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Sample GSM2080017 Query DataSets for GSM2080017
Status Public on May 08, 2016
Title WT Macrophage 0HR Rep1
Sample type SRA
 
Source name WT mouse bone marrow-derived macrophage
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: wild type
gender: female
cell type: macrophage
treated with: 100ng/ml LPS for 0h
Treatment protocol Cells were stimulated with 100ng/ml LPS for 0, 2, or 6 hours and subjected to ATAC-Seq
Growth protocol Bone marrow cells from WT or lincRNA-EPS KO mice were grown in L929 macrophage growth supplement (20%) for 9 days.
Extracted molecule genomic DNA
Extraction protocol 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit and sequenced using an Illumina NextSeq.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description WT_0h_Rep1
Data processing library strategy: ATAC-seq
ATAC-seq paired-end reads were trimmed for Illumina adapter sequences and transposase sequences using an in-house script and mapped to mm9 using Bowtie2 v2.1.0 with parameters –very sensitive. Duplicate reads were removed with Picard . Peak calling was performed by MACS2 narrow peak mode with parameters –q 0.01 –nomodel –shift 0.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files are ENCODE narrowPeak format. 1 chrom, 2 chromStart, 3 chromEnd, 4 name, 5 score, 6 strand, 7 signalValue, 8 pvalue, 9 qvalue
 
Submission date Mar 03, 2016
Last update date May 15, 2019
Contact name Howard Chang
Organization name Stanford University
Street address 269 Campus Dr. Stanford, CA
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL19057
Series (1)
GSE78873 A long noncoding RNA lincRNA-EPS acts as a transcriptional brake to restrain inflammation
Relations
BioSample SAMN04530896
SRA SRX1612910

Supplementary file Size Download File type/resource
GSM2080017_WT_0h_rep1_peaks.narrowPeak.gz 1.8 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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