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Sample GSM4564077 Query DataSets for GSM4564077
Status Public on Aug 30, 2021
Title Aire_KO_B6_2
Sample type SRA
 
Source name Aire_KO_B6_2
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: mTEChi
age: 4-7 weeks
genotype: Aire -/-
Extracted molecule genomic DNA
Extraction protocol Thymi were removed and enzymatically dissociated with Liberase TH and DNase. mTEChi were sorted and chromaton accessible regions purified.
ATAcseq libraries were prepared for sequencing using using a modified ATACseq protocol (Buenrostro et al., 2016, Lara-Astiaso et al., 2014)
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description nucleosome-free chromatin
Data processing Paired-end raw reads were trimmed using cutadapt (with the parameters -q 25 -m 30), and mapped to genome mm10 (Gencode) using bowtie2 (with the parameter --local).
Following alignment, mitochondrial genes are removed from the analysis, and duplicated reads were removed using picard-tools.
Nucleosome-free fragments at the length <120bp were selected from the remaining unique reads, and broad peaks were called using MACS2 (with the parameters --bw 120 -B -f BAMPE --SPMR –B --shift -50 --extsize 100 -keep-dup all -q 0.05).
Genome_build: mm10
Supplementary_files_format_and_content: Peaks detected by MACS2
 
Submission date May 21, 2020
Last update date Aug 30, 2021
Contact name Jakub Abramson
E-mail(s) jakub.abramson@weizmann.ac.il
Organization name Weizmann Institute of Science
Department Department of Immunology
Street address 234 Herzl st.
City Rehovot
ZIP/Postal code 7610001
Country Israel
 
Platform ID GPL19057
Series (2)
GSE151011 Mechanistic dissection of dominant AIRE mutations in mouse models reveals evidence for AIRE auto-regulation [ATAC-seq]
GSE151013 Mechanistic dissection of dominant AIRE mutations in mouse models reveals evidence for AIRE auto-regulation
Relations
BioSample SAMN14993001
SRA SRX8377824

Supplementary file Size Download File type/resource
GSM4564077_Aire_KO_B6_2_peaks.broadPeak.gz 2.2 Mb (ftp)(http) BROADPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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