|
| Status |
Public on Feb 07, 2017 |
| Title |
Patient 3 257015610720_S01_ALK-neg-3 |
| Sample type |
RNA |
| |
|
| Source name |
primary lung cancer
|
| Organism |
Homo sapiens |
| Characteristics |
plasma: primary lung cancer
age: 52 years
gender: Male
smoking history: Yes
histology: Adenocarcinoma
clinical stage: IIIB
alk mutational status: ALK negative
|
| Treatment protocol |
All the participants enrolled had 7ml peripheral venous blood samples collected in the fasting state at morning. Plasma was separated within 30 minutes since the sample collection with the centrifugation at 4,500×g for 10 minutes at 4 ℃ and then stored immediately at -80℃ for further measurements.
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA containing miRNAs was isolated from 200μl plasma with the QIAzol Lysis Reagent (QIAGEN) and purified with the miRNeasy Serum/Plasma Kit (QIAGEN) according to the manufacturer′s instructions.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression in human plasma
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 070156_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Feb 06, 2017 |
| Last update date |
Feb 07, 2017 |
| Contact name |
Xiao-Qing Liu |
| E-mail(s) |
[email protected]
|
| Organization name |
Affiliated Hospital of Academy of Military Medical Sciences
|
| Department |
Department of Lung Cancer
|
| Street address |
8 Dongda Road
|
| City |
Beijing |
| ZIP/Postal code |
100071 |
| Country |
China |
| |
|
| Platform ID |
GPL21576 |
| Series (1) |
| GSE94536 |
Gene expression-signatures for non-small cell lung cancer patients with different ALK mutational status. |
|
