Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of trans-vaccenic acid(TVA) diet on 16S ribosomal RNA (rRNA) expression of mouse gut microbiome

ABSTRACT: Effect of trans-vaccenic acid(TVA) diet on 16S ribosomal RNA (rRNA) expression of mouse gut microbiome

PROVIDER: PRJNA835303 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19091470_1.fastq.gz	Fastqsanger.gz
	SRR19091470_2.fastq.gz	Fastqsanger.gz
	SRR19091471_1.fastq.gz	Fastqsanger.gz
	SRR19091471_2.fastq.gz	Fastqsanger.gz
	SRR19091472_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 28

Similar Datasets

Effect of trans-vaccenic acid(TVA) diet on 16S ribosomal RNA (rRNA) expression of mouse gut microbiome

Project description:To investigate the TVA diet's effect on mouse gut microbiome, we fed C57/BL6 mice with TVA diet or CON diet for 18 days We then collected feces of the mice and performed 16S ribosomal RNA (rRNA) sequencing.

2023-09-21 | GSE202266 | GEO

Effect of trans-vaccenic acid(TVA) treatment on gene expression of mouse CD8+ T cells

Project description:To investigate the TVA's effect on mouse CD8+ T cells in vitro, we treated activated mouse CD8+ T cells with DMSO or 20 µM TVA for 24 hours. We then performed gene expression profiling analysis using data obtained from RNA-seq.

2023-09-21 | GSE202276 | GEO

Effect of trans-vaccenic acid(TVA) treatment on gene expression of mouse CD8+ T cells

Project description:To investigate the TVA's effect on mouse CD8+ T cells in vitro, we treated activated mouse CD8+ T cells with 20 µM TVA for various timepoints (or untreated cell control) followed by kethoxal labeling of single stranded DNA (ssDNA) We then performed differential analysis of ssDNA levels following the KAS-pipe pipeline

2023-05-08 | GSE202730 | GEO

Effect of trans-vaccenic acid(TVA) treatment on gene expression of mouse CD8+ T cells

Project description:Effect of trans-vaccenic acid(TVA) treatment on gene expression of mouse CD8+ T cells

| PRJNA835323 | ENA

Effect of trans-vaccenic acid(TVA) treatment on gene expression of mouse CD8+ T cells

Project description:Effect of trans-vaccenic acid(TVA) treatment on gene expression of mouse CD8+ T cells

| PRJNA837177 | ENA

Effect of Creb1 KD on TVA dependent CD8+ T cell activation

Project description:To investigate the role of Creb1 in TVA dependent CD8+ T cell activation, we knocked down Creb1 of mouse CD8+ T cells with siRNAs then treated with DMSO or TVA We then performed gene expression profiling analysis using data obtained from RNA-seq.

2023-09-21 | GSE202274 | GEO

ASLV vector infected 293t-TVA cells

Project description:Human 293T cells engineered to express the TVA receptor (see Mitchell et al., PLoS) infected with an ASLV vector. RNA isolated 48 hours later. ***PLEASE NOTE*** Series entries GSE1408 & GSE1409 no longer exist. All data discussed in the author's PLoS publication (PubMed ID 15314653) is available under GSE1407 & GSE1410. ***PLEASE NOTE*** Keywords: repeat sample

2004-05-19 | GSE1410 | GEO

Pytheas E. coli 16S rRNA sample analysis

Project description:Mass spectrometry remains an important method for analysis of modified nucleosides ubiquitously present in cellular RNAs, in particular for ribosomal and transfer RNAs that play crucial roles in mRNA translation and decoding. Furthermore, modifications have effect on the lifetimes of nucleic acids in plasma and cells and are consequently incorporated into RNA therapeutics. To provide an analytical tool for sequence characterization of modified RNAs, we developed Pytheas, an open-source software package for automated analysis of tandem MS data for RNA. This dataset contains the analysis of 14N and 15N-labeled 16S RNA from E. coli, including all the known RNA modifications (excluding pseudouridines). The analysis has been performed using three different protocols and instruments: Agilent Q-TOF, Waters Synapt G2-S, and Thermo Scientific Orbitrap Fusion Lumos.

2022-05-04 | PXD030538 | Pride

Role of 16S rRNA Helix 44 in Ribosomal Resistance to Hygromycin B.

Project description:Hygromycin B is an aminoglycoside antibiotic active against prokaryotic and eukaryotic ribosomes. Ribosomal alterations in bacteria conferring resistance to hygromycin B have not been described, prompting us to use a single rRNA allelic derivative of the gram-positive bacterium Mycobacterium smegmatis for investigation of the molecular mechanisms involved in ribosomal resistance to hygromycin B in eubacteria. Resistance mutations were found to localize exclusively in 16S rRNA. The mutations observed, i.e., 16S rRNA U1406C, C1496U, and U1498C (E. coli numbering), are in close proximity to the hygromycin B binding site located in conserved helix 44 of 16S rRNA. The 16S rRNA positions involved in hygromycin B resistance are highly conserved in all three domains of life, explaining the lack of specificity and general toxicity of hygromycin B.

| S-EPMC153343 | biostudies-literature

Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria).

Project description:A highly divergent 16S rRNA gene was found in one of the five ribosomal operons present in a species complex currently circumscribed as Scytonema hyalinum (Nostocales, Cyanobacteria) using clone libraries. If 16S rRNA sequence macroheterogeneity among ribosomal operons due to insertions, deletions or truncation is excluded, the sequence heterogeneity observed in S. hyalinum was the highest observed in any prokaryotic species thus far (7.3-9.0%). The secondary structure of the 16S rRNA molecules encoded by the two divergent operons was nearly identical, indicating possible functionality. The 23S rRNA gene was examined for a few strains in this complex, and it was also found to be highly divergent from the gene in Type 2 operons (8.7%), and likewise had nearly identical secondary structure between the Type 1 and Type 2 operons. Furthermore, the 16S-23S ITS showed marked differences consistent between operons among numerous strains. Both operons have promoter sequences that satisfy consensus requirements for functional prokaryotic transcription initiation. Horizontal gene transfer from another unknown heterocytous cyanobacterium is considered the most likely explanation for the origin of this molecule, but does not explain the ultimate origin of this sequence, which is very divergent from all 16S rRNA sequences found thus far in cyanobacteria. The divergent sequence is highly conserved among numerous strains of S. hyalinum, suggesting adaptive advantage and selective constraint of the divergent sequence.

| S-EPMC5658200 | biostudies-literature

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