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Sample GSM2053643 Query DataSets for GSM2053643
Status Public on Feb 01, 2020
Title DMSO_treated_Lo-Mnase_rep_2
Sample type SRA
 
Source name MCF-7
Organism Homo sapiens
Characteristics tissue: Breast
cell line: MCF-7
agent: DMSO
Treatment protocol To inhibit pol II, MCF7 cells were treated 1µM triptolide or 1µM flavopiridol for 30min
Growth protocol Cells were grown on 15 cm plates in DMEM medium with 10% FBS
Extracted molecule genomic DNA
Extraction protocol Libraries were constructed from Mnase digested DNA using NEXTflex Rapid Illumina DNA-Seq Library Prep Kit(Bioo)
 
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina NextSeq 500
 
Data processing Reads were filtered based on a mean base quality score >20. Reads were mapped to hg19 genome using Bowtie 0.12.8
Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package.
Non-duplicate, uniquely mapped paired-end reads were converted to a single fragment. BedGraph files contain genome coverage information
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph
 
Submission date Feb 03, 2016
Last update date Feb 01, 2020
Contact name Takashi Shimbo
E-mail(s) shimbot@niehs.nih.gov
Organization name NIH/NIEHS
Street address 111 TW Alexander Dr.
City RTP
ZIP/Postal code 27709
Country USA
 
Platform ID GPL18573
Series (1)
GSE77526 MNase-seq analysis in human breast cancer cells
Relations
BioSample SAMN04455074
SRA SRX1558856

Supplementary file Size Download File type/resource
GSM2053643_out_NS50054_150313_NS500489_AH5NJKBGXX.DMSO2-Lo.dedup.singleFrag.sort.bedGraph.gz 844.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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