ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens Drosophila melanogaster
PROVIDER: GSE194036 | GEO | 2022/12/23
REPOSITORIES: GEO
Similar Datasets
Project description:Connecting genes to their cis-regulatory elements has been enabled by genome-wide mapping of chromatin interactions using proximity ligation in ChIA-PET, Hi-C, and their derivatives. However, these methods require millions of input cells for high-quality data and thus are unsuitable for many studies when only limited cells are available. Conversely, epigenomic profiling via transposase digestion in ATAC-seq requires only hundreds to thousands of cells to robustly map open chromatin associated with transcription activity, but it cannot directly connect active genes to their distal enhancers. Here, we combine proximity ligation in ChIA-PET and transposase accessibility in ATAC-seq into ChIATAC to efficiently map interactions between open chromatin loci in low numbers of input cells. We validate ChIATAC in Drosophila cells and optimize it for mapping 3D epigenomes in human cells robustly. Applying ChIATAC to primary human T cells, we reveal mechanisms that topologically regulate transcriptional programs during T cell activation.
| S-EPMC9839710 | biostudies-literature
Project description:ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs
| PRJNA798774 | ENA
Project description:We describe the Bridge linker-Alul-Tn5 Hi-C (BAT Hi-C) method, which is a simple and efficient method for delineating chromatin conformational features of mouse embryonic stem (mES) cells and uncover DNA loops. This protocol combines Alul fragmentation and biotinylated linker-mediated proximity ligation to obtain kilobase (kb) resolution with a marked increase in the amount of unique read pairs. The protocol also includes chromatin isolation to reduce background noise and Tn5 tagmentation to cut down on preparation time.
2019-09-30 | GSE136756 | GEO
Project description:The analysis of chromatin features in single cells centers around the use of Tn5 transposase and exploits its activity to simultaneously fragment target DNA and integrate adapter sequences of choice. This reaction provides a direct readout in the transposase-accessible chromatin in single cells (scATAC-seq) assay to map open chromatin regions. Furthermore, by targeting Tn5 to antibody-bound chromatin epitopes, features like histone modifications can be mapped in single cells. Thus, enhancing Tn5 activity to improve genomic coverage for scATAC-seq or facilitating multi-omics readout of chromatin features via Tn5 together with the transcriptome is of great interest. Here, we address these issues by optimizing scATAC-seq for an increased number of integrations per cell. In addition, we provide a protocol that combines mapping of histone modification with scRNA-seq from the same cell. Our experimental workflows improve the results obtained from the downstream data analysis and serve to better resolve epigenetic heterogeneity and transcription regulation in single cells.
2023-11-08 | GSE235499 | GEO
Project description:The analysis of chromatin features in single cells centers around the use of Tn5 transposase and exploits its activity to simultaneously fragment target DNA and integrate adapter sequences of choice. This reaction provides a direct readout in the transposase-accessible chromatin in single cells (scATAC-seq) assay to map open chromatin regions. Furthermore, by targeting Tn5 to antibody-bound chromatin epitopes, features like histone modifications can be mapped in single cells. Thus, enhancing Tn5 activity to improve genomic coverage for scATAC-seq or facilitating multi-omics readout of chromatin features via Tn5 together with the transcriptome is of great interest. Here, we address these issues by optimizing scATAC-seq for an increased number of integrations per cell. In addition, we provide a protocol that combines mapping of histone modification with scRNA-seq from the same cell. Our experimental workflows improve the results obtained from the downstream data analysis and serve to better resolve epigenetic heterogeneity and transcription regulation in single cells.
2023-11-08 | GSE235497 | GEO
Project description:The analysis of chromatin features in single cells centers around the use of Tn5 transposase and exploits its activity to simultaneously fragment target DNA and integrate adapter sequences of choice. This reaction provides a direct readout in the transposase-accessible chromatin in single cells (scATAC-seq) assay to map open chromatin regions. Furthermore, by targeting Tn5 to antibody-bound chromatin epitopes, features like histone modifications can be mapped in single cells. Thus, enhancing Tn5 activity to improve genomic coverage for scATAC-seq or facilitating multi-omics readout of chromatin features via Tn5 together with the transcriptome is of great interest. Here, we address these issues by optimizing scATAC-seq for an increased number of integrations per cell. In addition, we provide a protocol that combines mapping of histone modification with scRNA-seq from the same cell. Our experimental workflows improve the results obtained from the downstream data analysis and serve to better resolve epigenetic heterogeneity and transcription regulation in single cells.
2023-11-08 | GSE235503 | GEO
Project description:The analysis of chromatin features in single cells centers around the use of Tn5 transposase and exploits its activity to simultaneously fragment target DNA and integrate adapter sequences of choice. This reaction provides a direct readout in the transposase-accessible chromatin in single cells (scATAC-seq) assay to map open chromatin regions. Furthermore, by targeting Tn5 to antibody-bound chromatin epitopes, features like histone modifications can be mapped in single cells. Thus, enhancing Tn5 activity to improve genomic coverage for scATAC-seq or facilitating multi-omics readout of chromatin features via Tn5 together with the transcriptome is of great interest. Here, we address these issues by optimizing scATAC-seq for an increased number of integrations per cell. In addition, we provide a protocol that combines mapping of histone modification with scRNA-seq from the same cell. Our experimental workflows improve the results obtained from the downstream data analysis and serve to better resolve epigenetic heterogeneity and transcription regulation in single cells.
2023-11-08 | GSE235502 | GEO
Project description:The analysis of chromatin features in single cells centers around the use of Tn5 transposase and exploits its activity to simultaneously fragment target DNA and integrate adapter sequences of choice. This reaction provides a direct readout in the transposase-accessible chromatin in single cells (scATAC-seq) assay to map open chromatin regions. Furthermore, by targeting Tn5 to antibody-bound chromatin epitopes, features like histone modifications can be mapped in single cells. Thus, enhancing Tn5 activity to improve genomic coverage for scATAC-seq or facilitating multi-omics readout of chromatin features via Tn5 together with the transcriptome is of great interest. Here, we address these issues by optimizing scATAC-seq for an increased number of integrations per cell. In addition, we provide a protocol that combines mapping of histone modification with scRNA-seq from the same cell. Our experimental workflows improve the results obtained from the downstream data analysis and serve to better resolve epigenetic heterogeneity and transcription regulation in single cells.
2023-11-08 | GSE235501 | GEO
Project description:The analysis of chromatin features in single cells centers around the use of Tn5 transposase and exploits its activity to simultaneously fragment target DNA and integrate adapter sequences of choice. This reaction provides a direct readout in the transposase-accessible chromatin in single cells (scATAC-seq) assay to map open chromatin regions. Furthermore, by targeting Tn5 to antibody-bound chromatin epitopes, features like histone modifications can be mapped in single cells. Thus, enhancing Tn5 activity to improve genomic coverage for scATAC-seq or facilitating multi-omics readout of chromatin features via Tn5 together with the transcriptome is of great interest. Here, we address these issues by optimizing scATAC-seq for an increased number of integrations per cell. In addition, we provide a protocol that combines mapping of histone modification with scRNA-seq from the same cell. Our experimental workflows improve the results obtained from the downstream data analysis and serve to better resolve epigenetic heterogeneity and transcription regulation in single cells.
2023-11-08 | GSE235504 | GEO
Project description:we developed a simple Digestion-Ligation-Only Hi-C (DLO Hi-C) technology to explore the 3D landscape of the genome
2018-02-27 | GSE89663 | GEO