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Status
Public on Dec 31, 2013
Title
TNFa_plastic_rep1
Sample type
RNA
Channel 1 Source name
IMR90, plastic, TNFa
Organism
Homo sapiens Characteristics
cell line: IMR90
Treatment protocol
Cells were treated for 24 hours with IL-4 (10 ng/ml), IL-13 (10ng/ml), or TNFa (10 ng/ml).
Growth protocol
IMR-90 cells (ATCC, Manassas, VA; Catalog # CCL-186) were cultured in DMEM medium supplemented with 10% FBS (Sigma, St. Louis, MO; Catalog # F2442) and Penicillin/Streptomycin (Invitrogen, Carlsbad, CA; Catalog # 15140) on a bed of growth factor reduced Matrigel (GFR Matrigel, BD Biosciences, Bedford, MA; Catalog No. 354230) or plastic.
Extracted molecule
total RNA
Extraction protocol
RNeasy Mini Kit (Qiagen).
Label
Cy5
Label protocol
Biotinylated cRNA were prepared according to the standard Agilent protocol.
Channel 2 Source name
Stratagene Universal Human Reference RNA
Organism
Homo sapiens Characteristics
sample type: reference
Extracted molecule
total RNA
Extraction protocol
Stratagene Universal Human Reference RNA (catalog number 740000).
Label
Cy3
Label protocol
Biotinylated cRNA were prepared according to the standard Agilent protocol.
Hybridization protocol
cRNA was hybridized on Agilent-014850 Whole Human Genome Microarray G4112F.
Scan protocol
Chips were scanned using the Agilent Surescan Microarray Scanner.
Description
SAM630166
Data processing
The data were processed with Agilent Feature Extraction software, version 10.7.3.1, using default settings, including linear and Lowess normalization.
Submission date
May 30, 2013
Last update date
Dec 31, 2013
Contact name
Alex Abbas
E-mail(s)
abbas@gene.com Organization name
Genentech, Inc.
Department
Bioinformatics
Street address
1 DNA Way
City
South San Francisco
State/province
CA
ZIP/Postal code
94080
Country
USA
Platform ID
GPL6480 Series (1)
GSE47542 IMR90 lung fibroblasts treated with IL-4 or IL-13
Data table header descriptions ID_REF VALUE Agilent log2 ratio, test channel (ch1)/reference channel (ch2).
Data table ID_REF VALUE A_23_P100001
-3.6279
A_23_P100011
0.41167
A_23_P100022
-0.94009
A_23_P100056
-1.4112
A_23_P100074
1.6829
A_23_P100092
0.54621
A_23_P100103
0.87545
A_23_P100111
0.547
A_23_P100127
0.28557
A_23_P100133
0.45367
A_23_P100141
0.44454
A_23_P100156
0.55556
A_23_P100177
-0.84065
A_23_P100189
-0.037983
A_23_P100196
-0.39579
A_23_P100203
0.39287
A_23_P100220
-3.0494
A_23_P100240
-2.7056
A_23_P10025
-2.3607
A_23_P100263
0.28438
41107 812 Kbytes .Supplementary file Size Download File type/resource GSM1151945_Agilent_251485053931_S01_GE2_107_Sep09_1_4.txt.gz
4.4 Mb
(ftp) (http) TXT
Processed data included within Sample table
