|
Status |
Public on Feb 01, 2020 |
Title |
Mnase_0.1U |
Sample type |
SRA |
|
|
Source name |
MCF-7
|
Organism |
Homo sapiens |
Characteristics |
tissue: Breast cell line: MCF-7 agent: Mnase_0.1U
|
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 |
SAMN04455090 |
SRA |
SRX1558871 |