|
| Status |
Public on Aug 03, 2022 |
| Title |
E15_2 [ATAC-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
TEC
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: TEC
age: embryonic 15
genotype: wild type
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Thymi were removed and enzymatically dissociated with Liberase TH and DNase. TEC populations 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 |
Jan 01, 2022 |
| Last update date |
Aug 03, 2022 |
| 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) |
| GSE192873 |
Transcriptional regulation of the thymus master regulator Foxn1 [ATAC-Seq] |
| GSE192875 |
Transcriptional regulation of the thymus master regulator Foxn1 |
|
| Relations |
| BioSample |
SAMN24563442 |
| SRA |
SRX13571897 |
