Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Soybean microbiome - temporal and spatial development

ABSTRACT: Soybean microbiome - temporal and spatial development

PROVIDER: PRJNA601979 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11314000_1.fastq.gz	Fastqsanger.gz
	SRR11314000_2.fastq.gz	Fastqsanger.gz
	SRR11314100_1.fastq.gz	Fastqsanger.gz
	SRR11314100_2.fastq.gz	Fastqsanger.gz
	SRR11314200_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 598

Similar Datasets

High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing

Project description:Inter-microbial and host–microbial interactions are thought to be critical for the functioning of the gut microbiome, but few substantive tools are available to measure these interactions. Here, we report a method for unbiased spatial sampling of microbiome-host interactions in the gut at high spatial resolution. This method combines enzymatic in situ polyadenylation of both bacterial and host transcripts with spatial RNA-sequencing. Application of this method revealed the biogeography of the mouse gut microbiome as function of location in the intestine, short-range intermicrobial interaction, local shaping of the microbiome by the host, and tumor-associated changes in the architecture of the host-microbiome interface. This method is compatible with broadly available commercial platforms for spatial RNA-sequencing, and can therefore be readily adopted to broadly study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.

2026-01-21 | GSE276866 | GEO

High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing (Stereoseq)

2026-01-21 | GSE308507 | GEO

High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing [Spatial transcriptomics]

Project description:Inter-microbial and host-microbial interactions are critical for the functioning of the gut microbiome, but few tools are available to measure these interactions in situ. Here, we report a method for broad spatial sampling of microbiome-host interactions in the gut at high resolution (1 µm). This method combines enzymatic in situ polyadenylation of both bacterial and host RNA with spatial RNA-sequencing to increase bacterial RNA recovery and enable transcriptomic analysis of low-abundance and spatially restricted microbial taxa. We benchmark the method against existing spatial transcriptomic workflows, demonstrating improved sensitivity and resolution. Application of this method in a mouse model of intestinal neoplasia revealed the biogeography of the mouse gut microbiome as function of location in the intestine, frequent strong inter-microbial interactions at short length scales, and tumor-associated changes in the architecture of the host-microbiome interface. This method is compatible with widely available commercial platforms for spatial RNA-sequencing and can therefore be readily adopted to study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.

2026-01-21 | GSE316608 | GEO

High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing [bulk RNA-Seq]

2026-01-21 | GSE316869 | GEO

High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing [Ileum, with in situ Polyadenylation]

2026-01-21 | GSE277197 | GEO

High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing [Ileum, without in situ Polyadenylation]

2026-01-21 | GSE277196 | GEO

Temporal and Spatial Transcriptomic Dynamics across Brain Development in Xenopus laevis tadpoles

Project description:Temporal and Spatial Transcriptomic Dynamics across Brain Development in Xenopus laevis tadpoles

| PRJNA759592 | ENA

Global Transcriptome Profiles in the Nodes of Rice During Spatial and Temporal Development

Project description:The following study was conducted to better understand the genetics of the spatial and temporal development of rice, especially as this relates to the development of lignocellulosic tissues. To do so, an oligonucleotide array was designed and created by the Plant Sciences Institute at Iowa State University. A total of 43,776 spots were printed on two separate platforms, the first contained 23,040 spots while the second contained 20,736. RNA was collected from nodes of rice seedlings at several different time points, as nodes are highly lignified tissues. Comparisons were performed to identify those genes exhibiting differential regulation across time at an anatomical position as well as across anatomical distance. For example, node 1 was compared across days 46, 53, 60, and 67 and at day 67 node 1 was compared to nodes 2, 3, and 4. Similar comparisons were performed for nodes 2, 3, and 4 where applicable. Keywords: Time course and anatomical development in rice For each comparison, 6 replicates and multiple power settings were considered. Dye-swaps were performed between replicates. A diagram of the comparisons made in this experiment may be found in ISU_RiceArray_LoopDesign.pdf (linked below as a Supplementary file).

2008-06-26 | E-GEOD-11896 | biostudies-arrayexpress

microbiome analysis of Soybean

Project description:microbiome analysis of root and nodule microbiome of soybean

| PRJEB44029 | ENA

Identification of Soybean AGL62-like binding sites in soybean seeds during seed development

Project description:To dissect the gene regulatory networks operating during soybean seed development, we identified the binding sites genome-wide for transcription factor in soybean seeds during seed development using ChIP-seq

2019-08-02 | GSE135265 | GEO

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