|
| Status |
Public on Mar 15, 2018 |
| Title |
BMDM LPS-EZH2_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow-derived macrophages
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
agent: LPS
tissue: bone marrow
cell type: bone marrow-derived macrophages
chip antibody: EZH2 (Active Motif, catalog# 39901, lot# 1)
|
| Treatment protocol |
non-treated (NT) or stimulated for 2 h with LPS
|
| Growth protocol |
bone marrow cells were isolated from femurs and tibias of adult mice and cultured for 5 days in a DMEM medium supplemented with M-CSF conditional medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The chromatin was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against EZH2 ( Active Motif 39901).
Libraries were prepared according to standard Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
stimulated for 2 h with LPS
|
| Data processing |
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis.
tags are extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp).To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
The two main peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009).
005WIHS_EZH2_ucsctracks.bed represents the custom track for UCSC browser to see location of Intervals and Active Regions. It contains the locations and names of all Intervals (shown as orange bars) and Active Regions (green). It also contains the location and values of the Interval summits (purple).
Genome_build: mm10
Supplementary_files_format_and_content: .bw and .bed
|
| |
|
| Submission date |
Jul 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xingli Zhang |
| E-mail(s) |
zhangxingli@sibs.ac.cn
|
| Organization name |
Institute of Health Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences
|
| Street address |
yueyang road 320
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE101320 |
EZH2 occupancy profiling by high throughput sequencing from macrophages non-treated (NT) or stimulated with LPS |
| GSE101383 |
Macrophage/microglial Ezh2 facilitates autoimmune inflammation through inhibition of Socs3 |
|
| Relations |
| BioSample |
SAMN07346465 |
| SRA |
SRX2997984 |
