|
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 |