ScATAC-seq of fetal thymus
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ABSTRACT:
PROVIDER: PRJEB53030 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To investigate the gene regulatory mechanisms driving T cell development, we generated single-cell transcriptomics and chromatin accessibility data from a human fetal thymus sample at 10 weeks of gestation.
2021-11-30 | E-MTAB-9828 | biostudies-arrayexpress
Project description:scRNA-seq of human fetal thymus
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Project description:To investigate the gene regulatory mechanisms driving T cell development, we generated single-cell transcriptomics and chromatin accessibility data from a human fetal thymus sample at 10 weeks of gestation.
2021-11-30 | E-MTAB-9840 | biostudies-arrayexpress
Project description:Plasmodium-specific CD4+ T cells from mice infected with Plasmodium chabaudi chabaudi AS parasites were recovered at Days 0, 4, 7, and 32 to undergo processing and to generate scATAC-seq dataset. At Day 7, CXCR5+ and CXCR6+ cells were recovered separately. At Day 32, mice were administered with either saline or artesunate (intermittent artesunate therapy - IAT). scATAC-seq dataset was analysed to investigate epigenomic landscapes of CD4+ T cells from effector to memory states.
2020-10-14 | E-MTAB-9402 | biostudies-arrayexpress
Project description:To study developmental trajectories in brain organoids, we conducted scRNA-seq and scATAC-seq in parallel on a dense timecourse of early development.
2022-08-18 | E-MTAB-11998 | biostudies-arrayexpress
Project description:Cell-to-cell variation is a universal feature of life that impacts a wide range of biological phenomena, from developmental plasticity to tumor heterogeneity. While recent advances have improved our ability to document cellular phenotypic variation the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of cellular DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells via assay of transposase accessible chromatin sequencing (ATAC-seq). Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single-cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provides insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type specific accessibility variance across 6 cell types. Targeted perturbations of cell cycle or transcription factor signaling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome topological domains de novo, linking single-cell accessibility variation to three-dimensional genome organization. All together, single-cell analysis of DNA accessibility provides new insight into cellular variation of the “regulome.” Profiles of single cell epigenomes, assayed using scATAC-seq, across 8 cell types and 4 targeted cell manipulations. The complete data set contains a total of 1,632 assayed wells.
2015-06-17 | E-GEOD-65360 | biostudies-arrayexpress
Project description:A mixture of Caki-1 and HeLa cells in known proportions (80:20) is profiled using 10x Chromium scATAC-seq or scGET-seq protocols.
2021-08-17 | E-MTAB-9650 | biostudies-arrayexpress
Project description:Thymic epithelial cells (TEC) control T cell development and play essential roles in establishing self-tolerance. Transcription factors controlling TEC development are poorly characterized. We report that Klf6 plays a critical role in TEC development. Mice deficient for Klf6 in TEC had a hypoplastic thymus - evident from fetal stages into adulthood. Proliferation of TEC was not reduced, but a dramatic increase in the frequency of apoptotic TEC in fetal and adult thymus was observed. Among cortical TEC (cTEC), we found expansion of a previously unreported cTEC population expressing the transcription factor Sox10. Medullary TEC (mTEC) subsets were not equally impacted with Ccl21a+ mTEC I and Tuft-like mTEC IV being disproportionately affected. Consistent with these TEC defects, naïve conventional T cells and NKT cells were reduced in the spleen, and signs of autoimmunity were evident. Thus, Klf6 has a pro- survival role in TEC and is also required for differentiation of the mTEC I and mTEC IV populations of TEC in adult mice. In this work, we report that mice with Foxn1-Cre mediated ablation of Klf6 in TEC demonstrate thymic hypoplasia beginning from prenatal life and extending through adulthood. Guided by single-cell transcriptional profiling, we determined that loss of Klf6 increased programmed cell death of TEC in prenatal and adult mice. In adult mice, thymic Klf6 deficiency severely impacted the mTEC I and mTEC IV populations. In addition, Klf6 deficiency led to the expansion of a previously uncharacterized cTEC population expressing Sox10 that is present in wild-type mice at very low frequencies. We observed concordant reductions of the naïve αβ T cell and iNKT pools in the periphery of young adult mice. Furthermore, we detected T cell infiltration in salivary and lacrimal glands, indicating defects in T cell tolerance.
2023-10-12 | GSE221073 | GEO
Project description:In the mouse thymus, invariant γδ T cells are generated at well-defined times during development and acquire effector functions before exiting the thymus. However, whether such thymic programming can occur in human is not known. Here we analyzed human fetal and post-natal γδ thymocytes and investigated the role of hematopoietic-stem-and-precursor-cells (HSPC) in the generation of human γδ T cells. Unlike post-natal γδ thymocytes, fetal γδ thymocytes were functionally programmed (e.g. IFNγ, granzymes), expressed low levels of terminal-deoxynucleotidyl-transferase (TdT) and were highly enriched for invariant/public germline-encoded CDR3 sequences (TRGV8-TRJP1-CATWDTTGWFKIF, TRDV2-TRDD3-CACDTGGY and TRDV1-TRDD3-CALGELGD, previously shown to be expanded in cytomegalovirus infection) composed of short-homology-repeat-containing gene segments. Furthermore, these unique characteristics were due to an intrinsic property of fetal HSPC caused by high expression of the RNA-binding protein Lin28b. In conclusion, our data indicate that the human fetal thymus generates, in a HSPC/Lin28b-dependent manner, invariant γδ T cells with programmed effector functions.
2019-11-21 | GSE128163 | GEO
Project description:Single cell sequencing technology has been widely used for understanding the heterogeneity of complex tissue and for identifying novel cell types or cell states. Previous efforts of single cell profiling are mostly performed by measuring transcriptomes using single cell RNA sequencing (scRNA-seq). scRNA-seq is relatively well developed and around 500 analysis tools are currently available for performing different tasks. In the past five years, assays for profiling the single cell chromatin accessibility landscape have emerged and provide extra information about gene regulation at the epigenetic level. Due to its simplicity and sensitivity, single cell Assays for Transposase-Accessible Chromatin using sequencing (scATAC-seq) is widely used to obtain chromatin accessibility. This data will be used to comprehensively evaluate scATAC-seq data analysis tools and gaps in analysis workflows together with publicly available bulk ATAC-Seq and scATAC-seq data using optimised universal evaluation metrics. Furthermore, this data will be used to validate novel isoforms identified from long-read scRNA-Seq study.
2019-12-19 | GSE142285 | GEO