Tn5 insertion in S.meliloti
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB60399 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We generated Tn5 segmentation data on naked genomic DNA to explore the intrinsic Tn5 insertion preference along the whole genome
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Project description:To be able to study where Tn5 inserts among repeat sequences of the genome, ATAC-seq was performed using a custom insert. The resulting DNA was then mechanically sheared and sequenced using PacBio
2024-07-19 | E-MTAB-14238 | biostudies-arrayexpress
Project description:This experiment includes the sequencing files for different hp1a-tn5 hybrids, together with standard ATAC-seq and ChIP-seq data used to evaluate the best construct.
2021-08-17 | E-MTAB-9648 | biostudies-arrayexpress
Project description:Tn5 transposase is used as a tool for detecting nucleosome-free regions of genomic DNA in eukaryotes, but its DNA target site in chromatin has not been understood. In the present study, the well-positioned dinucleosomes were reconstituted, and the Tn5 transposase target sites were mapped in the dinucleosomes in vitro. We found that Tn5 transposase preferentially targets near the entry-exit DNA region within the nucleosome, if the linker DNA exists between two nucleosomes. This specific DNA targeting by Tn5 did not depend on the linker DNA length and DNA sequence. Tn5 transposase becomes to target the middle of the linker DNA, in addition to the entry-exit site of the nucleosome, if the linker DNA length extends to 30 base pairs. These in vitro data provide direct evidence for the Tn5 target sites in the nucleosome, resulting important information for interpretation of the Tn5-transposase-based genomics methods, which have been interpreted as linker or nucleosome-free DNA regions in genomes.
2019-09-18 | GSE130322 | 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 | 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