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Sample GSM4831259 Query DataSets for GSM4831259
Status Public on Oct 14, 2020
Title LSK input [1296]
Sample type SRA
 
Source name LSK cells
Organism Mus musculus
Characteristics cell type: bone marrow derived progenitor cells
facs cell isolation sort markers: CD4-, CD8-, IL7Ra-, CD11b-, Ly6g-, CD45R-, Ter119-, cKit+, Sca1+
strain: C57BL/6
chip antibody: None
average chromatin size as measured between a 100-500 bp window using the agilent bioanalyzer 7500 chip: 231 bp
Extracted molecule genomic DNA
Extraction protocol Lysates were prepared from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq samples were prepared by end repair, 3’ adenylation, and adaptor ligation using Illumina’s TruSeq ChIP-seq Sample Preparation Kit.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Description 1296
1295.mm10.broadpeak.gz
1927.mm10.broadpeak.gz
Data processing Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm10 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWigs, signal from MACS.
Supplementary_files_format_and_content: broadpeaks, peak calls by MACS.
 
Submission date Oct 13, 2020
Last update date Nov 02, 2020
Contact name Ross Hardison
E-mail(s) rch8@psu.edu
Organization name Pennsylvania State University
Street address 303 Wartik Lab
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platform ID GPL16417
Series (1)
GSE159503 Effects of sheared chromatin length on ChIP-seq quality and sensitivity
Relations
Reanalysis of GSM4255730
BioSample SAMN16434214
SRA SRX9290379

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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