|
| Status |
Public on Jul 01, 2012 |
| Title |
CAP04.0648P |
| Sample type |
RNA |
| |
|
| Source name |
Control buffer exposed LCLs
|
| Organism |
Homo sapiens |
| Characteristics |
exposure: 90129
rna labeling batch: 10
hybridization batch: 4482545382
cell growth rate: 60
age (yrs): 46.95
gender: Female
bmi: 24.5
smoking status: 0
donor: CAP04.0648
|
| Treatment protocol |
Cells were exposed to 2micromolar activated beta-hydroxy simvastatin acid or control buffer for 24 hours.
|
| Growth protocol |
Cells were grown at 37C (95%O2, 5% CO2) in RPMI 1640 medium (Invitrogen) supplementded with 10% fetal bovine serum (HyClone), 500U/ml penicillin/streptomycin, and 2 nmol/L GlutaMAX (Invitrogen). Cells were normalized to a uniform density upon start of exposures
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in RNA later (Ambion) and RNA was isolated using the Qiagen miniprep RNA isolation kit with column DNAse treatment.RNA quality and quantity were assessed by Nanodrop ND-1000 spectrophotometer and Agilent bioanalyzer, respectively.
|
| Label |
biotin
|
| Label protocol |
RNA was amplified and biotin labeled using the Illumina TotalPrep-96 RNA amplification kit.
|
| |
|
| Hybridization protocol |
Samples were hybridized to Illumina HumanRef-8v3 beadarrays using standard Illumina protocols
|
| Scan protocol |
Beadarrays were scanned using BeadScanner using standard protocols.
|
| Description |
CAP04.0648 Control buffer exposed LCLs
|
| Data processing |
Data was read into GenomeStudio and quantile adjusted for between array intensity effects. Signal was averaged across probes within each gene as annotated based on ensMBL Build 54. Data was then normalized seperately for simvastatin treated and control treated samples. Within each subset, data was quantile normalized around the quantiles of the standard normal distribution for each gene and then adjusted for known covariates (exposure batch, RNA batch, hybridization batch, cell growth rate, and the age, gender, BMI, and smoking status of donors) using linear regression. Residuals were then adjusted using linear regression for unknown covariates as represented by the top 30 principal components. Residuals were than quantile normalized again.
|
| |
|
| Submission date |
Mar 28, 2012 |
| Last update date |
Jul 01, 2012 |
| Contact name |
Lara Mangravite |
| E-mail(s) |
lara.mangravite@sagebase.org
|
| Organization name |
Sage Bionetworks
|
| Street address |
1100 Fairview Ave North
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
| |
|
| Platform ID |
GPL6883 |
| Series (1) |
| GSE36868 |
Simvastatin treated Lymphoblastoid Cell lines from Cholesterol and Pharmacogenomics (CAP) Trial |
|
