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Sample GSM2175568 Query DataSets for GSM2175568
Status Public on Jul 26, 2016
Title hg19_shGFP_RNA_150331_rep1
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 lentiviral infected with non-targeting shRNA vector
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
E-mail(s) ash@northwestern.edu
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
Relations
BioSample SAMN05164194
SRA SRX1794283

Supplementary file Size Download File type/resource
GSM2175568_hg19_shGFP_RNA_150331_rep1.minus.bw 1.1 Gb (ftp)(http) BW
GSM2175568_hg19_shGFP_RNA_150331_rep1.plus.bw 1.1 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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