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Sample GSM2306629 Query DataSets for GSM2306629
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
Reanalyzed by GSE113533

Data table header descriptions
VALUE gProcessedSignal

Data table
1 49179.51
2 4.630378
3 4.620721
4 6820.435
5 4.600159
6 4.588606
7 4.578351
8 4.567273
9 123728.3
10 1642.423
11 286.194
12 4568.4
13 117.2914
14 4.496026
15 191.1378
16 12.92662
17 43.75329
18 288.0662
19 564.8431
20 7854.573

Total number of rows: 62976

Table truncated, full table size 904 Kbytes.

Supplementary file Size Download File type/resource
GSM2306629_SW480_KR12-Biotin_3.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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