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HDAC3 modulates enhancer activity to regulate terminal B cell differentiation

ABSTRACT: B220+GL7+ (GC) and B220+GL7- (non-GC) B cells were sorted from SRBC-immunized mice deficient for Hdac3 and wild type controls. RNA-sequencing revealed an upregulation of critical regulators of B cell differentiation in Hdac3-deleted animals.

ORGANISM(S): Mus musculus

PROVIDER: GSE77113 | GEO | 2016/09/02

SECONDARY ACCESSION(S): PRJNA309451

REPOSITORIES: GEO

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HDAC3 modulates enhancer activity to regulate terminal B cell differentiation

Project description:B220+GL7+ (GC) and B220+GL7- (non-GC) B cells were sorted from SRBC-immunized mice deficient for Hdac3 and wild type controls. RNA-sequencing revealed an upregulation of critical regulators of B cell differentiation in Hdac3-deleted animals. 10 days post-immunization with SRBCs, GC and non-GC B cells were sorted and RNA isolated by Trizol extraction for RNA-sequencing. 2 replicates were sequenced for each condition.

2016-09-02 | E-GEOD-77113 | biostudies-arrayexpress

Transcription profiling of mouseWT vs CD137L-/- GC B cells

Project description:WT and CD137L-/- mice of 8-12 weeks old were immunized intra-peritoneally with 50 Âµg chicken gamma- globulin conjugated to 4-hydroxy-3-nitrophenylacetyl (NP-CG) in alum or infected intranasally with 25 hemagglutinin units of influenza virus strain A/NT/60/68 in 50 Âµl HBSS. Nine days after immunization or infection, B cells were enriched from pooled spleens and lymph nodes of 4 mice per test group by means of magnetic labelled bead cell separation (MACS) using anti-mouse BD ImagTM CD45R/B220-particles DM. The B220+ MACS-sorted populations were stained with anti-GL7-FITC and anti-CD19-PE to sort CD19+GL7+ GC and CD19+GL7- non-GC B lymphocytes by flow cytometry on a FACSAria (BD). Around 1 million cells of each sample were obtained. These cells were spun down and the pellet was frozen in liquid nitrogen and kept at -80 ÂºC before RNA extraction.

2009-07-24 | E-NCMF-29 | biostudies-arrayexpress

Analysis of mouse antigen specific germinal centre B cell subset gene signatures in presence and absence of kidney disease during T dependent immunization

Project description:Wild type or Aristolochic acid (AAI) nephropathy (AAN) mice were immunized with NP-KLH in Alum (100ug/mouse) On day 12 post-immunization, live NP-GcB cells were FACS-sorted from spleen according to B220+ GL7+ CD95+ NP+ expression directly into SmartSeq low-input RNA kit lysis buffer

2024-01-01 | GSE237445 | GEO

Serine-threonine Kinase, ROCK2, Regulates Germinal Center B Cell Positioning and Cholesterol Biosynthesis

Project description:Splenic follicular B cells (FoB; B220+GL7-CD38hiCD23+) and Germinal Center B cells (GCB; B220+GL7+CD38lo) were FACS sorted from WT or CD23-Cre.Rock2 mice after 7d post-immunization with NP-CGG. RNA-seq was then employed to compare the transcriptome of GCBs from the indicated mice. Here we show that loss of ROCK2 leads to altered gene expression in GCBs. We also employed ATAC-seq analysis and found that differentially expressed genes from the ROCK2-deficient GC B cells contained loci that were enriched for IRF binding sites.

2020-05-22 | GSE141328 | GEO

Type 1 interferon signaling is crucial from the loss of tolerance nd the development of autoreactive B cells.

Project description:The transcriptomes of FACS-sorted B220+GL7+CD95+ germinal center B cells and B220+GL7-CD95- non-germinal center B cells from lupus-prone B6.Sle1b were compared to the same cell types in B6.Sle1b mice without the type 1 interferon receptor (B6.Sle1b.IFNaR1-/-).

2018-12-25 | GSE115349 | GEO

HDAC3 ensures stepwise epidermal stratification via NCoR/SMRT-reliant mechanisms independent of its histone deacetylase activity (HDAC3 NCoRSMRT microarray)

Project description:Chromatin modifiers play critical roles in epidermal development, but the functions of histone deacetylases in this context are poorly understood. We find that the Class I HDAC, HDAC3, is expressed broadly in embryonic epidermis, and is required for its orderly stepwise stratification. Stability of HDAC3 protein in vivo is reliant on NCoR and SMRT, which function redundantly in epidermal development. However, point mutations in the NCoR and SMRT Deacetylase Activating Domains, which are required for HDAC3’s enzymatic function, permit normal stratification, indicating that HDAC3’s roles in this context are independent of its histone deacetylase activity. HDAC3 functions both in conjunction with, and independent of, KLF4 to repress premature expression of different sets of terminal differentiation genes and suppresses expression of inflammatory cytokines through a RelA-dependent mechanism. These data identify HDAC3 as a hub coordinating multiple aspects of epidermal barrier acquisition. We used microarrays to determine transcriptional changes in Hdac3 deleted epidermis compared to control and Ncor1/Ncor2 deleted epidermis compared to control.

2020-08-23 | GSE137234 | GEO

LSD1 regulates the marginal zone B cell transcriptome

Project description:To understand the role of LSD1 in splenic B cell development, spleens from mice with B cell conditional deletion of LSD1 were harvested, B220+CD93–GL7–CD23–CD21hiCD1d+ marginal zone B cells and B220+CD93–GL7–CD23+CD21midCD1d– follicular B cells were FACS-sorted, and RNA-seq was performed to identify LSD1-target regulated genes.

2019-08-06 | GSE132197 | GEO

LSD1 regulates splenic B cell chromatin accessibility

Project description:To understand the role of LSD1 in splenic B cell development, spleens from mice with B cell conditional deletion of LSD1 were harvested, B220+CD93–GL7–CD23–CD21hiCD1d+ marginal zone B cells and B220+CD93–GL7–CD23+CD21midCD1d– follicular B cells were FACS-sorted, and ATAC-seq was performed to identify LSD1-target regulated chromatin.

2019-08-06 | GSE132196 | GEO

ScRNA-seq analysis of naive, germinal center and memory B cells of mice immunized with homologous and heterologous prime:boost combinations of whole-cell pertussis or acellular pertussis vaccines

Project description:Since the introduction of new generation pertussis vaccines, resurgence of pertussis is observed in many developed countries. Former whole-cell pertussis vaccines (wP) are able to protect against disease and transmission but have been replaced in several industrialized countries because of their reactogenicity and adverse effects. Current acellular pertussis vaccines (aP), made of purified proteins of Bordetella pertussis, are efficient at preventing disease but fail to induce long-term protection from infection. While the systemic and mucosal T cell immunity induced by the two types of vaccines has been well described, much less is known concerning B cell responses. Taking advantage of an inducible AID-Cre-EYFP fate-mapping mouse model, we sorted and analyzed by scRNAseq the transcriptomic profiles of memory B cells after a combination of prime:boost with the two classes of vaccines. B220+EYFP+GL7-PNA- memory B cells from the draining lymph nodes (dLNs) of tamoxifen-fed mice were FACS sorted 7 weeks after boost, alongside with B220+EYFP+GL7+PNA+ germinal center (GC) B cells and B220+GL7-PNA-EYFP-IgD+ naive B cells as a control population for the unsupervised clustering analysis. Single-cell mRNA sequencing was performed according to an adapted version of the SORT-seq protocol (Muraro et al., 2016, PMID: 27693023, with primers described in van den Brink et al. 2017), with cDNA libraries generation, sequencing and reads alignment performed at Single Cell Discoveries (Utrecht, Netherlands).

2022-09-12 | E-MTAB-12156 | biostudies-arrayexpress

Gene expression profiling of HDAC3-depleted mouse liver rescued with wild-type exogenous HDAC3

Project description:We have shown that intravenous injection of HDAC3 floxed mice with adeno-associated virus (AAV) expressing Cre depletes hepatic HDAC3, upregulates lipogenic gene expression, and causes fatty liver. When AAV-Flag-HDAC3 wild-type (WT) is co-injected along with AAV-Cre, the exogenous HDAC3 is expressed at endogenous levels and can completely rescue fatty liver phenotype. Here we profile transcriptome of the rescued WT livers in comparison with HDAC3-depleted (KO) livers. 4-months old C57BL/6 male mice were co-injected with AAV-Cre or AAV-Cre plus AAV-Flag-HDAC3. Mice were fed ad libitum and harvested at 5 pm (ZT10) at 2-weeks post-injection. Liver total RNA was extracted and hybridized to Affymetrix Mouse Gene 1.0ST array.

2013-11-25 | E-GEOD-49386 | biostudies-arrayexpress

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