Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatially-resolved chromatin accessibility profiling of the developing mouse embryo

ABSTRACT: Spatially-resolved chromatin accessibility profiling of the developing mouse embryo

PROVIDER: PRJNA888033 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR21836873_1.fastq.gz	Fastqsanger.gz
	SRR21836873_2.fastq.gz	Fastqsanger.gz
	SRR21836874_1.fastq.gz	Fastqsanger.gz
	SRR21836874_2.fastq.gz	Fastqsanger.gz
	SRR21836875_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Spatially-resolved chromatin accessibility profiling of the developing mouse embryo

Project description:We profiled the epigenetic landscape of the developing mouse embryo across three ages (E12.5, E13.5, and E15.5) using fresh frozen tissue sections processed with 10X Genomics's OMNI ATAC, which allows to record regions of open chromatin while retaining spatial resolution.

2022-11-03 | GSE214986 | GEO

Developing mouse embryo

Project description:Developing mouse embryo

| PRJNA888039 | ENA

Spatially uniform establishment of chromatin accessibility in the early Drosophila embryo

Project description:Spatially uniform establishment of chromatin accessibility in the early Drosophila embryo

| PRJNA414230 | ENA

A spatially resolved multiomic single-cell atlas of soybean development

Project description:Cis-regulatory elements (CREs) precisely control the spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression and chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) binding motifs controlling cell-type specification and maintenance. We identified non-cell autonomous activity of NIN-LIKE PROTEIN 7 (NLP7), the Nodule Inception (NIN) gene regulatory network and de novo enriched TF motifs in the nodule infected cells. With comprehensive developmental trajectories for endosperm and embryo, we found that 13 sucrose transporters, sharing the DOF11 binding motif, were co-up-regulated in late peripheral endosperm and identified the key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.

2024-07-05 | GSE270392 | GEO

Spatially resolved epigenomic profiling of single cells in complex tissues

Project description:The recent development of spatial omics enables single-cell profiling of the transcriptome and the 3D organization of the genome in a spatially resolved manner. A spatial epigenomics method would expand the repertoire of spatial omics tools and accelerate our understanding of the spatial regulation of cellular processes and tissue functions. Here, we developed an imaging approach for spatially resolved profiling of epigenetic modifications in single cells

2022-12-16 | GSE191069 | GEO

High-sensitive spatially resolved T cell receptor sequencing with SPTCR-seq

Project description:Understanding the spatial distribution of T cells is pivotal to decrypting immune dysfunction in cancer. Current spatially resolved transcriptomics fall short in directly annotating T cell receptors (TCRs), limiting the comprehension of anti-cancer immunity. We introduce a novel technology, Spatially Resolved T Cell Receptor Sequencing (SPTCR-seq), integrating target enrichment and long-read sequencing for highly sensitive TCR sequencing. This approach yields an on-target rate of ~85%, and via a bespoke computational pipeline, it provides meticulous spatial mapping, error correction, and UMI refinement. SPTCR-seq outperforms PCR-based methods, offering superior reconstruction of the complete TCR architecture, inclusive of V, D, J regions and the vital complementarity-determining region 3 (CDR3). Applying SPTCR-seq, we reveal local T cell diversity, clonal expansion, and transcriptional evolution across spatially distinct niches in glioblastoma, identifying critical involvement of NK and B cells in spatial T cell adaptation. SPTCR-seq, by bridging spatially resolved omics and TCR sequencing, stands as a robust tool for exploring T cell dysfunction in cancers and beyond.

2023-07-25 | GSE238071 | GEO

Spatially mapped single-cell chromatin accessibility

Project description:Spatially mapped single-cell chromatin accessibility

| PRJNA692203 | ENA

Spatially uniform establishment of chromatin accessibility in the early Drosophila embryo

Project description:As the Drosophila embryo transitions from the use of maternal RNAs to zygotic transcription, domains of “open” chromatin, with relatively low nucleosome density and specific histone marks, are established at promoters and enhancers involved in patterned embryonic transcription. However it remains unclear whether open chromatin is a product of activity - transcription at promoters and patterning transcription factor binding at enhancers - or whether it is established by independent mechanisms. Recent work has implicated the ubiquitously expressed maternal factor Zelda in this process. To assess the relative contribution of activity in the establishment of open chromatin , we have probed chromatin accessibility across the anterior-posterior axis of early Drosophila melanogaster embryos by applying a transposon based assay for chromatin accessibility (ATAC-seq) to anterior and posterior halves of hand-dissected, cellular blastoderm embryos. We find that genome-wide chromatin accessibility is remarkably similar between the two halves. Promoters and enhancers that are active in exclusively one half of the embryo have open chromatin in the other half, demonstrating that chromatin accessibility is not a direct result of activity. However there is a small skew at enhancers that drive transcription exclusively in either the anterior or posterior half of the embryo, with greater accessibility in the region of activity. Taken together these data support a model in which regions of chromatin accessibility are defined and established by ubiquitous factors, and fine tuned subsequently by activity.

2017-10-30 | GSE104957 | GEO

Spatially resolved multiomics of human cardiac niches - Visium

Project description:Spatially resolved multiomics of human cardiac niches - Visium

| PRJEB62497 | ENA

Chromatin accessibility profiling of the developing mouse embryo at the single nulceus level

Project description:Chromatin accessibility profiling of the developing mouse embryo at the single nulceus level

| PRJNA888035 | ENA