Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE219012 | GEO | 2023/09/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation [RNA-Seq]

Project description:Human B cell differentiation into antibody secreting plasma cells is a critical process in the adaptive immune response whose regulation at the genetic level remains incompletely understood. To reveal the temporal sequence of transcription factor driven cellular changes we generated chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) data from the in vitro differentiation of human B cells into plasma cells. Data was gathered from three biological replicates using a published 13-day protocol of cytokine addition to drive differentiation. Using a new computational method, cisREAD (cis-Regulatory Elements Across Differentiation), we defined a core set of cis regulatory elements that are confidently linked to the dynamic binding of transcription factors and changes in gene expression. This confirmed known aspects of the differentiation process and revealed novel understanding, including a switch from PU.1/SPIB-driven to AP-1-driven genetic regulation associated with B cell activation.

2023-09-21 | GSE219011 | GEO

Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation [ATAC-Seq]

2023-09-21 | GSE219009 | GEO

Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation

Project description:Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation

| PRJNA906582 | ENA

Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation [ATAC-Seq]

Project description:Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation [ATAC-Seq]

| PRJNA906586 | ENA

Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation [RNA-Seq]

| PRJNA906585 | ENA

GENE-SWitCH Chicken chromatin accessibility profiling by ATAC-seq

Project description: Not available

| S-BSST901 | biostudies-other

GENE-SWitCH Pig chromatin accessibility profiling by ATAC-seq

Project description: Not available

| S-BSST903 | biostudies-other

GENE-SWitCH Pig chromatin accessibility profiling by ATAC-seq

Project description: Not available

| S-BSST905 | biostudies-other

GENE-SWitCH Pig chromatin accessibility profiling by ATAC-seq

Project description: Not available

| S-BSST899 | biostudies-other

Environmental sensing by mature B cells is controlled by the transcription factors PU.1 and SpiB.

Project description:Humoral immunity requires B cells to respond to multiple stimuli, including antigen, membrane and soluble ligands, and microbial products. Ets family transcription factors regulate many aspects of haematopoiesis, although their functions in humoral immunity are difficult to decipher as a result of redundancy between the family members. Here we show that mice lacking both PU.1 and SpiB in mature B cells do not generate germinal centers and high-affinity antibody after protein immunization. PU.1 and SpiB double-deficient B cells have a survival defect after engagement of CD40 or Toll-like receptors (TLR), despite paradoxically enhanced plasma cell differentiation. PU.1 and SpiB regulate the expression of many components of the B cell receptor signaling pathway and the receptors for CD40L, BAFF and TLR ligands. Thus, PU.1 and SpiB enable B cells to appropriately respond to environmental cues.

| S-EPMC5681560 | biostudies-literature

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