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Sample GSM891172 Query DataSets for GSM891172
Status Public on Mar 09, 2012
Title beta-TC3 cells, 24-hr treatment, 2.4uM, PXD101, Replicate3, Batch_10, HTA2_A02
Sample type RNA
 
Source name beta-TC3 cells
Organism Mus musculus
Characteristics treatment: 24 hrs with 2.4uM, PXD101
Treatment protocol Compounds dissolved at 1000-fold the profiling concentration in DMSO were diluted 1:10 with media and 10 µl were added per well. At the indicated time point (1, 6, 24 h, respectively), cells were lysed in 900 µl buffer RLT (Qiagen) by shaking for 30s, and lysates were immediately frozen in liquid nitrogen.
Growth protocol Cell lines αTC1 and βTC3 were cultured in low-glucose DMEM supplemented by 10% FBS, 10 U/ml penicillin and 50 µg/ml streptomycin. 24 h prior to compound treatment, 3 mio. cells were plated per well in a 6-well plate in 1 ml medium.
Extracted molecule total RNA
Extraction protocol RNA was prepared using Qiagen RNeasy kits according to the manufacturer’s protocol.
Label biotin
Label protocol 1 µg 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). Total RNA was first reverse transcribed using a T7-Oligo(dT) promoter primer in the first strand cDNA synthesis reaction. Following RNAse H-mediated second strand cDNA synthesis, the double-stranded cDNA was purified and served as a template for an in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for cRNA amplification and biotin labeling.
 
Hybridization protocol The biotinylated cRNA targets were normalized, fragmented and hybridized to Affymetrix HT Mouse 430 A peg arrays (Affymetrix 901045). The hybridization and subsequent washing and staining were performed on the Affymetrix GeneChip® Array Station (GCAS) automation platform.
Scan protocol The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332).
Description beta-TC3 cells
Data processing Expression data (in the form of CEL files) from eight 96-well Affymetrix HT_MG-430A arrays was background corrected, normalized and summarized with RMA using GenePattern.
 
Submission date Mar 08, 2012
Last update date Mar 09, 2012
Contact name Paul A Clemons
E-mail(s) pclemons@broadinstitute.org
Phone 617-714-7346
Organization name Broad Institute of Harvard and MIT
Department Chemical Biology Program
Street address 7 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02143
Country USA
 
Platform ID GPL8759
Series (1)
GSE36379 Expression data from mouse pancreatic cell lines treated with chromatin-targeting small molecules

Data table header descriptions
ID_REF
VALUE RMA-normalized signal intensity using GenePattern software

Data table
ID_REF VALUE
1415670_at 356.7230208
1415671_at 1164.01762
1415672_at 294.3241483
1415673_at 277.41832
1415674_a_at 210.4774429
1415675_at 155.6031588
1415676_a_at 545.628061
1415677_at 277.157085
1415678_at 523.7700835
1415679_at 720.1133511
1415680_at 194.4641995
1415681_at 474.1061525
1415682_at 91.80657905
1415683_at 453.8758133
1415684_at 75.34220548
1415685_at 52.09582067
1415686_at 60.13490333
1415687_a_at 1221.901972
1415688_at 387.339617
1415689_s_at 100.092038

Total number of rows: 22716

Table truncated, full table size 522 Kbytes.




Supplementary file Size Download File type/resource
GSM891172.CEL.gz 2.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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