Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In vitro generation of mature murine plasma cells uncovers adaptive Prdm1 expression

ABSTRACT: In vitro generation of mature murine plasma cells uncovers adaptive Prdm1 expression

PROVIDER: PRJNA674599 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12979700.fastq.gz	Fastqsanger.gz
	SRR12979701.fastq.gz	Fastqsanger.gz
	SRR12979702.fastq.gz	Fastqsanger.gz
	SRR12979703.fastq.gz	Fastqsanger.gz
	SRR12979704.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 45

Similar Datasets

In vitro generation of mature murine plasma cells uncovers adaptive Prdm1 expression

Project description:Upon encounter with antigen, B cells undergo a sequential process of differentiation to become antibody-secreting plasma cells. While the key drivers of differentiation have been identified, research has been limited by the lack of in vitro models recapitulating the full process for murine B cells. Here we describe methodology using BCR or TLR ligation to obtain plasma cells that are phenotypically mature, have exited cell cycle and express a gene signature concordant with long-lived plasma cells. Dependent on the initial stimuli, the transcriptomes also show variation, suggestive of unique functional properties for the resultant plasma cells. Moreover, using the new culture conditions we demonstrate that alternative promoter choice regulating the expression of the master transcription factor Blimp-1 can be observed. Thus, our novel system provides a readily tractable model for furthering our understanding of plasma cell biology.

2021-11-03 | GSE160823 | GEO

Prdm1

Project description:Prdm1

| PRJNA300302 | ENA

A System for In Vitro Generation of Mature Murine Plasma Cells Uncovers Differential <i>Blimp-1</i>/<i>Prdm1</i> Promoter Usage.

Project description:Upon encounter with Ag, B cells undergo a sequential process of differentiation to become Ab-secreting plasma cells. Although the key drivers of differentiation have been identified, research has been limited by the lack of in vitro models recapitulating the full process for murine B cells. In this study, we describe methodology using BCR or TLR ligation to obtain plasma cells that are phenotypically mature, have exited cell cycle and express a gene signature concordant with long-lived plasma cells. Dependent on the initial stimuli, the transcriptomes also show variation including the enhanced expression of matrisome components after BCR stimulation, suggestive of unique functional properties for the resultant plasma cells. Moreover, using the new culture conditions we demonstrate that alternative promoter choice regulating the expression of the master transcription factor Blimp-1/Prdm1 can be observed; when the canonical B cell promoter for Prdm1 is deleted, differentiating B cells exhibit flexibility in the choice of promoter, dictated by the initiating stimulus, with preferential maintenance of expression following exposure to TLR ligation. Thus our system provides a readily tractable model for furthering our understanding of plasma cell biology.

| S-EPMC7612223 | biostudies-literature

Expression data from murine bone marrow-resident plasma cells and spleen mature follicular B cells

Project description:CD138+ B220- plasma cells were sorted from bone marrow and B220+ CD23+ mature follicular B cells were sorted from the spleens. Plasma cells were sorted from C57BL/6 mice 7 days after boosting with antigen, with mice first primed with an i.p. injection of KLH/IFA followed by boost at day 21 with KLH/PBS i.p. Mature B cells were sorted from antigen-naïve C57BL/6 mice. We compared expression profiles of plasma cells and mature B cells to identify differentially expressed transcripts. Seven days after boosting with KLH, plasma cells were enriched by CD138-PE/anti-PE magnetic bead enrichment and then sorted to purity. Affymetrix microarrays were performed on 50,000-70,000 plasma cells and 2,000,000-3,000,000 naïve B cells.

2012-08-06 | E-GEOD-39916 | biostudies-arrayexpress

Expression data from murine bone marrow-resident plasma cells and spleen mature follicular B cells

2012-08-07 | GSE39916 | GEO

Analysis of interleukin-21-induced Prdm1 gene regulation reveals functional cooperation of STAT3 and IRF4 TFs

Project description:Interleukin-21 (IL-21) is a pleiotropic cytokine that induces expression of transcription factor BLIMP1 (encoded by Prdm1), which regulates plasma cell differentiation and T cell homeostasis. We identified an IL-21 response element downstream of Prdm1 that binds the transcription factors STAT3 and IRF4, which are required for optimal Prdm1 expression. Genome-wide ChIP-Seq mapping of STAT3- and IRF4-binding sites showed that most regions with IL-21-induced STAT3 binding also bound IRF4 in vivo, and furthermore, revealed that the noncanonical TTCnnnTAA GAS motif critical in Prdm1 was broadly used for STAT3 binding. Comparing genome-wide expression array data to binding sites revealed that most IL-21-regulated genes were associated with combined STAT3-IRF4 sites rather than pure STAT3 sites. Correspondingly, ChIP-Seq analysis of Irf4_/_ T cells showed greatly diminished STAT3 binding after IL-21 treatment, and Irf4_/_ mice showed impaired IL- 21-induced Tfh cell differentiation in vivo. These results reveal broad cooperative gene regulation by STAT3 and IRF4. Affymetrix expression data: Prepare CD4+ T cells from spleen. CD4+ T cells were preactivated, rested, and treated with IL-21 for 1, 6, and 24 hours. ChIP-seq data: Profiling of IRF4 and Stat3 binding with and without IL-21 stimulation in wild type and IRF4 KO mice.

2010-01-08 | E-GEOD-19198 | biostudies-arrayexpress

The transcriptional repressor Blimp1/Prdm1 regulates post-natal reprogramming of intestinal enterocytes

Project description:Expression profiling of Prdm1 mutant E18.5 small intestine was performed using Illumina whole genome V2 arrays. The hypothesis tested in the present study was that Blimp1 regulates the transcription of key genes involved in enterocyte differentiation and survival. Results identify substantial and premature activation of key components of the adult enterocyte biochemical signature. Villin-Cre and Prdm1BEH/+ animals were intercrossed to generate heterozygous Villin-Cre, Prdm1BEH males that were then mated with homozygous Prdm1 CA/CA females carrying the R26R allele to generate Prdm1+/+ (Prdm1CA/+) or Prdm1-/- (Villin-Cre, Prdm1CA/BEH) offspring. Total RNA obtained from 11 Prdm1+/+ and 10 Prdm1-/- E18.5 small intestine samples was hybridized to Illumina WG6_V2 beadchips.

2011-06-02 | E-GEOD-29658 | biostudies-arrayexpress

Molecular function of Prdm1/Blimp1 in trophoblast giant cell differentiation.

Project description:Expression profiling of wild-type and Prdm1 null mouse trophoblast giant cell cultures using Illumina whole genome mouse V2 arrays. The hypothesis tested was that Prdm1/Blimp1 regulates expression of genes required for spiral artery trophoblast giant cell function. Prdm1 null and littermate control wild-type trophoblast stem cell clones were generated from blastocyst outgrowths. Total RNA was obtained from multiple replicates of four wild-type TS cell clones and four Prdm1 null TS cell clones differenitated for zero, two, four and six days by growth factor withdrawal and hybridized to Illumina WG6_V2 arrays

2016-03-14 | E-GEOD-74409 | biostudies-arrayexpress

Analysis of interleukin-21-induced Prdm1 gene regulation reveals functional cooperation of STAT3 and IRF4 TFs

2010-01-08 | GSE19198 | GEO

PRDM1 inhibits proliferation of human colon cancer organoids

Project description:We reports the transcript landscape of PR Domain Containing 1, with ZNF domain (PRDM1) in RKO colon cancer cells. We show that PRDM1 alpha and PRDM1 beta transcript isoforms repress and activate a largely overlapping suite of genes, many of which belong to the embryonic stem cell core transcript program.

2017-07-21 | GSE101668 | 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