|
| Status |
Public on Mar 06, 2020 |
| Title |
1101Cvs1101P |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Lung cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lung adenocarcinoma (LADC)
gender: female
tissue: 60
tumor stage: Ⅱb
alternative id: 151483A_1101C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was first extracted from the specimens using Trizol reagent and purified with Total RNA was first extracted from the specimens using Trizol reagent and purified with NucleoSpin ® RNA clean-up
|
| Label |
Cy5
|
| Label protocol |
1.5 ug of Cy3 or Cy5-labelled cRNA (specific activity >10.0 pmol Cy3 or Cy5/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.
|
| |
|
| Channel 2 |
| Source name |
adjacent to carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: paired paracancerous tissue
gender: female
tissue: 60
tumor stage: Ⅱb
alternative id: 151483A_1101P
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was first extracted from the specimens using Trizol reagent and purified with Total RNA was first extracted from the specimens using Trizol reagent and purified with NucleoSpin ® RNA clean-up
|
| Label |
Cy3
|
| Label protocol |
1.5 ug of Cy3 or Cy5-labelled cRNA (specific activity >10.0 pmol Cy3 or Cy5/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.
|
| |
|
| |
| Hybridization protocol |
cDNA labeled with a fluorescent dye (Cy3 or Cy5-dCTP) was produced by the Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. After purification with Nucleospin ® Extract II kit, the elution volume was about 30 L.Two tubes of cy3 or Cy5-dCTP labeled purified products were mixed.Hybrid system and hybrid reaction.Chip cleaning and scanning.
|
| Scan protocol |
Agilent chip scanner (G2565CA) was used to scan the cleaned chip and obtain the hybrid picture
|
| Description |
JD-YX-2015-1483-JSFU-01
1101Cvs1101P:cy5ByCy3Signal(normalized)
|
| Data processing |
Agilent Feature Extraction (v10.7) software was used to analyze the hybrid images and extract the data.Then, Agilent GeneSpring software was used to normalize and analyze the data.
Scan the tiff image with the Feature Extraction software to obtain the original data file (.txt). Import the original data file (.txt) into GeneSpring software and write the grouping and other parameter information.Conduct data normalization and QC analysis for each sample.Normalization (standardization) method: The default method is the normalization of GeneSpring GX's Percentile 75 method (with each chip itself) Divide the 75 percentile values of the data to get the ratio), and then take the value generated after log2;Another alternative approach. The other method is the normalization of Quantile method of GeneSpring GX software, and then the value generated after log2.
|
| |
|
| Submission date |
Mar 05, 2020 |
| Last update date |
Mar 06, 2020 |
| Contact name |
chunyang jiang |
| E-mail(s) |
chunyangjiang@126.com
|
| Phone |
022-27557493
|
| Organization name |
Tianjin Union Medical Center
|
| Street address |
190 Jieyuan Road, Hongqiao District, Tianjin
|
| City |
Tianjin |
| ZIP/Postal code |
300121 |
| Country |
China |
| |
|
| Platform ID |
GPL20115 |
| Series (2) |
| GSE146459 |
Differentially RNA expression of lung adenocarcinoma and paired paracancerous tissue |
| GSE146461 |
RNA expression of lung adenocarcinoma and paired paracancerous tissue |
|
