Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide identification of codanin-1 binding sites in human K562 erythroleukemia cells with chromatin immunoprecipitation coupled with next-generation sequencing

ABSTRACT: Genome-wide identification of codanin-1 binding sites in human K562 erythroleukemia cells with chromatin immunoprecipitation coupled with next-generation sequencing

PROVIDER: PRJNA543943 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9094410.fastq.gz	Fastqsanger.gz
	SRR9094420.fastq.gz	Fastqsanger.gz
	SRR9094411.fastq.gz	Fastqsanger.gz
	SRR9094421.fastq.gz	Fastqsanger.gz
	SRR9094412.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 22

Similar Datasets

Genome-wide binding sites of NF90/ILF3 in K562 erythroleukemia cells

Project description:We used ChIP-seq to characterize the genome-wide binding sites of NF90/ILF3 in K562 erythroleukemia cells.

2018-03-01 | E-MTAB-6042 | biostudies-arrayexpress

Global analysis of in vivo EGR1-binding sites in erythroleukemia cell K562 using chromatin immunoprecipitation and massively parallel sequencing

Project description:Early growth response gene 1 (EGR1) has been implicated in megakaryocyte differentiation induced by PMA (phorbol 12-myristate 13-acetate). The identification of direct EGR1 target genes in global scale is critical for our understanding of how EGR1 contributes to this process. In this study, we provide a global survey on the binding location of EGR1 in the K562 cell treated by PMA using chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq). K562 is a human erythroleukemia cell line, which is situated in the common progenitor stage of megakaryocytic and erythroid lineages of the hematopoietic stem cell differentiation and its normally following differentiation is blockaded. Upon exposure to PMA stimuli, K562 cell can be induced into megakaryocytic cell, which provides a model for the study of transcriptional control networks. Over 14 000 highly confident in vivo EGR1 binding sites were identified in PMA treated K562 cell. More than 70% of these genomic sites associated with EGR1 binding were located around annotated gene regions. This whole genome study on the EGR1 targets may help a better understanding of the EGR1 regulated genes and the downstream pathway in megakaryocyte differentiation. The in vivo binding locations of EGR1 in K562 cell treated with PMA (phorbol 12-myristate 13-acetate, 10 ng/ml for 2 hours) were identified using chromatin immunoprecipitation combing with massively parallel sequencing (ChIP-Seq) based on AB SOLiD System 2.0.

2010-09-08 | E-GEOD-21665 | biostudies-arrayexpress

Global analysis of in vivo EGR1-binding sites in erythroleukemia cell K562 using chromatin immunoprecipitation and massively parallel sequencing

2010-09-08 | GSE21665 | GEO

Transcription profiling of human erythroleukemia K562 cells during TPA-induced megakaryocyte differentiation

Project description:Analysis of differential gene expression during TPA-induced megakaryocyte differentiation of human erythroleukemia K562 cells. The transcription profile of untreated vs TPA-treated K562 cells for 2 days was compared using gene microarrays.

2009-09-01 | E-MEXP-2213 | biostudies-arrayexpress

Genome-wide identification of codanin-1 binding sites in human K562 erythroleukemia cells with chromatin immunoprecipitation coupled with next-generation sequencing

Project description:Congenital dyserythropoietic anemia type I (CDA-I) is an autosomal recessive disorder marked by ineffective erythropoiesis, abnormal morphology of bone marrow erythroblasts, and iron overload. Most cases of CDA-I are caused by mutations in the CDAN1 gene, which encodes for a ubiquitous protein of unknown function, codanin-1. To study the function of codanin-1 in CDA-I erythroid pathophysiology several erythroid models were developed. Here we show that codanin-1 expression is required for erythroid progenitor development and normal erythroid cell differentiation. Erythroid cells lacking codanin-1 demonstrated morphologic changes similar to that observed in CDA-I. Global gene expression changes after codanin-1 knockdown revealed alterations in a set of key erythroid genes. In particular, the AHSP gene, which showed decreased mRNA expression after codanin-1 knockdown in CD34+ cells, also demonstrated increased codanin-1 occupancy at its gene regulatory region by chromatin immunoprecipitation coupled to high-throughput sequencing. Using cell models recapitulating many features of CDA-I, we have confirmed the importance of codanin-1 during erythroid differentiation and provide mechanistic insight into how loss of codanin-1 expression results in CDA-I.

2022-05-19 | GSE131510 | GEO

Genome-wide binding sites of NF90/ILF3 in K562 erythroleukemia cells

Project description:Genome-wide binding sites of NF90/ILF3 in K562 erythroleukemia cells

| PRJEB22363 | ENA

Heat-induced transcriptional memory profiled in human K562 erythroleukemia cells.

Project description:Heat-induced transcriptional memory profiled in human K562 erythroleukemia cells.

| PRJNA525636 | ENA

Heat-induced transcriptional memory profiled in human K562 erythroleukemia cells.

Project description:Precision run-on sequencing (PRO-seq) of nascent RNA synthesis across the human genome. The PRO-seq data was generated from human K562 erythroleukemia cells that were either unconditioned (unCond) or preconditioned with multiple heat shock exposures (preCond). After two day recovery from the preconditioning, during which the cells underwent two mitotic divisions, the cells were additionally subjected to a single heat shock to measure nascent transcription in response to heat shock in unconditioned versus preconditioned cells.

2020-03-04 | GSE127844 | GEO

Heat-induced transcriptional memory profiled in human K562 erythroleukemia cells [PRO-seq]

Project description:Heat-induced transcriptional memory profiled in human K562 erythroleukemia cells [PRO-seq]

| PRJNA647374 | ENA

Heat-induced transcriptional memory profiled in human K562 erythroleukemia cells [PRO-seq]

Project description:Precision run-on sequencing (PRO-seq) of nascent RNA synthesis across the human genome. The PRO-seq data was generated from human K562 erythroleukemia cells that were either unconditioned (unCond) or preconditioned with a single heat shock exposure (preC). After two day recovery from the preconditioning, during which the cells underwent two mitotic divisions, the cells were additionally subjected to a single heat shock to measure nascent transcription in response to heat shock in unconditioned versus preconditioned cells.

2021-04-01 | GSE154746 | 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