|
| Status |
Public on Apr 25, 2016 |
| Title |
ZC-03 |
| Sample type |
RNA |
| |
|
| Source name |
primary tumor, lymphnode postive subgroup, replicate 1
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: stage IV colorectal cancer
tissue: primary tumor
age: 45y
gender: female
subgroup: lymph node positive
|
| Treatment protocol |
In our center, 15 patients with resectable mCRC were analyzed, with 7 patients in lymph node negative subgroup and 8 patients in lymph node positive subgroup. Fresh-frozen tissue samples of primary colorectal cancer were obtained. All tissue samples were collected and immediately snap-frozen in liquid nitrogen, and stored at -80˚C until RNA extraction. Written informed consent from each patient was obtained according to the institutional regulations.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation was done with TRIzol (Invitrogen, Carlsbad, CA) according to the instructions of the manufacturer. RNA was quantified using a NanoDrop-1000 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 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 |
1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 52.8ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2600D) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 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 (G2600D) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression of human primary tumor tissue in lymph node positive subgroup in the resectable stage IV colorectal cancer.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Nov 24, 2014 |
| Last update date |
Apr 23, 2018 |
| Contact name |
jianfie fu |
| E-mail(s) |
nuifu@sina.com
|
| Organization name |
The Second Affiliated Hospital of Zhejiang University School of Medicine
|
| Department |
Cancer Institute
|
| Lab |
Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China
|
| Street address |
88 Jiefang Road,
|
| City |
Hangzhou |
| ZIP/Postal code |
310009 |
| Country |
China |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE63596 |
The status of lymph node of resectable distant metastaticcolorectal cancer (stage Ⅳ) as a prognostic predictor |
|
| Relations |
| Reanalyzed by |
GSE113533 |
