|
| Status |
Public on Sep 25, 2015 |
| Title |
Lung_Squamous_Carcinoma_Patient1 |
| Sample type |
RNA |
| |
|
| Source name |
Lung Squamous Carcinoma Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Cancer tissue obtained from bronchoscopy
status: Mild-moderate dysplasia
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen tissues using the TRIzol RNA isolation reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s specifications. RNA integrity was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). If the RNA integrity number was greater than or equal to 6.5, the total RNA was purified using the RNeasy Mini Kit (Cat No.74106, Qiagen, Germany). The RNA concentration was determined with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, USA).
|
| Label |
Cy3
|
| Label protocol |
CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent, version 6.6) according to manufacturer's instructions, followed by RNeasy column purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (Nanodrop ND1000, Labtech) and with the Agilent 2100 Bioanalyser.
|
| |
|
| Hybridization protocol |
600 ng of CTP-Cy3-labelled cRNA (specific activity > 10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 25 µl containing 25 x Agilent fragmentation buffer and 10 x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2 x Agilent hybridization buffer were added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent) and 1 min with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief passage in acetonitrile.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides: scan area was 61x21.6 mm, scan resolution 3 µm, dye channel was set to Green, Tiff file dynamic range was 20 bits and Green PMT was set to 100 %.
|
| Description |
Gene expression of lung squamous carcinoma precancerous and cancer tissue
|
| Data processing |
Normalized expression data were extracted with R package “limma” using cyclic loess method, and the ComBat algorithm was utilized to eliminate potential batch effects
|
| |
|
| Submission date |
Sep 24, 2015 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Ning An |
| E-mail(s) |
nick_anning@sina.com
|
| Phone |
86-1087788409
|
| Organization name |
Chinese academy of medical sciences
|
| Street address |
NO.17 Pan Jiayuan Nan Li, Chao Yang District
|
| City |
Beijing |
| ZIP/Postal code |
100021 |
| Country |
China |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE73402 |
Sixty-two lung squamous precancerous and cancer samples obtained from brochoscopy |
|
| Relations |
| Reanalyzed by |
GSE113533 |
