|
| Status |
Public on May 08, 2016 |
| Title |
KO Macrophage 6HR Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
LincRNA-EPS KO mouse bone marrow-derived macrophage
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: LincRNA-EPS KO
gender: female
cell type: macrophage
treated with: 100ng/ml LPS for 6h
|
| 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 |
lincRNA-EPS_KO_6h_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 |
SAMN04530894 |
| SRA |
SRX1612920 |
