|
| Status |
Public on Jul 04, 2020 |
| Title |
OC17N: Adjacent normal tissue paired with OC17T |
| Sample type |
RNA |
| |
|
| Source name |
Ovarian normal tissue
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
age: 58y
tissue: Ovarian normal tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the Trizol reagent (Invitrogen) following the manufacturer's protocol. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng total RNA using the One-Color Low Input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-2000 spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K V2 Microarray (G4851B) 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 naturally.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using G3 one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression of ovarian normal tissue
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol: GE1_107_Sep09 and Grid: 039494_D_F_20150609) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Jul 05, 2019 |
| Last update date |
Jul 05, 2020 |
| Contact name |
kexin chen |
| E-mail(s) |
chenkexin@tjmuch.com
|
| Organization name |
Tianjin Medical University Cancer Institute and Hospital
|
| Street address |
huanhu road, tiyuanbei, hexi district
|
| City |
tianjin |
| ZIP/Postal code |
300060 |
| Country |
China |
| |
|
| Platform ID |
GPL16699 |
| Series (1) |
| GSE133859 |
Tumor specific methylome in Chinese high-grade serous ovarian cancer characterized by gene expression profile |
|
