1415683_at 3123.366714
1415684_at 505.5917138
1415685_at 782.5036035
1415686_at 1301.096511
1415687_a_at 6263.765737
1415688_at 1723.972486
1415689_s_at 795.2387171

Total number of rows: 22690

Table truncated, full table size 513 Kbytes.




Supplementary file Size Download File type/resource
GSM770006.CEL.gz 2.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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