IRF4-dependent division-coupled reprogramming events [IRF4cKO.ATACseq]
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PROVIDER: PRJNA725526 | ENA |
REPOSITORIES: ENA
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Project description:IRF4-dependent division-coupled reprogramming events [IRF4cKO.RNAseq]
| PRJNA725527 | ENA
Project description:To assess the timing and scope of IRF4–dependent reprogramming in vivo, CTV-labeled IRF4–sufficient and –deficient B cells were transferred into mMT hosts. One day later, hosts were challenged with 50 mg LPS. Three days post-LPS challenge, transferred cells were recovered and sorted from divisions 0, 1, 3, 4, 5, and 6 as determined by CTV dilution for RNA–seq.
2021-07-30 | GSE173436 | GEO
Project description:To assess the timing and scope of IRF4–dependent reprogramming in vivo, CTV-labeled IRF4–sufficient and –deficient B cells were transferred into mMT hosts. One day later, hosts were challenged with 50 mg LPS. Three days post-LPS challenge, transferred cells were recovered and sorted from divisions 0, 1, 3, 4, 5, and 6 as determined by CTV dilution for ATAC–seq.
2021-07-30 | GSE173435 | GEO
Project description:B cells provide humoral immunity by differentiating into antibody secreting plasma cells. Differentiation is dependent upon division and transcriptional changes, with commitment to B cell lineages associated with epigenetic changes. Analysis of early transcriptional and epigenetic events in B cell differentiation revealed that plasmablasts and plasma cells undergo dynamic changes in gene expression and a progressive DNA hypomethylation targeted to at least 10% of genes/loci. Of the differentially methylated loci, more than 99.7% were demethylated during differentiation and these clustered in cis-regulatory features such as enhancers and transcription factor binding sites. Changes in gene expression and DNA methylation coincided with each other at specific divisions during differentiation and inhibition of DNA methylation resulted in augmented plasma cell commitment in a division-dependent manner. These data identify a major epigenetic reprogramming event during early B cell differentiation coupled division and provide an approach to modulating humoral immune responses.
2016-05-01 | GSE78815 | GEO
Project description:B cells provide humoral immunity by differentiating into antibody secreting plasma cells. Differentiation is dependent upon division and transcriptional changes, with commitment to B cell lineages associated with epigenetic changes. Analysis of early transcriptional and epigenetic events in B cell differentiation revealed that plasmablasts and plasma cells undergo dynamic changes in gene expression and a progressive DNA hypomethylation targeted to at least 10% of genes/loci. Of the differentially methylated loci, more than 99.7% were demethylated during differentiation and these clustered in cis-regulatory features such as enhancers and transcription factor binding sites. Changes in gene expression and DNA methylation coincided with each other at specific divisions during differentiation and inhibition of DNA methylation resulted in augmented plasma cell commitment in a division-dependent manner. These data identify a major epigenetic reprogramming event during early B cell differentiation coupled division and provide an approach to modulating humoral immune responses.
2016-05-01 | GSE78816 | GEO
Project description:Transcriptional profiling of T-cells isolated from spleen of IRF4 -/- mice and cultured under Th17 polarizing conditions for 42 hrs compared to cells similarly isolated and cultured from spleen of IRF4 +/- mice. The aim of the study was to identify global misexpression of genes in IRF4 -/- cells and hence identify key pathways regulated by IRF4 during Th17 differentiation. Two-condition experiment, IRF4 -/- vs IRF4 +/- Th17 cells at 42hrs. Biological replicates: 3 for each condition
2012-09-13 | E-GEOD-40726 | biostudies-arrayexpress
Project description:Abiotic stress-response reprogramming events underlie successful initiation of apomixis
| PRJEB14921 | ENA
Project description:Fibroblasts are the most commonly used model in probing the complex process of somatic reprogramming. Although hematopoietic cells represents a more convenient and accesible/ or “an excellent alternative” starting cell type, the molecular mechanisms in hematopoietic reprogramming are poorly defined. In the present study, we showed that hematopoietic stem and progenitor cells (HSPCs) with long term repopulating potential, among several HSPC populations, are more amenable for reprogramming, and exhibit an efficient induction of transcriptional program involved in the promation of cell prolifieration and inhibition of apoptosis. In sharp comparison with fibroblasts, HSPCs possess distinct requirements for the activation of Tgf-b and wnt pathways in the initiation phase of reprograming, which can be attributable, at lease partially, to differentiall expression of key signaling genes in these two cell types. Our data demonstrate that lineage and developmental/differentiation stage-specific context define key early events in the reprogramming of hematopoietic cells to pluripotency. Examine the differential global gene expression among different hematopietic cells in reprogramming. LT-HSC, ST-HSC, MP and fibroblasts were used in this study. Doxcycline addition could induce expression of oct4, sox2, klf4 and c-myc, consequently reprogramming these cells into iPS cells. Hematopietic cells cultured with doxcycline for 0, 2, 4 days were sampled, and samples at the same timepoint without doxcycline were also taken to exclude vast gene expression change in hematopoietic cell in-vitro culture. Fibroblast samples induced by doxcycline for 0, 2, 4 days were also introduced to provide comparism between lineages.
2015-04-07 | E-GEOD-54462 | biostudies-arrayexpress
Project description:Plasma cell differentiation is coupled to division-dependent DNA hypomethylation and gene regulation.
| PRJNA288178 | ENA
Project description:Transcriptional profiling of T-cells isolated from spleen of IRF4 -/- mice and cultured under Th17 polarizing conditions for 42 hrs compared to cells similarly isolated and cultured from spleen of IRF4 +/- mice. The aim of the study was to identify global misexpression of genes in IRF4 -/- cells and hence identify key pathways regulated by IRF4 during Th17 differentiation.
2012-09-13 | GSE40726 | GEO