|
| Status |
Public on Dec 01, 2011 |
| Title |
PRE_03 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral Blood Mononuclear Cells (PBMC) from Non-small Cell Lung Cancer (NSCLC) patients taken before and after surgery.
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Non-small Cell Lung Cancer (NSCLC)
cell type: Peripheral Blood Mononuclear Cells (PBMC)
surgery: PRE
smoking: S
race: W
Sex: M
age: 68
copd: N
dx: NSCLC
Stage: 3B
days between sample collection: 36
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA purification was carried out at Wistar using TriReagent Molecular Research) as recommended and controlled for quality using the Bioanalyzer. Only samples with 28S/16S ratios >0.75 were used for further studies. A constant amount (500ng) of total RNA was amplified as recommended by Illumina.
|
| Label |
biotin
|
| Label protocol |
Illumina Label Protocol
|
| |
|
| Hybridization protocol |
Samples were hybridized to the human Illumina MicroRNA v2 (Universal 12 Beadchip 1536 bead type) Sentrix Beadchip Array (http://www.illumina.com/pages.ilmn?ID=240) according to standard Illumina protocol.
|
| Scan protocol |
Illumina Setting with PMTFactor=2
|
| Description |
pre- surgery sample
|
| Data processing |
Illumina BeadStudio v.3.0 software was used to export expression levels and detection p-values for each probe of each sample. Arrays were quantile normalized and filtered to remove non-informative miRNA probes. A probe was called non-informative if it had expression signals with detection p-value>0.05 in all samples or if it had expression signals less than 2 average background levels in all samples.
|
| |
|
| Submission date |
Mar 01, 2011 |
| Last update date |
Dec 01, 2011 |
| Contact name |
Louise C Showe |
| E-mail(s) |
lshowe@wistar.org
|
| Phone |
215-898-3791
|
| Organization name |
The Wistar Institute
|
| Lab |
Dr. Louise Showe
|
| Street address |
3601 Spruce St
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL8179 |
| Series (1) |
| GSE27606 |
Resection of Non-Small Cell Lung Cancers Reverses Tumor-Induced Gene Expression Changes in the Peripheral Immune System |
|
