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Sample GSM898220 Query DataSets for GSM898220
Status Public on May 24, 2012
Title RNA-Seq_HCT116-WT_no-treatment_rep2
Sample type SRA
Source name human colorectal carcinoma cell line HCT116
Organism Homo sapiens
Characteristics celll line: HCT116
genotype/variation: Wild type
stimulation: none
chip antibody: none
data processing (alignment) algorithm: Bowtie
Treatment protocol Cells were treated with 10 ng/ml TNF-alpha for 30-60 mins.
Growth protocol HCT116 cells were grown in McCoys media, supplemented with 10% FBS and 1% pen-strep.
Extracted molecule total RNA
Extraction protocol See
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Reads were mapped by bowtie to hg18, keeping only uniquely mapping genes and discarding all but one of clonal reads. RPKM was calculated as the number of reads per kilo base of exon model per million reads mapped. BEDGRAPH files were generated using bed files as the input files. Only chromosome positions with at least 5 monoclonal reads are retained
Genome_build: hg18
Supplementary_files_format_and_content: bed files, BEDGRAPH files: standard UCSC genome browser format
Submission date Mar 21, 2012
Last update date May 15, 2019
Contact name Bing Ren
Organization name University of California, San Diego
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platform ID GPL11154
Series (1)
GSE28115 CBX3 Regulates Efficient RNA Processing Genome Wide
SRA SRX130491
BioSample SAMN00829241

Supplementary file Size Download File type/resource
GSM898220_RZY92.BEDGRAPH.gz 1.5 Mb (ftp)(http) BEDGRAPH
GSM898220_RZY92.bed.gz 51.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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