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| Status |
Public on Mar 27, 2024 |
| Title |
RNA-seq, LaminB1 ChIP-seq and in situ Hi-C of double positive thymocytes from control and Suv39h1/Suv39h2 double knockout mice |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
Genome binding/occupancy profiling by high throughput sequencing
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| 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. We investigated the effects of loss of H3K9me3-dependent heterochromatin in primary immune cells deficient in both Suv39h1 and Suv39h2 (Suv39DKO), the major mammalian histone methyltransferase enzymes which catalyse heterochromatic H3K9me3 deposition.
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| Overall design |
CD4+CD8+ double positive thymocyte cells from control and Suv39h1/Suv39h2 double knockout mice were analysed by RNA-seq, LaminB1 ChIP-seq and in situ Hi-C. Three biological replicates were undertaken for RNA-seq and two biological replicates for LaminB1 ChIP-seq and Hi-C.
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| Contributor(s) |
Garnham AL, Coughlan HD, Keenan CR, Smyth GK, Allan RS |
| Citation(s) |
38719473 |
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| Submission date |
Aug 14, 2020 |
| Last update date |
Jun 26, 2024 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
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| Phone |
(+61 3) 9345 2326
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| Fax |
(+61 3) 9347 0852
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| URL |
http://www.wehi.edu.au
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| Organization name |
Walter and Eliza Hall Institute of Medical Research
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| Department |
Bioinformatics
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| Lab |
Smyth
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| Street address |
1G Royal Pde
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| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
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| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL30172 |
NextSeq 2000 (Mus musculus) |
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| Samples (34)
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| GSM4728469 |
Control LaminB1 ChIP replicate 2 |
| GSM4728470 |
Suv39h1, Suv39h2 double knock-out whole cell extract replicate 1 |
| GSM4728471 |
Suv39h1, Suv39h2 double knock-out whole cell extract replicate 2 |
| GSM4728472 |
Suv39h1, Suv39h2 double knock-out LaminB1 ChIP replicate 1 |
| GSM4728473 |
Suv39h1, Suv39h2 double knock-out LaminB1 ChIP replicate 2 |
| GSM4728474 |
Control, replicate 1 |
| GSM4728475 |
Control, replicate 2 |
| GSM4728476 |
Suv39h1, Suv39h2 double knock-out, replicate 1 |
| GSM4728477 |
Suv39h1, Suv39h2 double knock-out, replicate 2 |
| GSM4728486 |
Control, RNA-Seq replicate 1 |
| GSM4728487 |
Control, RNA-Seq replicate 2 |
| GSM4728488 |
Control, RNA-Seq replicate 3 |
| GSM4728489 |
Suv39h1, Suv39h2 double knock-out, RNA-Seq replicate 1 |
| GSM4728490 |
Suv39h1, Suv39h2 double knock-out, RNA-Seq replicate 2 |
| GSM4728491 |
Suv39h1, Suv39h2 double knock-out, RNA-Seq replicate 3 |
| GSM8091847 |
CON ATAC-seq replicate 1 |
| GSM8091848 |
CON ATAC-seq replicate 2 |
| GSM8091849 |
DKO ATAC-seq replicate 1 |
| GSM8091850 |
DKO ATAC-seq replicate 2 |
| GSM8091851 |
CON H3K4me3 replicate |
| GSM8091852 |
CON H3K27ac replicate |
| GSM8091853 |
CON H3K27me3 replicate |
| GSM8091854 |
CON whole cell extract replicate |
| GSM8091855 |
CON IgG replicate |
| GSM8091856 |
DKO H3K4me3 replicate |
| GSM8091857 |
DKO H3K27ac replicate |
| GSM8091858 |
DKO H3K27me3 replicate |
| GSM8091859 |
DKO whole cell extract replicate |
| GSM8091860 |
DKO IgG replicate |
| GSM8091861 |
CON H3K9me3 replicate |
| GSM8091862 |
CON H3K9me3 whole cell extract |
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| This SuperSeries is composed of the following SubSeries:
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| GSE156293 |
LaminB1 ChIP-seq of DP thymocytes from wildtype and Suv39h1 and Suv39h2 double knockout mice |
| GSE156294 |
in situ Hi-C profiles of DP thymocyltes from control and Suv39h1/Suv39h2 double knockout mice |
| GSE156296 |
RNA-seq profiles of DP thymocytes from control and Suv39h1/Suv39h2 double knockout mice |
| GSE256244 |
ATAC-seq of DP thymocytes from Suv39h1 and Suv39h2 double knockout chimeric mice |
| GSE256245 |
ChIP-seq of histone marks of DP thymocytes from Suv39h1 and Suv39h2 double knockout chimeric mice |
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| Relations |
| BioProject |
PRJNA657281 |
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