|
| Status |
Public on Mar 27, 2024 |
| Title |
ChIP-seq of histone marks of DP thymocytes from Suv39h1 and Suv39h2 double knockout chimeric mice |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
H3K9me3-dependent heterochromatin is critical for the silencing of repeat-rich pericentromeric regions and also has key roles in repressing lineage-inappropriate protein-coding genes for healthy cellular function. Within all eukaryotic nuclei, heterochromatin and euchromatin are spatially segregated, with euchromatin typically located in the nuclear interior and heterochromatin at the nuclear periphery. Here we investigate the histone modifications (H3K27ac, H3K27me3, H3K4me3 and H3K9me3) in the absence of H3K9me3-dependent heterochromatin by performing ChIP-seq in primary immune cells deficient in both Suv39h1 and Suv39h2 (Suv39DKO), the major mammalian histone methyltransferase enzymes which catalyse heterochromatic H3K9me3 deposition.
|
| |
|
| Overall design |
CD4+CD8+ double positive mouse thymocyte cells were flow-sorted (Ly5.2+CD19-CD4+CD8+) and analysed. H3K27ac, H3K27me3, H3K4me3 and H3K9me3 ChIP-seq libraries from Suv39h1+/y Suv39h2+/- (control) mice were prepared and sequenced along with an IgG and whole-cell extract (input) library. H3K27ac, H3K27me3 and H3K4me3 ChIP-seq libraries from Suv39h1-/y Suv39h2-/- double knock-out (Suv39DKO) mice were prepared and sequenced along with an IgG and whole-cell extract (input) library. For the bioinformatics analysis, the reads were aligned to mm10 and duplicates were removed.
|
| |
|
| Contributor(s) |
Keenan CR, Coughlan HD, Smyth GK, Allan RS |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Feb 21, 2024 |
| Last update date |
Mar 28, 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 |
| |
|
| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL30172 |
NextSeq 2000 (Mus musculus) |
|
| Samples (12)
|
|
| This SubSeries is part of SuperSeries: |
| GSE156297 |
RNA-seq, LaminB1 ChIP-seq and in situ Hi-C of double positive thymocytes from control and Suv39h1/Suv39h2 double knockout mice |
|
| Relations |
| BioProject |
PRJNA1078778 |
Less...
More...