|
| Status |
Public on Aug 28, 2019 |
| Title |
DN3a_TCF1KO_2 |
| Sample type |
SRA |
| |
|
| Source name |
DN3a thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell type: T cells
genotype: Tcf1-/-
markers: Lin - CD25+ CD44- CD27-
|
| Growth protocol |
DN thymocytes (CD8 - CD4 - ) from Tcf1-/- and wildtype littermates were sorted and subsequently crosslinked with formaldehyde (Sigma). Crosslinking was quenched with Glycine and after cell lysis chromatin was sonicated into fragments.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sonicated chromatin was precleared and incubated with antibodies. TCF-1 (C46C7; #2206 Cell Signalling Technologies).
Nextera DNA Library Prep Kit; Illumina
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The reads were filtered by quality using Trim-galore tool (Krueger, 2015) (default values) and the quality control was driven by FastQC (Andrews, 2010) and MultiQC (Ewels, 2016).
The remained reads were mapped to mm10 using bowtie2 (Langmead et al, 2012) with –very-sensitive parameter. After all, before the peak calling, the read duplicates and multiple mapping reads were removed using Picard tools (http://broadinstitute.github.io/picard).
The peaks for 2 WT and 2 Tcf1 -/- samples were called using MACS2 (Zhang et al, 2008) with the following parameters: -g mm -B –shift -100 -ext 200 –nomodel –q
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with RPKM tracks
|
| |
|
| Submission date |
Sep 04, 2018 |
| Last update date |
Mar 09, 2021 |
| Contact name |
Martijn Cordes |
| E-mail(s) |
[email protected]
|
| Organization name |
Leiden University Medical Centre
|
| Department |
Immunology
|
| Lab |
Staal
|
| Street address |
Albinusdreef 2
|
| City |
Leiden |
| State/province |
Zuid-Holland |
| ZIP/Postal code |
2333 ZA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE119469 |
Tcf1 regulates T lymphocyte lineage fidelity through its target genes Gata3 and Bcl11b |
|
| Relations |
| BioSample |
SAMN09954660 |
| SRA |
SRX4640102 |
