Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multiome in the same cell revealed the impact of osmotic stress on Arabidopsis root tip development at single-cell level

ABSTRACT: Multiome in the same cell revealed the impact of osmotic stress on Arabidopsis root tip development at single-cell level

PROVIDER: PRJNA986159 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Multiome in the same cell revealed the impact of osmotic stress on Arabidopsis root tip development at single-cell level [RNA]

Project description:Cell-specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single-cell mono-omics techniques are unable to fully capture the relationships and dynamics of molecular information within cells. While data integration algorithm facilitates the merging of single-cell RNA-seq and single-cell ATAC-seq data, ensuring the accuracy of the integration process remains a challenge, particularly when investigating cell-type-specific TRNs. In this study, we aimed to elucidate the TRNs of Arabidopsis under osmotic stress at the single-cell level by employing single-cell multi-omics technology to simultaneously examine gene expression and chromatin accessibility of 16,670 Arabidopsis root tip nuclei. We performed 12,968 peak-to-gene linkage at bona fide single-cell level, instead of previous computational integration at cell type level, which enabled us to obtain an unprecedented resolution to reconstruct transcriptional regulation. Pseudotime developmental trajectories revealed that osmotic stress led to shift the developmental status of Suberin synthetic endodermis (Suberin-endo) and trichoblast cells. We identified candidate stress-related cell-specific enhancers and cis-regulatory elements as well as potential target genes, and uncovered large cellular heterogeneity. We also found that cis-regulatory elements became accessible prior to gene expression and these cis-regulatory elements could form a positive feedback loop with epigenetic modification H3K4me3 in response to osmotic stress in columella cells.

2024-04-25 | GSE235495 | GEO

Multiome in the same cell revealed the impact of osmotic stress on Arabidopsis root tip development at single-cell level [ATAC]

2024-04-25 | GSE235494 | GEO

Multiome in the same cell revealed the impact of osmotic stress on Arabidopsis root tip development at single-cell level [Cut&Tag]

2024-04-25 | GSE235509 | GEO

Multiome in the same cell revealed the impact of osmotic stress on Arabidopsis root tip development at single-cell level

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-04-25 | GSE235510 | GEO

Multiome RNA+ATAC on human PBMCs (snATAC-seq data)

Project description:We generated Multiome RNA+ATAC data from the same cell from human PBMC. This served as a gold benchmark for a novel integration method for multi-omics data that we developed.

2021-12-02 | E-MTAB-11226 | biostudies-arrayexpress

Multiome RNA+ATAC on human PBMCs (snRNA-seq data)

Project description:We generated Multiome RNA+ATAC data from the same cell from human PBMC. This served as a gold benchmark for a novel integration method for multi-omics data that we developed.

2021-12-02 | E-MTAB-11225 | biostudies-arrayexpress

Transcriptome gene expression analysis of root tip, leaf tip, shoot tip, root (without root tip) and leaf (without leaf tip) from Ceratopteris richardii sporophytes

Project description:To study genes specially expressed in root tip, leaf tip, shoot tip, root (without root tip) and leaf (without leaf tip) of Ceratopteris richardii, we carried out an RNA-seq to analyze gene expression levels from these five tissues.

2019-10-22 | GSE139160 | GEO

single cell multiome for MSCs

Project description:we used single-cell multiome analysis to profile the transcriptome and epigenome of MSCs from four healthy donors.

2023-11-09 | GSE228669 | GEO

smRNA under high osmotic stress

Project description:To identifiy osmotic stress responsive smRNAs, we used a deep-sequencing technique to profile small RNA populations in leaf and root tissues of plants under high osmotic stress and control conditions. We treated 30day-old plants with high osmotic stress and sampled leaves and roots from the same plant with 3 biologial replicates. Then, 3 replicates were pooled and total RNA was extracted and prepared for smRNA deep sequencing. After normalization and annotation, we selected potential osmotic stress responsive smRNAs.

2012-09-19 | E-GEOD-36560 | biostudies-arrayexpress

Transcriptome gene expression analysis of root tip, leaf tip, shoot tip, root (without root tip) and leaf (without leaf tip) from Ceratopteris richardii sporophytes

Project description:Transcriptome gene expression analysis of root tip, leaf tip, shoot tip, root (without root tip) and leaf (without leaf tip) from Ceratopteris richardii sporophytes

| PRJNA578676 | ENA

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