|
| Status |
Public on Aug 06, 2019 |
| Title |
ATACseq_BMDM_KO_IL4 |
| Sample type |
SRA |
| |
|
| Source name |
ATACseq_BMDM_KO
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype: Slc6a8-/y
cell type: Bone marrow-derived macrophages
treatment: IL4 (10 ng/mL) for 6 hrs
|
| Treatment protocol |
Bone marrow-derived macrophages were untreated or treated with IL4 (10 ng/mL) for 6 hours.
|
| Growth protocol |
Bone marrow isolated from WT and KO mice were cultured with 10% M-CSF for 5 days to differentiate into macrophages.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed by PBS and 50000 cell were re-suspended in 50 μL of lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.5% NP-40) and nuclei were digested with Tn5 enzyme.
DNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina protocols.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using Real Time Analysis.
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.2.5
Reads were filtered as the unsure bases less than 10% and low quality (I<10) bases less than 50%.
Peaks were called using MACS (version1.4.2) with the following setting: P-value < 10^-5)
Annotation was done by using script annotatePeaks.pl in HOMER
Genome_build: mm10
|
| |
|
| Submission date |
Feb 09, 2018 |
| Last update date |
Aug 06, 2019 |
| Contact name |
Liangliang Ji |
| E-mail(s) |
jll14@mails.tsinghua.edu.cn
|
| Organization name |
Institute for Immunology
|
| Department |
School of Medicine
|
| Lab |
Xiaoyu Hu
|
| Street address |
Tsinghua University
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE110403 |
Metabolic reprogramming of macrophage polarization by creatine [ATAC-seq] |
| GSE110456 |
Metabolic reprogramming of macrophage polarization by creatine |
|
| Relations |
| BioSample |
SAMN08513265 |
| SRA |
SRX3677298 |
