|
| Status |
Public on Dec 09, 2013 |
| Title |
1tumor |
| Sample type |
RNA |
| |
|
| Source name |
human gastric adenocarcinoma tissue
|
| Organism |
Homo sapiens |
| Characteristics |
sample pair: 1
tissue: gastric adenocarcinoma tissue
gender: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from two pool of snap frozen colon cancer tissues and one pool of normal tissues using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.
|
| 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 8x60k array slides
|
| Description |
lncRNA expression
|
| Data processing |
Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies)
|
| |
|
| Submission date |
Dec 09, 2013 |
| Last update date |
Dec 09, 2013 |
| Contact name |
wei gu |
| E-mail(s) |
guwei1206@hotmail.com
|
| Organization name |
ruijin hospital
|
| Street address |
No.197,Rui Jin Er Road
|
| City |
shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL15314 |
| Series (1) |
| GSE53137 |
lncRNAs expression signatures of gastric cancer |
|
