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The transcriptional regulation analysis of ETS2 in mouse BMM cells (Cut&Tag)

ABSTRACT: The transcriptional regulation analysis of ETS2 in mouse BMM cells (Cut&Tag)

PROVIDER: PRJNA1219400 | ENA |

REPOSITORIES: ENA

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The transcriptional regulation analysis of ETS2 in mouse BMM cells (Cut&Tag)

Project description:The transcription factor ETS2 was identified as a hub gene that promotes osteoclast differentiation during the progression of osteoarthritis (OA). Virtual perturbation and in vitro perturbation experiments demonstrated that knockdown of ETS2 can inhibit osteoclast differentiation. Transcriptional regulatory network analysis and combined CUT&Tag with ATAC-seq analysis results indicate that ETS2 promotes osteoclast differentiation by targeting and enhancing the expression of CEBPB.

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Project description:This study uses Cleavage Under Targets and Tagmentation (Cut&Tag) chromatin profiling to map genome-wide binding sites of TES (TEAD1 Epigenetic Silencer, an engineered epigenetic silencer factor consisting of KRAB-hTEAD1(1-166)-DNMT3A/3L with V5 tag) and overexpressed wild-type TEAD1 (HA-tagged) in SNB19 glioblastoma cells. Cut&Tag was performed using the CUTANA protocol (EpiCypher). Three biological replicates were prepared for TES (detected via anti-V5) and TEAD1 (detected via anti-HA), with mouse IgG and rabbit IgG as negative controls. Peak calling identified binding sites for both factors, showing that TES largely preserves the DNA-binding specificity of wild-type TEAD1 while converting it into a transcriptional repressor.

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Project description:HIF2A(EPAS1) geenome_wide localization by Cut & Tag in MRC5 human fibroblasts ectopically expressing HIF2A in the pBabe vector, and in control MRC5 human fibroblasts containing only the pBabe vector. 2 biological replicates were done for the MRC5-HIF2A cells. Cut & Tag with an anti-H3-K27me3 Ab was done as a positive control for the Cut & Tag experiments.

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Bulk Cut&run and Cut&tag

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Transcriptional regulation by TES and TEAD1 in SNB19 glioblastoma cells: Cut&Tag

Project description:Transcriptional regulation by TES and TEAD1 in SNB19 glioblastoma cells: Cut&Tag

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scNanoSeq-CUT&Tag: a long-read single-cell CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells

Project description:We developed scNanoSeq-CUT&Tag, a streamlined method by adapting a modified CUT&Tag protocol to Oxford Nanopore sequencing platform for efficient chromatin modification profiling at single-cell resolution. We firstly tested the performance of scNanoSeq-CUT&Tag on six human cell lines: K562, 293T, GM12878, HG002, H9, HFF1 and adult mouse blood cells, it showed that scNanoSeq-CUT&Tag can accurately distinguish different cell types in vitro and in vivo. Moreover, scNanoSeq-CUT&Tag enables to effectively map the allele-specific epigenomic modifications in the human genome andallows to analyze co-occupancy of histone modifications. Taking advantage of long-read sequencing,scNanoSeq-CUT&Tag can sensitively detect epigenomic state of repetitive elements. In addition, by applying scNanoSeq-CUT&Tag to testicular cells of adult mouse B6D2F1, we demonstrated that scNanoSeq-CUT&Tag maps dynamic epigenetic state changes during mouse spermatogenesis. Finally, we exploited the epigenetic changes of human leukemia cell line K562 during DNA demethylation, it showed that NanoSeq-CUT&Tag can capture H3K27ac signals changes along DNA demethylation. Overall, we prove that scNanoSeq-CUT&Tag is a valuable tool for efficiently probing chromatin state changes within individual cells.

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