|
| Status |
Public on Mar 27, 2024 |
| Title |
Control whole cell extract replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
genotype: Suv39h1+/y Suv39h2+/-
gender: Male
cell type: CD4+CD8+ double positive thymocytes
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Flow cytometrically sorted DP thymocyte cells (CD45.2+CD19-CD4+CD8+) were fixed in 1% formaldehyde. Chromatin was Mnase digested then immunoprecipitated using anti-LaminB1 antibody. Chromatin was reverse cross-linked and purified using Zymo ChIP clean and concentrator kit.
Libraries were prepared using Illumina TruSeq DNA kit. Libraries were sequenced on an Illumina NextSeq 500 to produce paired-end 81bp reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The replicates FASTQ files were merged, then reads were aligned to the mouse genome (mm10) with Rsubread.
Bam files were sorted with Rsamtools and duplicate reads were removed with MarkDuplicates from Picard tools.
WCE samples were down sampled to the size of the ChIP libraries (~53 million reads) using DownsampleSam from Picard tools.
The Enriched Domain Detector (EDD) tool (https://github.com/CollasLab/edd) was used to call LADs on the bam files using the WCE to the corresponding ChIP (WT: gap penalty 4.79 and bin size 6 kbp, KO: gap penalty 9.1 and bin size 8 kbp). This produced two BED files of peaks, one or control mice and one the DKO mice.
Genome_build: mm10
Supplementary_files_format_and_content: Bed format file containing LADs called by EDD (a tab-delimited text file specifying genomic regions by chromosome name, start position, end position).
|
| |
|
| Submission date |
Aug 14, 2020 |
| Last update date |
Mar 27, 2024 |
| 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) |
| GSE156293 |
LaminB1 ChIP-seq of DP thymocytes from wildtype and Suv39h1 and Suv39h2 double knockout mice |
| GSE156297 |
RNA-seq, LaminB1 ChIP-seq and in situ Hi-C of double positive thymocytes from control and Suv39h1/Suv39h2 double knockout mice |
|
| Relations |
| BioSample |
SAMN15824101 |
| SRA |
SRX8949743 |
