Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Microbiome sequencing data -- NSF Dimensions 2020

PROVIDER: PRJNA1006419 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR25674100_1.fastq.gz	Fastqsanger.gz
	SRR25674100_2.fastq.gz	Fastqsanger.gz
	SRR25674200_1.fastq.gz	Fastqsanger.gz
	SRR25674200_2.fastq.gz	Fastqsanger.gz
	SRR25674300_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 1920

Similar Datasets

Nassar2022 - Microbiome sequencing NER model

Project description:Microbiome sequencing model is a Named Entity Recognition (NER) model that identifies and annotates microbiome nucleic acid sequencing method or platform in texts. This is the final model version used to annotate metagenomics publications in Europe PMC and enrich metagenomics studies in MGnify with sequencing metadata from literature. For more information, please refer to the following blogs: http://blog.europepmc.org/2020/11/europe-pmc-publications-metagenomics-annotations.html https://www.ebi.ac.uk/about/news/service-news/enriched-metadata-fields-mgnify-based-text-mining-associated-publications

2022-02-21 | MODEL2202170012 | BioModels

A Pilot Study to Explore the Role of Gut Flora in Colorectal Cancer

Project description:This study seeks to correlate microbiome sequencing data with information provided by patients and their medical records regarding colorectal cancer.

| 2320796 | ecrin-mdr-crc

The effect of very-high-molecular-mass hyaluronan (vHMM-HA) on IMR90 transcriptome

Project description:Naked mole-rat skin fibroblasts (NSF) produces vHMM-HA. Although NSF-HA has been shown to suppress NSF transformation, it is still unclear if exceptional polymer length of vHMM-HA is important for its functions. Here, we compared the effect of intact control NSF-HA (cNSF-HA) and partially fragmented NSF-HA (fNSF-HA) on the transcriptome of IMR90 cells. Related RNA-Seq datasets are deposited in ArrayExpress (E-MTAB-8943).

2019-01-01 | GSE116759 | GEO

The effect of very-high-molecular-mass hyaluronan (vHMM-HA) on CD44-overexpressing IMR90 cells

Project description:Naked mole-rat skin fibroblasts (NSF) produces vHMM-HA. Although NSF-HA has been shown to suppress NSF transformation, it is still unclear if exceptional polymer length of vHMM-HA is important for its functions. Here, we compared the effect of intact control NSF-HA (cNSF-HA) ) on the transcriptome of CD44-overexpressing IMR90 cells.

2020-04-25 | E-MTAB-8943 | biostudies-arrayexpress

Nitrogen signaling factor changes gene expression and binding of transcription factors [ChIP-seq]

Project description:High quality nitrogen sources such as NH4+ and glutamate inhibit the uptake of poor nitrogen sources including amino acids (leucine etc.), which is called “nitrogen catabolite repression (NCR)”. We found a cell-to-cell communication system in fission yeast that inactivates NCR and enables cells to take up leucine even on high NH4+ medium (referred to as adaptive growth). Furthermore, we identified novel oxylipins responsible for the adaptive growth, which are secreted from cells and are referred to as nitrogen signaling factors (NSF). RNA-seq analyses showed that mitochondrial respiratory-related genes are differentially expressed upon addition of synthetic NSF. These results suggest that the cell-to-cell communication via NSF reprograms the metabolic preference from glycolysis to mitochondrial respiration. Moreover, we also performed ChIP-seq of transcription factors (TFs) and found that bindings of several TFs on DNA are regulated by NSF.

2024-06-25 | GSE250092 | GEO

Methylation orofiling of human stem cell reprogramming by targeted bisulfite sequencing

Project description:We report a method for specific capture of an arbitrary subset of genomic targets for single molecule bisulfite sequencing, and for digital quantitation of DNA methylation at a single nucleotide resolution. We used targeted bisulfite sequencing to characterize the changes of DNA methylation during the de-differentiation of human fibroblasts into hybrid stem cells, and into induced pluripotent stem cells. We compared the methylation level of approximately 66,000 CpG sites within 2020 CpG islands on chromosome 12, chromosome 20, and 34 selected regions. A total of 288 differentially methylated regions were identified between fibroblasts and pluripotent cells. Methylation cluster analysis revealed distinct methylation patterns between fibroblasts and pluripotent cells. Furthermore iPS cells are globally more methylated than human embryonic stem cells, which could be due to the reprogramming process. This targeted bisulfite sequencing method is particularly useful for efficient and large-scale analysis of DNA methylation in organisms with large genomes. Experiment Overall Design: Comparison of DNA methylation on 2020 CpG islands and 34 other selected regions among eleven human ES, iPS and fibroblast lines.

2009-08-28 | E-GEOD-15007 | biostudies-arrayexpress

The effect of very-high-molecular-mass hyaluronan (vHMM-HA) on CD44 protein-protein interactions.

2020-03-24 | PXD013445 | Pride

Galdieria sulphuraria strain:074W

Project description:NSF funded genome sequencing project

| PRJNA13023 | ENA

Project description:Dimensions 4A

| PRJNA648993 | ENA

Amplicon based single molecule footprinting on ES cells and derivatives

Project description:Single Molecule Footprinting (SMF) data from Sonmezer et al., 2020. SMF data is obtained by treating isolated nuclei with methyltransferases, where binding of proteins on DNA, e.g. nucleosomes and TFs, leave behind unmethylated cytosines as footprints. Data in this experiment comprises SMF data obtained from ES cells and various derivatives of ES cells, such DNMT-null, REST-knockout ES cells, neural progenitors and ES cells treated with NRF1 sirNA.

2020-12-26 | E-MTAB-9033 | 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