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Sample GSM544408 Query DataSets for GSM544408
Status Public on Aug 03, 2015
Title 41-FB#02-DMSO-SS-6h
Sample type RNA
Source name primary fibroblast, DMSO and serum starved,
Organism Homo sapiens
Characteristics individual id: FB#02
cell type: primary fibroblast
agent: DMSO, 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 in presence of DMSO
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
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)

Data table
AFFX-BioB-5_at 534.729 P 6.02111e-05
AFFX-BioB-M_at 904.011 P 4.42873e-05
AFFX-BioB-3_at 452.597 P 4.42873e-05
AFFX-BioC-5_at 1513.21 P 4.42873e-05
AFFX-BioC-3_at 1836.5 P 4.42873e-05
AFFX-BioDn-5_at 3607.39 P 4.42873e-05
AFFX-BioDn-3_at 6913.96 P 4.42873e-05
AFFX-CreX-5_at 18546.4 P 5.16732e-05
AFFX-CreX-3_at 20954.4 P 4.42873e-05
AFFX-DapX-5_at 0.474253 A 0.971554
AFFX-DapX-M_at 19.2134 A 0.440646
AFFX-DapX-3_at 14.3476 A 0.645559
AFFX-LysX-5_at 10.5504 A 0.275129
AFFX-LysX-M_at 1.79603 A 0.973889
AFFX-LysX-3_at 11.4783 A 0.175328
AFFX-PheX-5_at 2.31078 A 0.953518
AFFX-PheX-M_at 0.983984 A 0.963443
AFFX-PheX-3_at 26.7055 A 0.313723
AFFX-ThrX-5_at 12.3296 A 0.382599
AFFX-ThrX-M_at 1.83313 A 0.949771

Total number of rows: 22277

Table truncated, full table size 677 Kbytes.

Supplementary file Size Download File type/resource
GSM544408.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM544408.CHP.gz 202.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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