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Sample GSM2306618 Query DataSets for GSM2306618
Status Public on Nov 01, 2016
Title LS180-DMSO-6h-sample2-rep1
Sample type RNA
Source name LS180 cultures, DMSO treatment, 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 LS180 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)
GSE86597 Alkylating pyrrole-imidazole polyamide KR12 binding in colorectal cancer genomes (LS180)
GSE86599 Alkylating pyrrole-imidazole polyamide KR12 binding in colorectal cancer genomes
Reanalyzed by GSE113533

Data table header descriptions
VALUE gProcessedSignal

Data table
1 55350.63
2 3.749917
3 3.747559
4 7615.868
5 3.741464
6 3.736918
7 10.59935
8 3.724225
9 30194.21
10 3.710199
11 474.2314
12 12059.58
13 81.72335
14 4.741517
15 5.370162
16 3.649573
17 346.6518
18 158.0293
19 4.640162
20 6197.242

Total number of rows: 62976

Table truncated, full table size 904 Kbytes.

Supplementary file Size Download File type/resource
GSM2306618_LS180_DMSO2_1.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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