Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: A spatially resolved multiomic single-cell atlas of soybean development

PROVIDER: PRJNA1124403 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR29429300_1.fastq.gz	Fastqsanger.gz
	SRR29429300_2.fastq.gz	Fastqsanger.gz
	SRR29429301_1.fastq.gz	Fastqsanger.gz
	SRR29429301_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 117

Similar Datasets

Project description:Time-resolved single-cell Multiomic zebrafish atlas

| PRJNA1164307 | ENA

A spatially resolved single cell atlas of human gastrulation

Project description:A spatially resolved single cell atlas of human gastrulation

| PRJEB40781 | ENA

A single-cell and spatially resolved atlas of human breast cancers

Project description:A single-cell and spatially resolved atlas of human breast cancers

| PRJNA734812 | ENA

Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics

Project description:Non-hematopoietic cells contribute essentially to hematopoiesis. However, heterogeneity and spatial organization of these cells in human bone marrow remain largely uncharacterized. We used single-cell RNA sequencing (scRNA-Seq) to profile 29,325 non-hematopoietic cells and discovered nine transcriptionally distinct subtypes. We simultaneously profiled 53,417 hematopoietic cells and predicted their interactions with non-hematopoietic subsets. We employed Co-Detection by Indexing (CODEX) to spatially profile over one million single cells with a novel 53-antibody panel. We integrated scRNA-Seq and CODEX data to link cellular signaling and spatial proximity. Spatial analysis also revealed a hyperoxygenated arterio-endosteal niche for early myelopoiesis, and an adipocytic, but not endosteal or perivascular, localization for early hematopoietic stem and progenitor cells. We used our CODEX atlas to automatically annotate cell types in new bone marrow images and uncovered MSC expansion and leukemic blast/MSC-enriched spatial neighborhoods in AML patient samples. This comprehensive, spatially-resolved multiomic atlas of human bone marrow serve as a reference for future investigation of cellular interactions that drive hematopoiesis.

2024-04-24 | GSE253355 | GEO

A spatially resolved single cell genomic atlas of the adult human breast

Project description:A spatially resolved single cell genomic atlas of the adult human breast

| PRJNA801681 | 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

A spatially resolved single cell genomic atlas of the adult human breast [snRNA_nuclei]

Project description:A spatially resolved single cell genomic atlas of the adult human breast [snRNA_nuclei]

| PRJNA983286 | ENA

A spatially resolved single cell genomic atlas of the adult human breast [visium]

Project description:A spatially resolved single cell genomic atlas of the adult human breast [visium]

| PRJNA983280 | ENA

A spatially resolved single cell genomic atlas of the adult human breast [scRNA_cells]

Project description:A spatially resolved single cell genomic atlas of the adult human breast [scRNA_cells]

| PRJNA985695 | ENA

Genome-wide RNA tomography in the zebrafish embryo

Project description:Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome-wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes, they are unable to yield spatially resolved information in embryos or tissues. Microscopy-based approaches, using for example in situ hybridization, can provide spatial information about gene expression, but are limited to analyzing one or a few genes at a time. Here, we present a method where we combine traditional histological techniques with low-input RNA sequencing and mathematical image reconstruction to generate a high-resolution genome-wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially-resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly, our method enables searching for genes that are expressed in specific spatial patterns without manual image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. To generate spatially-resolved RNA-seq data for zebrafish embryos (shield stage, 10 somites, 15 somites, 18 somites) and mouse forelimbs (E10.5), we cryosectioned samples, extracted RNA from the individual sections, and amplified and barcoded mRNA using the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012) with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired-end to improve 3' annotations.

2014-10-23 | E-GEOD-59873 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data