|
| Status |
Public on Mar 27, 2024 |
| Title |
DKO IgG replicate |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Thymus
cell type: CD4+CD8+ double positive thymocytes
antibody: Rabbit IgG pAb (Abcam ab46540)
strain: C57BL/6
genotype: Suv39h1-/y Suv39h2-/-
Sex: Male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq was performed as per (Lee et al. 2006) with amendments as follows: 1) sonication was performed using a Covaris S220 focused-ultrasonicator with the following settings to shear DNA to a size of 300-500 bp suitable for high-throughput sequencing: Fill Level 10, Duty Cycle 10, PIP 175, Cycles/Burst 200 for 60 seconds. 2) Immunoprecipitation was performed overnight at 4degC with rotation using ProteinG Dynabeads (50μL per IP) pre-coupled with antibody (5μL per IP) in 0.5% BSA/PBS for >5h. 3) Final immunoprecipitated DNA was purified using Zymo ChIP DNA Clean & Concentrator kit.
Illumina Tru-seq (1/2 reaction) library preparation was performed.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Libraries were sequenced on an Illumina NextSeq 500, generating 76 bp paired-end reads or Illumina NextSeq 2000 generating 66 bp paired-end reads.
Reads were aligned to the mouse genome mm10 by Rsubread with duplicates removed with Picard tools MarkDuplicates command
BigWig files were generated with BamCoverage from Deeptools with bamCoverage normalizeUsing RPGC, bs 10 and effectiveGenomeSize 2652783500.
Assembly: mm10
Supplementary files format and content: BigWig, a coverage track generated from the mapped read fragments. The coverage is calculated as the number of reads per 10 bp bin. Coverage was normalization by reads per genomic content (RPGC).
|
| |
|
| Submission date |
Feb 21, 2024 |
| 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 |
GPL30172 |
| Series (2) |
| GSE156297 |
RNA-seq, LaminB1 ChIP-seq and in situ Hi-C of double positive thymocytes from control and Suv39h1/Suv39h2 double knockout mice |
| GSE256245 |
ChIP-seq of histone marks of DP thymocytes from Suv39h1 and Suv39h2 double knockout chimeric mice |
|
| Relations |
| BioSample |
SAMN40018449 |
| SRA |
SRX23682313 |
