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Genome-wide maps of H3K27ac in HDAC3 knockout bone marrow pDCs compared with control pDCs

ABSTRACT: Genome-wide maps of H3K27ac in HDAC3 knockout bone marrow pDCs compared with control pDCs

PROVIDER: PRJNA809374 | ENA |

REPOSITORIES: ENA

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Genome-wide maps of H3K27ac in HDAC3 knockout bone marrow pDCs compared with control pDCs

Project description:Hdac3 is highly expressed in pDCs, and its deficiency led to substantially impaired development of pDCs, but not cDCs in bone marrow (BM) and spleen. Meanwhile,further investigation demonstrated that HDAC3 was required for the differentiation of pDC from progenitors at different differentiation stages in vitro. Cut & Tag analysis of H3K27ac level in HDAC3 deficient bone marrow pDCs compared with control pDCs, showed that H3K27ac level significantly increased on cDC related genes with PU.1 binding sites in HDAC3 knockout pDCs.

2022-05-27 | GSE197212 | GEO

Next Generation Sequencing of transcriptomes to reveal the role of HDAC3 in regulating the development of LMPP and CD115- CDP and bone marrow pDCs

Project description:Hdac3 is highly expressed in pDCs, and its deficiency led to substantially impaired development of pDCs, but not cDCs in bone marrow (BM) and spleen. Meanwhile, the hematopoietic progenitors with DC differentiation potential, including CMP, CLP and CD115+ CDP were significantly decreased. Although the number of HSC and CD115− CDP were increased, their differentiation potential toward pDCs were abolished. Further investigation demonstrated that HDAC3 was required for the differentiation of pDC from progenitors at different differentiation stages.

2022-05-27 | GSE197207 | GEO

Changes of H3K9ac and H3K27ac recruitment in pachytene spermatocytes and round spermatids from testes-specific HDAC3-depleted mice and genome-wide maps of HDAC3,NCOR and Sox30 in wild-type and Sox30 KO testes

Project description:We reported changes in the recruitment of H3K9ac and H3K27ac in HDAC3-depleted mouse testes in the late meiotic and early haploid stages. We also investigated genome-wide occupancy of HDAC3, NCOR and Sox30 to the mouse testes from wild-type and Sox30 KO mice.

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Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes

Project description:Histone deacetylase inhibitors are efficacious epigenetic-based therapies for some cancers and neurological disorders; however, these drugs inhibit multiple Hdacs and have detrimental effects on the pre- and post-natal skeleton. To better understand how Hdac inhibitors affect the skeleton, we focused on understanding the role of one of their targets, Hdac3, in endochondral bone formation by deleting it in immature murine chondrocyte micro masses with Adeno-Cre. Hdac3-deficient chondrocytes expressed higher levels of pro-inflammatory and matrix degrading genes (e.g., Il-6, Mmp3, Mmp13, Saa3) and lower levels of genes related to the extracellular matrix production, bone development and ossification (e.g., Acan, Col2a1, Ihh, Col10a1). Histone acetylation was increased in and around genes with elevated expression. This SuperSeries is composed of the SubSeries listed below. High Throughput RNA sequencing and Chromatin immunopreciptation sequencing experiments were performed in chondrocyte cultures. Differential analysis was conducted on ChIP-seq and RNA-seq data to identify H3K27Ac profiles for up and down-regulated genes in Hdac3-deficient murine chondrocytes. mm10 was used as reference genome. Refer to individual Series

2016-08-10 | E-GEOD-75552 | biostudies-arrayexpress

Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes[RNA-Seq]

Project description:Histone deacetylase inhibitors are efficacious epigenetic-based therapies for some cancers and neurological disorders; however, these drugs inhibit multiple Hdacs and have detrimental effects on the pre- and post-natal skeleton. To better understand how Hdac inhibitors affect the skeleton, we focused on understanding the role of one of their targets, Hdac3, in endochondral bone formation by deleting it in immature murine chondrocyte micro masses with Adeno-Cre. Hdac3-deficient chondrocytes expressed higher levels of pro-inflammatory and matrix degrading genes (e.g., Il-6, Mmp3, Mmp13, Saa3) and lower levels of genes related to the extracellular matrix production, bone development and ossification (e.g., Acan, Col2a1, Ihh, Col10a1). Histone acetylation was increased in and around genes with elevated expression. High Throughput RNA sequencing and Chromatin immunopreciptation sequencing experiments were performed in chondrocyte cultures. Differential analysis was conducted on ChIP-seq and RNA-seq data to identify H3K27Ac profile for up and down regulated genes in Hdac3-deficient murine chondrocytes.

2016-08-10 | E-GEOD-75549 | biostudies-arrayexpress

Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes[ChIP-Seq]

Project description:Histone deacetylase inhibitors are efficacious epigenetic-based therapies for some cancers and neurological disorders; however, these drugs inhibit multiple Hdacs and have detrimental effects on the pre- and post-natal skeleton. To better understand how Hdac inhibitors affect the skeleton, we focused on understanding the role of one of their targets, Hdac3, in endochondral bone formation by deleting it in immature murine chondrocyte micro masses with Adeno-Cre. Hdac3-deficient chondrocytes expressed higher levels of pro-inflammatory and matrix degrading genes (e.g., Il-6, Mmp3, Mmp13, Saa3) and lower levels of genes related to the extracellular matrix production, bone development and ossification (e.g., Acan, Col2a1, Ihh, Col10a1). Histone acetylation was increased in and around genes with elevated expression. High Throughput RNA sequencing and Chromatin immunopreciptation sequencing experiments were performed in chondrocyte cultures. Differential analysis was conducted on ChIP-seq and RNA-seq data to identify H3K27Ac profile for up and down regulated genes in Hdac3-deficient murine chondrocytes.

2016-08-10 | E-GEOD-75547 | biostudies-arrayexpress

RNA sequencing of bone marrow WT and SLAMF9-/- pDCs

Project description:SLAMF9 belongs to the conserved lymphocytic activation molecule family (SLAMF). Unlike other SLAMs, which have been extensively studied, the role of SLAMF9 in the immune system remained mostly unexplored. By generating CRISPR/CAS9 SLAMF9 knockout mice, we analyzed the role of this receptor in plasmacytoid dendritic cells (pDCs), which preferentially express the SLAMF9 transcript and protein. These cells display a unique capacity to produce type I interferon and bridge between innate and adaptive immune response. Analysis of pDCs in SLAMF9-/- mice revealed an increase of immature pDCs in the BM and enhanced accumulation of pDCs in the lymph nodes. In the periphery, SLAMF9 deficiency resulted in lower levels of the transcription factor SPIB, elevation of pDC survival, and attenuated IFNand TNFproduction. To define the role of SLAMF9 during inflammation, pDCs lacking SLAMF9 were followed during induced experimental autoimmune encephalomyelitis (EAE). SLAMF9-/- mice demonstrated attenuated disease and delayed onset, accompanied by a prominent increase of immature pDCs in the LN, with a reduced co-stimulatory potential and enhanced infiltration of pDCs into the central nervous system (CNS). These results suggest the crucial role of SLAMF9 in pDC differentiation, homeostasis and function in the steady state and during EAE.

2019-08-22 | GSE131633 | GEO

Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes

Project description:Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes

| PRJNA304512 | ENA

ChIPseq for histone marks in WT and Hdac3 knock-out clones of TNG-A derived mESCs in 2iLIF and SL differentiation conditions

Project description:H3K27ac and H4K5ac ChIPseq in WT and Hdac3-/- mESCs in order to determine the role of Hdac3 on the activity of cis-regulatory elements during differentiation.<br>This experiment is part of the study: "Mechanistic framework of lineage restriction in embryonic stem cells" by Olivieri et al.

2021-03-15 | E-MTAB-9450 | biostudies-arrayexpress

Comparison of pDCs isolated from recipients of STAT1+/+ vs. STAT1-/- bone marrow

Project description:The goal of this study is to determine if pDCs reconstituted from T cell depleted allogeneic STAT1-/- bone marrow express genes that contribute to Graft versus host disease (GVHD) resistance as compared to STAT1+/+ bone marrow Lethally irradiated B6 x C3H.SW mice were transplanted with T cell depleted 129 or 129 STAT1-/- bone marrow. 14 days later, pDCs were isolated from spleens by magnetic cell selection, and pooled from 12 mice/group. cDNA was generated and hybridized to an Affymetrix genechip mouse genome 430 2.0 array. Samples were normalized by RMA algorithm to a log2 intensity value and analyzed by Ingenuity Pathway Analysis v8.5 software.

2014-07-25 | E-GEOD-59731 | biostudies-arrayexpress

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