Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A soil-grown wheat root atlas with validated cross-species cluster annotations allows to delineate conserved tissue specific marker genes [Spatial Transcriptomics]

ABSTRACT: A soil-grown wheat root atlas with validated cross-species cluster annotations allows to delineate conserved tissue specific marker genes [Spatial Transcriptomics]

PROVIDER: PRJNA1132997 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR29761155_1.fastq.gz	Fastqsanger.gz
	SRR29761155_2.fastq.gz	Fastqsanger.gz
	SRR29761156_1.fastq.gz	Fastqsanger.gz
	SRR29761156_2.fastq.gz	Fastqsanger.gz
	SRR29761157_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

A soil-grown wheat root atlas with validated cross-species cluster annotations allows to delineate conserved tissue specific marker genes

Project description:A soil-grown wheat root atlas with validated cross-species cluster annotations allows to delineate conserved tissue specific marker genes

| PRJNA1126233 | ENA

A soil-grown wheat root atlas with validated cross-species cluster annotations allows to delineate conserved tissue specific marker genes

Project description:Despite the broad use of single-cell and single-nucleus RNA sequencing in plant research, accurate cluster annotation in less studied plant species remains a major challenge due to the lack of validated marker genes. Here, using soil-grown wheat roots as a model, we generated a single-cell RNA-sequencing (scRNA-seq) atlas and annotated cluster identities in an unbiased way by transferring existing annotations from publicly available datasets in wheat, rice, maize and Arabidopsis. These cross-species orthology-based predictions were next validated using untargeted spatial transcriptomics. This information refined existing cluster annotations for different datasets across key plant model species. We then used the validated clusters to generate cell type-specific gene regulatory networks for root tissues of wheat and two other monocot crop species. By integrating all available data, including homeolog expression in wheat, we predicted reliable tissue-specific markers which are conserved across different species. In summary, we provided an annotated and validated single cell transcriptomic resource for soil-grown wheat root apical meristems and revealed conserved cell type-specific regulators and markers across species. These data expand upon previous root single cell atlas resources in crops, and will facilitate cell type annotation in non-model plant species in the future.

2025-01-06 | GSE270342 | GEO

A soil-grown wheat root atlas with validated cross-species cluster annotations allows to delineate conserved tissue specific marker genes [Spatial Transcriptomics]

2025-01-06 | GSE271725 | GEO

Striga hermonthica kibos ecotype microRNA annotations

Project description:Striga hermonthica kibos ecotype microRNA annotations

| PRJNA1188022 | ENA

Structural variants annotations

Project description:This resource contains the SV annotations using the AnnotSV tool. The description of annotations can be found in AnnotSV web page https://lbgi.fr/AnnotSV/ or GCAT-BSC web page: http://cg.bsc.es/GCAT_BSC_iberianpanel

| EGAD00010002152 | EGA

Metagenome-validated Parallel Amplicon Sequencing and Text Mining-based Annotations for Simultaneous Profiling of Bacteria and Fungi: Vaginal Microbiome and Mycobiota in Healthy Women

Project description:Metagenome-validated Parallel Amplicon Sequencing and Text Mining-based Annotations for Simultaneous Profiling of Bacteria and Fungi: Vaginal Microbiome and Mycobiota in Healthy Women

| PRJEB43447 | ENA

Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation

Project description:Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation

| PRJNA587064 | ENA

Refining mouse annotations via targeted RNA sequencing

2016-04-04 | GSE72311 | GEO

A validated regulatory network for Th17 cell specification

Project description:Th17 cells have critical roles in mucosal defense and are major contributors to inflammatory disease. Their differentiation requires the nuclear hormone receptor RORγt working with multiple other essential transcription factors (TFs). We have used an iterative systems approach, combining genome-wide TF occupancy, expression profiling of TF mutants, and expression time series to delineate the Th17 global transcriptional regulatory network. We find that cooperatively-bound BATF and IRF4 contribute to initial chromatin accessibility, and with STAT3 initiate a transcriptional program that is then globally tuned by the lineage-specifying TF RORγt, which plays a focal deterministic role at key loci. Integration of multiple datasets allowed inference of an accurate predictive model that we computationally and experimentally validated, identifying multiple new Th17 regulators, including Fosl2, a key determinant of cellular plasticity. This interconnected network can be used to investigate new therapeutic approaches to manipulate Th17 functions in the setting of inflammatory disease. 143 RNA-seq, 83 ChIP-seq, 65 ChIP-seq controls, and 16 FAIRE-seq

2012-09-20 | E-GEOD-40918 | biostudies-arrayexpress

Refining mouse annotations via targeted RNA sequencing

Project description:In this work we aim to improve the understanding of the mouse transcriptome complexity, investigate the expressed fraction of the genome and ameliorate the available mouse annotations. We utilized CatureSeq, a recently described strategy meant to enhance the sequencing coverage of low abundant genes. In our experimental design we generated oligonucleotide probes to select annotated and putative long-noncoding RNA and splice junctions. This allowed us to improve dramatically the sequencing throughput of the targeted regions. As a consequence our approach permitted the simultaneous identification of thousands of exons and the expansion of the already known ones The mouse gene assembly is anlaysed by targeted RNA sequencing of lncRNA and splice junctions. 8 mouse tissues and 16 samples are considered in the analysis. Each sample was added with external RNA controls. The controls are polyadenylated transcripts of known concentration designed to be added to an RNA analysis experiment after sample isolation.

2016-04-04 | E-GEOD-72311 | 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