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Sample GSM544342 Query DataSets for GSM544342
Status Public on Aug 03, 2015
Title FB3158_0m_20
Sample type RNA
 
Source name primary fibroblast, serum starved
Organism Homo sapiens
Characteristics individual id: FB3158
cell type: primary fibroblast
agent: no insulin
time point (insulin treatment): baseline
Treatment protocol To minimize technical variability, fibroblasts from the 35 individuals were passaged, treated and harvested in one batch for the signaling assays and microarray experiments. Fibroblasts from 35 individuals were serum starved for 18 hours and treated with 100nM insulin for one hour and 6 hours. In the ERK inhibition studies, cells from 4 individuals were treated with 10 uM UO126 (Cell Signaling) or DMSO (Sigma-Aldrich) for 1 hour before 100nM insulin or ddH2O (mock treatment) was added, and cells were incubated for another 1 hour or 6 hours before being harvested.
Growth protocol Primary fibroblasts were cultured at 37°C in 5% CO2 in MEM medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 U/mL penicillin and 100 μg/ml streptomycin, and were passaged every 3 days.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cells before or after treatment using RNeasy Micro Kit (QIAGEN).
Label biotin
Label protocol 500ng of total RNA was used for each sample. cRNA was amplified and biotin-labeled following manufacturer's protocol using MessageAmp™ Premier RNA Amplification Kits (Ambion).
 
Hybridization protocol cRNA was fragmented in 1X Fragmentation buffer (Ambion). 10 ug of cRNA were hybridized for 16 hours at 45C on GeneChip Human Genome HG-U133A_2 Arrays (GEO Platform GPL571). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Description primary fibroblast, serum starved
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date May 18, 2010
Last update date Aug 03, 2015
Contact name Isabel Xiaorong Wang
Organization name HHMI/University of Michigan
Department Pediatrics&Genetics
Lab Dr. Vivian G. Cheung Lab
Street address 210 washtenaw ave
City Ann Arbor
State/province Michigan
ZIP/Postal code 48109
Country USA
 
Platform ID GPL571
Series (1)
GSE21891 Expression data from insulin-treated human primary fibroblasts and effects of U0126 on insulin-induced gene expression

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 527.014 P 6.01289e-05
AFFX-BioB-M_at 699.802 P 4.42873e-05
AFFX-BioB-3_at 411.858 P 5.16732e-05
AFFX-BioC-5_at 1356.29 P 4.42873e-05
AFFX-BioC-3_at 1495.71 P 4.42873e-05
AFFX-BioDn-5_at 3473.45 P 4.42873e-05
AFFX-BioDn-3_at 7516.46 P 7.00668e-05
AFFX-CreX-5_at 20445.3 P 5.16732e-05
AFFX-CreX-3_at 23116.2 P 4.42873e-05
AFFX-DapX-5_at 0.782085 A 0.921998
AFFX-DapX-M_at 29.865 A 0.287743
AFFX-DapX-3_at 3.56148 A 0.876428
AFFX-LysX-5_at 1.63315 A 0.804816
AFFX-LysX-M_at 2.24083 A 0.712257
AFFX-LysX-3_at 1.16216 A 0.760937
AFFX-PheX-5_at 1.01919 A 0.984817
AFFX-PheX-M_at 1.03429 A 0.979978
AFFX-PheX-3_at 15.2352 A 0.544587
AFFX-ThrX-5_at 12.2019 A 0.440641
AFFX-ThrX-M_at 1.46537 A 0.883969

Total number of rows: 22277

Table truncated, full table size 677 Kbytes.




Supplementary file Size Download File type/resource
GSM544342.CEL.gz 1.9 Mb (ftp)(http) CEL
GSM544342.CHP.gz 203.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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