Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Hi-C to compare 3D genome organisation in WT to HIRA KO HeLa cells

ABSTRACT: Hi-C to compare 3D genome organisation in WT to HIRA KO HeLa cells

PROVIDER: PRJEB79848 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Hi-C to compare 3D genome organisation in HIRA KO HeLa cells rescued with HIRA

Project description:Hi-C to compare 3D genome organisation in HIRA KO HeLa cells rescued with HIRA

| PRJEB79847 | ENA

Hi-C to compare 3D genome organisation in HIRA KO HeLa cells rescued with HIRA

Project description:We performed Hi-C in asynchronous HeLa cells that knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene transfected with HIRA-YFP (HIRA) or YFP only (control) plasmid.

2025-08-07 | E-MTAB-14431 | biostudies-arrayexpress

Hi-C to compare 3D genome organisation in WT to HIRA KO HeLa cells

Project description:We performed Hi-C in asynchronous HeLa cells that are wild-type (WT) or knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene.

2025-08-07 | E-MTAB-14433 | biostudies-arrayexpress

EdU-seq and H3 variant SNAP capture-seq in HIRA KO HeLa cells rescued with HIRA

Project description:Our previous work on the histone H3.3 chaperone HIRA revealed its importance for maintaining the targeting of H3.3 to its pre-existing sites. In concert with replication fork-coupled deposition of the replicative H3.1 variant, this establishes boundaries of H3.3/H3.1, which define early replication initiation zones, which are disrupted in the absence of HIRA (Gatto et al., 2022). We have also recently shown a role of HIRA for active gene organisation and compartment A interactions by Hi-C. Here, we performed a HIRA rescue experiment in HIRA KO HeLa cells combined with a G1/S synchronisation to assay the recovery of H3.1 and H3.3 distribution (prior to S phase entry) by SNAP capture-seq and the pattern of nascent DNA synthesis in early S phase (2h) by EdU-seq. We also include H3.3 SNAP capture-seq from an asynchronous HIRA rescue we performed to assay recovery of genome organisation by Hi-C (submitted as a separate ArrayExpress entry).

2025-08-07 | E-MTAB-14419 | biostudies-arrayexpress

Total RNA-seq in WT and HIRA KO HeLa cells

Project description:We performed total RNA-seq of G1/S-synchronised HeLa cells that are wild-type (WT) or knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene.

2025-08-07 | E-MTAB-14417 | biostudies-arrayexpress

Hi-C from Primate iPSC derived Astrocytes (iAstrocytes)

Project description:Hi-C experiment was performed to map and compare potential evolutionary changes in chromatin structural organisation of human, chimpanzee and macaque iAstrocytes.

2025-03-06 | E-MTAB-13259 | biostudies-arrayexpress

Chromatin accessibility by ATAC-seq in WT and HIRA KO HeLa cells

Project description:We profiled accessibility by ATAC-seq of G1/S-synchronised HeLa cells that are wild-type (WT) or knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene.

2025-08-07 | E-MTAB-14415 | biostudies-arrayexpress

Distribution of active (H3K4me1, H3K4me3, H3K27ac) and inactive (H3K9me3, H3K27me3) histone PTMs in WT and HIRA KO HeLa cells

Project description:We profiled the enrichment of active (H3K4me1, H3K4me3, H3K27ac) and inactive (H3K9me3, H3K27me3) histone PTMs in cells that are wild-type (WT) or knock-out (KO) for the H3.3-specific chaperone HIRA. We performed native ChIP-seq following MNase digestion to isolate nucleosomes in H3.1-SNAP and H3.3-SNAP-bearing HeLa cells. We had previously assayed the distribution of the H3.1 and H3.3 histone variants (Gatto et al., 2022) in the same cell lines, so we generated this PTM ChIP-seq data to compare the behaviour of the variants with that of H3 modifications.

2025-08-07 | E-MTAB-14416 | biostudies-arrayexpress

EdU-seq and H3 variant SNAP capture-seq in HIRA KO HeLa cells rescued with HIRA

Project description:EdU-seq and H3 variant SNAP capture-seq in HIRA KO HeLa cells rescued with HIRA

| PRJEB79724 | ENA

Total RNA-seq in WT and HIRA KO HeLa cells

Project description:Total RNA-seq in WT and HIRA KO HeLa cells

| PRJEB79723 | ENA