|
Status |
Public on Feb 24, 2021 |
Title |
cDC1 zfp366 KO CUT&Tag replicate 2 |
Sample type |
SRA |
|
|
Source name |
Splenic conventional dendritic cells 1
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 genotype: zfp366-/- gender: Female biological replicates (mouse pool): 2
|
Treatment protocol |
cDC1/cDC2 isolated from the spleen using collagenase/dnase.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Ampure XP beads As described by Mezger et al., High-throughput chromatin accessibility profiling at single-cell resolution, Nature Communications 9, 3647 (2018).
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
cDC1_WTvsKO_peaks.txt.gz
|
Data processing |
Library strategy: CUT&Tag Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using Rsubread::align. BAM files were sorted with Sambamba v0.6.6 (Tarasov et al., 2015). Duplicate reads were removed and reads were filtered to retain reads with template length between 10 and 300 bp. Biological replicates were combined. For each cDC type, the HOMER pipeline used to call peaks in the wildtype samples with the corresponding knockout samples as the input. Genome_build: GRCm38/mm10 Supplementary_files_format_and_content: HOMER peak files, one for cDC1s and one for cDC2s.
|
|
|
Submission date |
Jan 19, 2021 |
Last update date |
Feb 24, 2021 |
Contact name |
Gordon K Smyth |
E-mail(s) |
smyth@wehi.edu.au
|
Phone |
(+61 3) 9345 2326
|
Fax |
(+61 3) 9347 0852
|
URL |
http://www.wehi.edu.au
|
Organization name |
Walter and Eliza Hall Institute of Medical Research
|
Department |
Bioinformatics
|
Lab |
Smyth
|
Street address |
1G Royal Pde
|
City |
Parkville |
State/province |
Vic |
ZIP/Postal code |
3052 |
Country |
Australia |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE165138 |
DC-SCRIPT (Zpf366) binding in cDC1 and cDC2 cells from wildtype and DC-SCRIPT knockout mice |
GSE165361 |
RNA-seq and CUT&Tag analysis of mouse cDC1 and cDC2 populations upon DC-SCRIPT depletion |
|
Relations |
BioSample |
SAMN17385131 |
SRA |
SRX9898904 |