|
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)
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|
|
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
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|
|
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 |