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Sample GSM2306623 Query DataSets for GSM2306623
Status Public on Nov 01, 2016
Title LS180-KR12-500nM-6h-sample2-rep2
Sample type RNA
 
Source name LS180 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 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
Relations
Reanalyzed by GSE113533

Data table header descriptions
ID_REF
VALUE gProcessedSignal

Data table
ID_REF VALUE
1 55896.35
2 3.670389
3 3.676333
4 6551.507
5 3.68363
6 3.686075
7 4.544206
8 4.09871
9 46079.38
10 3.689191
11 596.9827
12 11259.79
13 52
14 3.680909
15 3.677367
16 4.87131
17 291.9606
18 120.0781
19 3.907103
20 6970.528

Total number of rows: 62976

Table truncated, full table size 904 Kbytes.




Supplementary file Size Download File type/resource
GSM2306623_LS180_KR12-Biotin2_2.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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