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Genome-wide maps of chromatin state in human primary CAR-T cells [scRNA-seq]

ABSTRACT: We report the single-cell transcriptomic profile of human primary T cells specifc for NY-ESO-1.

ORGANISM(S): Homo sapiens

PROVIDER: GSE213015 | GEO | 2022/09/09

REPOSITORIES: GEO

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Genome-wide maps of chromatin state in human primary CAR-T cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-09-02 | GSE174282 | GEO

Genome-wide maps of chromatin state in human primary CAR-T cells [RNA-seq]

Project description:We report the transcriptomic and epigentic profile of human primary CD19-28z CAR-T cells.

2022-09-06 | GSE174279 | GEO

Genome-wide maps of chromatin state in human primary CAR-T cells [ChIPseq, ATAC-seq]

Project description:We report the transcriptomic and epigentic profile of human primary CD19-28z CAR-T cells.

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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

Project description: Not available

| S-EPMC2921165 | biostudies-literature

TCR affinity-dependent functional inhibition via PD-1 and SHP-1 phosphatase

Project description:To investigate gene expression changes associated with stimulation of TCRs of different affinity, primary CD8 T cells were transduced with sequence optimized TCRs of various affinities and stimulated for 6h. Gene expression was measured at baseline (0h) and after 6h after stimulation with low dose NY-ESO-1 multimer

2013-02-11 | E-GEOD-42922 | biostudies-arrayexpress

Genome-wide maps of chromatin state in primary MLL-AF9 AML

Project description:Here we describe the development of CKIα inhibitors, which co-target the transcriptional kinases CDK7 and CDK9, thereby augmenting CKIα-induced p53 activation and its anti-leukemic activity. Oncogene-driving super-enhancers (SEs) are highly sensitive to CDK7/9 inhibition. We identified multiple newly-gained SEs in primary mouse AML cells and demonstrate that the inhibitors abolish many SEs and preferentially suppress the transcription elongation of SE-driven oncogenes. We show that blocking CKIα together CDK7 and/or CDK9 synergistically stabilize p53, deprive leukemia cells of survival and proliferation-maintaining SE-driven oncogenes, and induce apoptosis.

2018-08-23 | GSE117443 | GEO

Vaccine Therapy With or Without Sirolimus in Treating Patients With NY-ESO-1 Expressing Solid Tumors

Project description:This phase I trial studies the side effects and best schedule of vaccine therapy with or without sirolimus in treating patients with cancer-testis antigen (NY-ESO-1) expressing solid tumors. Biological therapies, such as sirolimus, may stimulate the immune system in different ways and stop tumor cells from growing. Vaccines made from a person’s white blood cells mixed with tumor proteins may help the body build an effective immune response to kill tumor cells that express NY-ESO-1. Infusing the vaccine directly into a lymph node may cause a stronger immune response and kill more tumor cells. It is not yet known whether vaccine therapy works better when given with or without sirolimus in treating solid tumors.

| 2119578 | ecrin-mdr-crc

Genome-wide maps of chromatin state in human primary airway smooth muscle cells.

Project description:We generated genome-wide chromatin-state maps of human airway smooth muscle cells. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, Lysine 4 monomethylation was used to highlight the location of potential regulatory domains in these cells.

2017-12-31 | GSE43357 | GEO

Genome-wide maps of chromatin state in NCCIT cells

Project description:H2B mono-ubiquitylation is required for multiple methylations of both H3K4 and H3K79 and has been implicated in gene expression from yeast to human. However, molecular crosstalk between H2BUb1 and other modifications, especially H3K4 and H3K79 methylations, remains unclear in vertebrates. To understand the functional role of H2BUb1, genome-wide histone modification patterns were measured in human cells. This study proposes dual roles of H2BUb1 that are both H3 methylation dependent and independent. First, H2BUb1 is a 5'-enriched active transcription mark and is co-occupied with H3K79 methylations in actively transcribed regions. Importantly, this study found a unique role of H2BUb1 in chromatin architecture independent of histone H3 methylations. H2BUb1 is well positioned in exon-intron boundaries of highly expressed exons and is specifically enriched in 5'-biased exons. Furthermore, H2BUb1 demonstrates increased occupancy in skipped exons compared to flanking exons for the human and mouse genome. Our findings suggest that a potentiating mechanism links H2BUb1 to both H3K79 methylations in actively transcribed regions and the exon-intron structure of highly expressed exons through the regulation of nucleosome dynamics during transcription elongation. We generated high-throughput sequencing (ChIP-seq) data for genome-wide occupancy of H2BUb1, nucleosome, H3K4me3, H3K36me3, H379me1/2/3, H3Ac, and mRNA in human embryonic carcinoma cells. We performed ChIP-seq for seven different histone modifications, MNase-seq, mRNA-seq (two replications), and inputDNA-seq in NCCIT cell lines (human embryonic carcinoma cell lines). We also performed mRNA-seq for RNF20-siRNA transfected NCCIT cells, where H2BUb1 signals decreased.

2012-03-07 | E-GEOD-25882 | biostudies-arrayexpress

Genome-wide maps of chromatin state in rice endosperm

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone H3 trimethylation in rice endosperm. By obtaining about four hundred million bases of sequence from rice chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of rice endosperm. We find that the presence of H3K27me3 in either upstream or downstream of a gene is predominately associated with repression of the gene, while its absence is mainly associated with high gene expression. Examination of Histone H3 lysine 27 trimethylation in rice endosperm.

2011-12-06 | E-GEOD-27048 | biostudies-arrayexpress

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