Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SERBP1 iCLIP in mitotic and asynchronous cells with Blu577 treatment

ABSTRACT: SERBP1 iCLIP in mitotic and asynchronous cells with Blu577 treatment

PROVIDER: PRJEB46913 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR6465070.fastq.gz	Fastqsanger.gz
	ERR6465071.fastq.gz	Fastqsanger.gz
	ERR6465072.fastq.gz	Fastqsanger.gz
	ERR6465073.fastq.gz	Fastqsanger.gz
	ERR6465074.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 11

Similar Datasets

SERBP1 iCLIP in mitotic and asynchronous cells with Blu577 treatment

Project description:In the associated paper, SERBP1 is shown to form granules in mitotic cells in a PKCɛ-dependent manner (M-bodies). We performed SERBP1 iCLIP in DLD1 cells that were either asynchronous or enriched for mitotic cells and after treatment with 2 hours of 500nM Blu577 or equivalent DMSO. We found that SERBP1 alters its positioning on rRNA in mitosis in a Blu577-dependent manner, identifying an alternative binding position that coincides with the formation of M-bodies. Mitotic enrichment was performed by single thymidine block, release in to G2 block with RO3306, and release and mitotic shake-off. The fastq files provided are demultiplexed, with adapters and barcodes trimmed and UMI sequences are found in the fastq headers.

2021-10-05 | E-MTAB-10830 | biostudies-arrayexpress

The study of ESRRB occupancy in asynchronous and mitotic mESCs.

Project description:We performed ChIP-seq for ESRRB and investigated its deposition in asynchronous and mitotic cells.

2023-09-22 | GSE243808 | GEO

The study of histone modifications and SOX2 occupancy in asynchronous and mitotic mESCs.

Project description:We performed ChIP-seq for H3K4me3, H3K27ac, H3K4me1, H3K27me3, H3K36me3, H3K9me3, and H4K20me3 to characterize chromatin states and investigated SOX2 deposition in asynchronous and mitotic cells.

2023-03-19 | GSE189561 | GEO

Genome-wide analysis of SOX2 binding in asynchronous and mitotic mouse embryonic stem cells.

Project description:SOX2 is part of the core network of transcription factors regulating embryonic stem cell pluripotency. We found that SOX2 has the ability to remain bound to mitotic chromosomes, in contrast to most transcription factors that are excluded from mitotic chromatin as transcription shuts down. We obtained a highly purified population of mitotic mouse embryonic stem cells and compared the genome-wide binding profile of SOX2 to that in asynchronous cells by Chromatin Immunoprecipitation followed by high throughput sequencing (ChIP-seq), and show that SOX2 remains bound to a small set of genes during mitosis.

2016-11-07 | GSE89599 | GEO

Expression and FoxA1 binding in asynchronous and mitotic HUH7 cells

Project description:Expression and FoxA1 binding in asynchronous and mitotic HUH7 cells

| PRJNA170313 | ENA

The study of ESRRB occupancy in asynchronous and mitotic mESCs.

Project description:The study of ESRRB occupancy in asynchronous and mitotic mESCs.

| PRJNA1020083 | ENA

Enhanced crosslinking and immunoprecipitation of SERBP1 in Hela cells

Project description:Purpose:We used eCLIP experiment to analyze binding profile of SERBP1 and its relationship with G4. Result: we found 505 high-confidence SERBP1 binding sites in Hela cells, and the analysis of sequence revealed transcriptome-wide enrichment of PQS in SERBP1-binding regions

2020-10-27 | GSE156015 | GEO

ATAC-seq on mouse embryonic stem cells for asynchronous cells, mitotic cells and purified mitotic chromosomes.

Project description:ATAC-seq on mouse embryonic stem cells for asynchronous cells, mitotic cells and purified mitotic chromosomes.

| PRJNA615279 | ENA

The study of SOX2 deposition in asynchronous and mitotic E14TG2a cells

Project description:The study of SOX2 deposition in asynchronous and mitotic E14TG2a cells

| PRJNA894707 | ENA

The study of SWI/SNF subunits and other transcription factors deposition in asynchronous and mitotic mESCs and cells released from mitosis

Project description:We executed CUT&RUN-seq for SWI/SNF components ARID1A, BRD9, SMARCA4, SMARCB1, SMARCE1, as well as ESRRB, SOX2, and EZH2 in asynchronous and mitotic cells and reported that, in asynchronous cells, ARID1A localized primarily at enhancer regions and EZH2 preferentially deposited at bivalent promoters and silent enhancer domains. The remaining factors were enriched at both TSS/promoters and to varying degrees at active enhancers. Unexpectedly, in mitosis, the chromatin regulatory factors almost all tethered at proximal gene regions with very little binding at enhancers. While the SWI/SNF subunits were bound principally at promoters, EZH2, the catalytic subunit of Polycomb Repressive Complex 2 was bound at both promoters and silent enhancers in mitotic cells. Moreover, we reported that upon the degradation of SMARCE1 in mitosis, the occupancy of SOX2, ESRRB, and EZH2 on mitotic chromatin was disrupted.

2023-03-19 | GSE189560 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data