GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2175548 Query DataSets for GSM2175548
Status Public on Jul 26, 2016
Title hg19_WT_DMSO_RNA_160219_rep2
Sample type SRA
Source name HCT116
Organism Homo sapiens
Characteristics cell type: Human colorectal tumor
passages: Low passages (6-10)
cell line: HCT116
chip antibody: N/A
Treatment protocol Treatment with GSK126[5uM] or DMSO was administrated at 0- and 48-hour; harvesting cells at 96-hours.
Growth protocol Cell medium was composed as follow: DMEM 1X (Thermo Fisher), 10% serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C
Extracted molecule total RNA
Extraction protocol RNA was extracted using QIAGEN RNeasy kit.
Stranded Total RNA Preparation Kit with
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Cells treated with DMSO for 4 days
Data processing Basecalls were performed using Casava v1.8 and bcl2fastq v2.17 for Illumina HiSeq and NextSeq output,respectively.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
RNA-seq reads were aligned to UCSC hg19 and dm3 using Tophat version 2.0.9. Only uniquely mapping reads with at most two mismatches were retained.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
genome build: hg19
processed data files format and content: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.
Submission date May 23, 2016
Last update date May 15, 2019
Contact name Ali Shilatifard
Organization name Northwestern University Feinberg School of Medicine
Department Department of Biochemistry and Molecular Genetics
Lab Shilatifard Lab
Street address 320 E Superior St
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
Platform ID GPL18573
Series (1)
GSE81795 An epigenetic mark of polycomb response elements implemented by Trx/MLL/COMPASS
BioSample SAMN05164174
SRA SRX1794263

Supplementary file Size Download File type/resource 41.0 Mb (ftp)(http) BW 42.9 Mb (ftp)(http) BW
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