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Status |
Public on Feb 05, 2014 |
Title |
GM19238_Kd_ARNTL2_1 |
Sample type |
RNA |
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Source name |
LCL GM19238, Kd ARNTL2, 72hrs
|
Organism |
Homo sapiens |
Characteristics |
chip number: 9 transfection plate: 1 target gene: ARNTL2 kd level: 0.84 rin: 9.2 transfection date: 2011-03-29
|
Biomaterial provider |
Coriell, http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM19238
|
Treatment protocol |
Cells were transfected with Lonza 96-well Nucleofector system, using solution SF and program DN-100. For each knockdown, 1 million cells were transfected with 50pmol of siRNA and total RNA was extracted 72 hours later.
|
Growth protocol |
Cells were grown at 37°C with 5% CO2 in RPMI-1640 (containing L-glutamine) supplemented with 15% FBS, 100 IU/ml penicilin and 100 µg/ml streptomycin.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy Plus 96 extraction kit. RNA quality was assessed with Agilent Bioanalyzer.
|
Label |
Biotin
|
Label protocol |
Standard protocol
|
|
|
Hybridization protocol |
Standard protocol
|
Scan protocol |
Standard protocol
|
Data processing |
First, probes overlapping SNPs were filtered out and the 3'-most probe for each gene was chosen. Then probes not meeting the detection threshold in at least one individual were filtered out. Intensity values were then log-transformed and quantile normalized using the 'lumi' package in R. Finally, the samples were corrected using the RUV-2 method.
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|
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Submission date |
Sep 04, 2013 |
Last update date |
Feb 05, 2014 |
Contact name |
Darren A. Cusanovich |
E-mail(s) |
darrenc@arizona.edu
|
Organization name |
University of Arizona
|
Department |
Cellular and Molecular Medicine
|
Street address |
1230 N Cherry Avenue, BSRL 421
|
City |
Tucson |
State/province |
AZ |
ZIP/Postal code |
85721 |
Country |
USA |
|
|
Platform ID |
GPL10558 |
Series (1) |
GSE50588 |
The Functional Consequences of Variation in Transcription Factor Binding |
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