|
| Status |
Public on Sep 18, 2012 |
| Title |
Primary_Fibroblast_p4_631.1768.1.1 |
| Sample type |
RNA |
| |
|
| Source name |
primary fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary fibroblast
gender: MALE
passage number: 4
loring pipeline sample id: 631.1768.1.1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the MirVana RNA extraction kit (Ambion), quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
Primary_Fibroblast_p4_631.1768.1.1wq
SAMPLE 12
|
| Data processing |
The unnormalized data (for both v3 and v4 platform) were filtered in GenomeStudio for pvalue<=0.01 using OR clause. This resulted in 19015 probes for v3 platform and 25413 probes for v4 platform. The common probes between the 2 platforms were matched by sequence \(100% match\) and one single file was produced for all the samples under study. Only the common probes between the two platforms were normalized using robust spline normalisation (RSN) with lumi in R. The processed data are on the Series record.
|
| |
|
| Submission date |
Sep 11, 2012 |
| Last update date |
Sep 18, 2012 |
| Contact name |
Rathi D Thiagarajan |
| E-mail(s) |
rthiagarajan@ucsd.edu
|
| Organization name |
UCSD
|
| Department |
Reproductive Medicine
|
| Lab |
Louise Laurent
|
| Street address |
2880 Torrey Pines Scenic Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE40793 |
Conversion of human fibroblasts into vascular cells (gene expression) |
| GSE40927 |
Conversion of human fibroblasts into vascular cells |
|
