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Sample GSM1667173 Query DataSets for GSM1667173
Status Public on Jun 02, 2016
Title shNT, normoxia, replicate 1
Sample type SRA
Source name HCT116_shNT_normoxia
Organism Homo sapiens
Characteristics cell line: HCT116
cell type: colorectal carcinoma cell line
shRNA: non-targeting
culture condition: normoxia
Treatment protocol untreated/normoxia: normal growth conditions; hypoxia: 24hrs 1% O2
Growth protocol HCT116 cells were plated in McCoy's 5A medium supplemented with 10%FBS 24hrs prior to treatment
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using TRI reagent according to manufacturer's instructions and quality assessed using Bioanalyzer RNA Pico chips (Agilent). PolyA RNA was purified using the Dynabeads mRNA Direct micro kit (Life Technologies) according to manufacturer's instructions and ribosomal RNA contamination assessed using Bioanalyzer RNA Pico chips.
Libraries for Ion Torrent sequencing were prepared using the Ion Total RNAseq v2 kit (Life Technologies), according to manufactorer's instructions. Yeild and insert-size distribution were measured using Bioanalyzer High Sensitivity DNA chips (Agilent). The final Ion Torrent RNAseq libraries were subjected to an additional size-selection for 120-200bp on a Blue Pippin (Sage Science). Ion Torrent template preparation was carried out using the Ion PI Template OT2 200 Kit v2 and library sequencing carried out on an Ion Torrent Proton sequencer using the Ion PI Sequencing 200 Kit v2 (Life Technologies) according to manufacturer's instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description polyA RNA from HCT116 cells harboring non-targeting shRNA in untreated/normoxic condition
Data processing Signal processing, base calling and removal of barcode and adapter sequences was carried out automatically by the Torrent Suite Software (Life Technologies).
Data quality was assessed using custom scripts and the Fastx toolkit (version, hannonlab.cshl.fastx_toolkit.html). Reads shorter than 30 nt were removed and long reads trimmed to 150nt
Alignment to the human genome (hg19/GRCh37) was carried out using GSNAP (version 2013-10-28) with a mismatch setting of 3%.
Gene level counts were obtained using htseq-count (version 0.5.4p5) with a custom modified GTF annotation file based on an hg19 RefSeq gene list obtained from UCSC table browser (Karolchik et al., 2004).
Differential gene expression was assessed using DESeq (version 1.14.0) in R (version 3.0.3)
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Gene level count data; tab-delimited text
Submission date Apr 27, 2015
Last update date May 15, 2019
Contact name Matthew D Galbraith
Organization name University of Colorado Anschutz Medical Campus
Department Pharmacology & Linda Crnic Institute for Down Syndrome
Street address RC1-N, Mail Stop 8303, Rm. P18-6114 12800 E. 19th Ave.
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
Platform ID GPL17303
Series (1)
GSE68297 PolyA RNAseq from HCT116 cells in normoxia and hypoxia
BioSample SAMN03569159
SRA SRX1011329

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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