GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2136448 Query DataSets for GSM2136448
Status Public on Jul 31, 2017
Title RKOparental-1
Sample type SRA
Source name RKOparental-1
Organism Homo sapiens
Characteristics cell line: human colorectal cancer cell line RKO
genotype/variation: parental control
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using an RNeasy Plus Mini kit (Qiagen). The RNA integrity and concentration was determined on a Bioanalyzer instrument (Agilent) using an RNA 6000 Nano kit.
For preparation of samples for RNA sequencing, 1 x10e6 cells were plated and grown for 48 h. The cells were then detached by trypsination and 2 106 cells were pelleted for RNA isolation. RNA samples were prepared using the Qiagen RNeasy Mini kit with on-column DNase treatment according to the provided protocol. RNA quality and concentration was determined by analysis on a Bioanalyzer 2100 instrument using the RNA 6000 nano chip (Agilent).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description RKOparental-1
Data processing The reads were aligned to the human genome hg19 assembly ( using Tophat2 software (version 2.0.4)
The normalized counts summary and statistical tests were performed using the Cufflinks tool (version 2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with normalized counts values for each Sample.
Submission date Apr 28, 2016
Last update date May 15, 2019
Contact name L. H.
Organization name Uppsala University
Street address Dag Hammarskjölds Väg 20
City Uppsala
ZIP/Postal code 751 85
Country Sweden
Platform ID GPL17303
Series (1)
GSE80746 Gene regulation of candidate cancer gene DIP2C
BioSample SAMN04910142
SRA SRX1734394

Supplementary file Size Download File type/resource
GSM2136448_Sample1_counts.txt.gz 125.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap