|
| Status |
Public on Feb 05, 2014 |
| Title |
GM19238_Kd_NR3C1_2 |
| Sample type |
RNA |
| |
|
| Source name |
LCL GM19238, Kd NR3C1, 72hrs
|
| Organism |
Homo sapiens |
| Characteristics |
chip number: 22
transfection plate: 4
target gene: NR3C1
kd level: 0.63
rin: 9.1
transfection date: 2011-10-17
|
| 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.
|
| |
|
| 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 |
|
