|
| Status |
Public on Nov 01, 2016 |
| Title |
SW480-KR12-500nM-6h-rep3 |
| Sample type |
RNA |
| |
|
| Source name |
SW480 cultures, 500 nM biotinylated KR12 incubation, 6 h
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colon
|
| Treatment protocol |
Samples were administered 500 nM KR12 or 0.05% DMSO for 6 h prior to extraction.
|
| Growth protocol |
SW480 cultures at 9.6 × (10^4) cells per sample were plated in a 6-well microtiter plate for overnight attachment prior to treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Samples at 100 ng were labeled with RNA Spike-In Kit.
|
| |
|
| Hybridization protocol |
Sample preparations were performed on SurePrint G3 Human GE 8x60K V2 microarrays per Agilent Technologies’ recommendations.
|
| Scan protocol |
Data acquisition was performed on an Agilent SureScan microarray scanner.
|
| Description |
RNA Spike-In Kit
|
| Data processing |
Differential expressions of microarray data were calculated by the LIMMA package in R. Replicates underwent background correction by the “normexp” method with an offset of 16, and scale-normalized for replicate spots between arrays. After a linear model fit for each gene was determined, statistical evaluations and differential expressions were compiled via the method of empirical Bayes, with fold changes calculated based on difference in responses between DMSO and KR12 treatments. Spots with matching RefSeq mRNA and ncRNA identifiers were filtered and retained for subsequent analyses.
|
| |
|
| Submission date |
Sep 08, 2016 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Jason Lin |
| Organization name |
Chiba Cancer Center Research Institute
|
| Street address |
666-2 Nitona-cho, Chuo-ku
|
| City |
Chiba |
| State/province |
Chiba |
| ZIP/Postal code |
260-8717 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16699 |
| Series (2) |
| GSE86598 |
Alkylating pyrrole-imidazole polyamide KR12 binding in colorectal cancer genomes (SW480) |
| GSE86599 |
Alkylating pyrrole-imidazole polyamide KR12 binding in colorectal cancer genomes |
|
| Relations |
| Reanalyzed by |
GSE113533 |
