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Status
Public on Dec 31, 2013
Title
TNFa_plastic_rep2
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
SAM630167
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
-3.585
A_23_P100011
0.11145
A_23_P100022
-0.72288
A_23_P100056
-1.3591
A_23_P100074
1.7134
A_23_P100092
0.57309
A_23_P100103
0.96727
A_23_P100111
0.46182
A_23_P100127
0.52342
A_23_P100133
0.21134
A_23_P100141
0.66084
A_23_P100156
0.27055
A_23_P100177
-1.0169
A_23_P100189
0.05452
A_23_P100196
-0.65
A_23_P100203
0.44541
A_23_P100220
-2.8703
A_23_P100240
-3.2193
A_23_P10025
-3.2782
A_23_P100263
0.45072
41107 810 Kbytes .Supplementary file Size Download File type/resource GSM1151946_Agilent_251485053932_S01_GE2_107_Sep09_1_4.txt.gz
4.4 Mb
(ftp) (http) TXT
Processed data included within Sample table
