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Effect of Arid1a deletion on chromatin accessibility in antiviral effector CD8+ T cells. [Cut & Run]

ABSTRACT: To investigate the role of ARID1A in the regulation of transcription factor binding and histone modifications in effector CD8+ T cell responses, we crossed GzmB-Cre P14 Thy1.1 mice with Arid1a-fl/fl mice to generate Arid1a KO mice. We then performed CUT&RUN against ARID1A, BATF, ETS, Tbet, H3K27ac, H3K27me3 in WT, Arid1a KO, or Tbx21 (Tbet) KO cells in vivo at d0, 48h in vitro activated, d5, and d8 post-LCMV Armstrong infection.

ORGANISM(S): Mus musculus

PROVIDER: GSE228380 | GEO | 2023/06/13

REPOSITORIES: GEO

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Effect of Arid1a deletion in antiviral effector CD8+ T cells. [RNA-seq]

Project description:To investigate the roll of ARID1A in the regulation of effector CD8+ T cell responses, we crossed GzmB-Cre P14 Thy1.1 mice with Arid1a-fl/fl mice to generate Arid1a Het and KO mice. We then performed gene expression profiling analysis of WT, Het, and KO cells in vivo at d3, d5, and d8 post-LCMV Armstrong infection.

2023-06-13 | GSE227634 | GEO

Effect of Arid1a deletion on chromatin accessibility in antiviral effector CD8+ T cells. [ATAC-Seq]

Project description:To investigate the role of ARID1A in the regulation of effector CD8+ T cell responses, we crossed GzmB-Cre P14 Thy1.1 mice with Arid1a-fl/fl mice to generate Arid1a Het and KO mice. We then performed chromatin accessibility profiling analysis by ATAC-seq in WT, Het, and KO cells in vivo at d0, 48h in vitro activated, d3, d5, and d8 post-LCMV Armstrong infection.

2023-06-13 | GSE228171 | GEO

Kinetics of Tbet+ B cells during LCMV infection

Project description:Inflammatory (B220+ CD19+ CD44+ CD11c+ Tbet-AmCyanhi) B cells were sorted from female Tbet-AmCyan reporter mice at day 8, 10, and 15 post infection with LCMV-Armstrong. RNA-seq was employed to assess transcriptional changes in inflammatory B cells throughout the infection.

2022-01-27 | GSE192765 | GEO

Kinetics of Tbet+ B cells during LCMV infection

2022-01-27 | GSE150139 | GEO

Genome-wide maps of chromatin state in naïve CD4+ T cells, WT/EZH2-null TFH and TH1 cells

Project description:ATAC-Seq experiments were performed to elucidate the chromatin state changes among naïve CD4+ T cells, WT follicular helper T (TFH) cells and WT type 1 helper T (TH1) cells Day2 (D2), Day5 (D5), Day8 (D8) post-LCMV-Armstrong infection, as well as EZH2-null (KO) TFH and TH1 at Day8 post-LCMV-infection. The analysis suggested stringent lineage-specific mode of chromatin accessibility in each group, indicating chromatin remodeling is tightly associated with TFH versus TH1 lineage differentiation in response to acute viral infection. Furthermore, the comparison between wild-type and EZH2-null TFH cells showed that less-opening state of certain chromatin accessible region in TFH-differentiation associated genes in the formers, suggesting EZH2 led to permissive chromatin accessibility primarily at specific regions of TFH-associated genes. H3K27me3-ChIP-seq was performed in WT TFH and TH1 cells to confirm the deposition of the histone marks at those loci.

2018-12-31 | GSE120532 | GEO

Expression profile of miR-17-92a-MSCV-IRES-Thy1.1 transduced P14 CD8+ T cells

Project description:During acute viral infections, effector CD8+ T cells differentiate into memory precursors or short-lived terminal effectors. miR-17-92a over-expression skews CD8+ effector cells to the terminal differentiation. We used microarray to identify the genes that are differentially expressed caused by miR-17-92a over-expression. CD8+ T cells from P14 TCR transgenic mice were infected with miR-17-92a-MSCV-IRES-Thy1.1 vector and transfer to C57BL6 recipients. Chimeras were infected with LCMV Armstrong. Thy1.1+ miR-17-92a-MSCV-IRES-Thy1.1 transduced P14 cells and Thy1.1- non-transduced P14 cells were sorted by FACS. RNA was extracted from samples, labeled, and hybridized to Affymetrix microarrays.

2012-06-04 | E-GEOD-34217 | biostudies-arrayexpress

Transcriptional profile of B cell susbets

Project description:Inflammatory (B220+ CD19+ CD44+ CD11c+ Tbet-AmCyanhi), GC (B220+ IgDlo CD95+ GL-7+), and naive follicular B cells (B220+ CD19+ IgDhi CD23+) were sorted from male Tbet-AmCyan reporter mice at day 12 post infection with LCMV-Armstrong. RNA-seq was employed to compare the transcriptomes of these three B cell populations.

2022-01-19 | GSE150124 | GEO

Gene Expression in d5 wound-edge tissues of MFG-E8 WT and MFG-E8 KO mice

Project description:Gene Expression in d5 wound-edge tissues of MFG-E8 WT and MFG-E8 KO mice Affymetrix GeneChipÂ® Mouse Genome 430 array was used to study the gene expression in d5 wound-edge tissues of MFG-E8 WT and MFG-E8 KO mice Gene Expression in d5 wound-edge tissues of MFG-E8 WT and MFG-E8 KO mice

2016-07-21 | E-GEOD-73229 | biostudies-arrayexpress

Gene Expression in d5 wound-edge tissues of MFG-E8 WT and MFG-E8 KO mice

Project description:Gene Expression in d5 wound-edge tissues of MFG-E8 WT and MFG-E8 KO mice Affymetrix GeneChip® Mouse Genome 430 array was used to study the gene expression in d5 wound-edge tissues of MFG-E8 WT and MFG-E8 KO mice

2016-07-21 | GSE73229 | GEO

The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation

Project description:T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during infection. We find that at high concentrations T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin immunoprecipitation sequencing (ChIP-seq) showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential. Splenocyte derived CD8+ T cells from C57BL/6 mice with either a wildtype (WT) (GzmB-Cre Zeb2+/+) or GzmB-Cre Zeb2-fl/fl (Zeb2-/-) backgrounds, following 8 days post infection with LCMV-Armstrong, were subsetted into KLRG1-hi/IL-7R-lo populations (terminal effectors, TE) or KLRG1-lo/IL-7R-hi (memory precursors, MP) populations. Four experimental groups, each with 3 samples, comprised of TE+WT, MP+WT, TE+ZEB2-/-, and MP+ZEB2-/-, were profiled for gene expression utilizing a polyA RNA prep and hybridized to the Illumina microarray platform IlluminaWG-v2.0.

2015-09-15 | E-GEOD-72408 | biostudies-arrayexpress

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