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Sample GSM770007 Query DataSets for GSM770007
Status Public on Aug 02, 2011
Title aTC1_d5_gw8510_3.3uM_bio rep3
Sample type RNA
 
Source name aTC1 cells, 5-day treatment, 3.3 uM GW8512
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 3
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 1319.312343
1415671_at 5866.240993
1415672_at 4796.972678
1415673_at 946.8167138
1415674_a_at 820.4271043
1415675_at 791.8241637
1415676_a_at 3148.72908
1415677_at 440.5952227
1415678_at 1856.327541
1415679_at 3058.758726
1415680_at 879.1965667
1415681_at 2387.583788
1415682_at 214.541541
1415683_at 3006.358669
1415684_at 534.7131201
1415685_at 880.4044162
1415686_at 1308.203133
1415687_a_at 6235.941714
1415688_at 1634.166714
1415689_s_at 800.1705562

Total number of rows: 22690

Table truncated, full table size 512 Kbytes.




Supplementary file Size Download File type/resource
GSM770007.CEL.gz 2.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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