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Sample GSM5026913 Query DataSets for GSM5026913
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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