|
| Status |
Public on Oct 12, 2012 |
| Title |
Donor5_control |
| Sample type |
RNA |
| |
|
| Source name |
Donor5_control
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary CD4+ T cells
batch: 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Total RNA (100-200 ng per sample) was used for preparation of biotin-labeled targets (cRNA) using Illumina® TotalPrep™ RNA Amplification Kit (Life Technologies Inc., Austin, TX) and one round of amplification. The cRNA yields were quantified by UV spectrophotometry and the distribution of transcript sizes was assessed using the Agilent Bioanalyzer 2100 capillary electrophoresis system.
|
| |
|
| Hybridization protocol |
Hybridization of labeled cRNA to the BeadChip, and washing and scanning were performed according to the manufacturer's instructions.
|
| Scan protocol |
BeadArrays were scanned using an Illumina BeadArray Reader. Scanner settings were set at a default for DirectHyb.
|
| Description |
5590177038.sdf
|
| Data processing |
Raw data were extracted using Illumina Genometudio Gene Expression Module v1.1. The data were transformed using variance stabilizing transformation (vst), normalised using robust spline normalisation with Bioconductor package lumi in R and adjusted for batch effect using ComBat (http://statistics.byu.edu/johnson/ComBat/Usage.html). Genes that were not expressed in any of the samples were removed prior to the identification of differentially expressed genes.
|
| |
|
| Submission date |
Oct 11, 2012 |
| Last update date |
Oct 12, 2012 |
| Contact name |
Nadejda S. Beliakova-Bethell |
| E-mail(s) |
nbeliako@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Department |
Medicine
|
| Street address |
9500 Gilman Dr.
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL6947 |
| Series (1) |
| GSE41504 |
Suberoylanilide hydroxamic acid (SAHA) induces limited changes in the transcriptome of primary CD4+ T cells |
|
