Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Experimental identification of small non-coding RNAs in the model marine bacterium Ruegeria pomeroyi DSS-3

ABSTRACT: Experimental identification of small non-coding RNAs in the model marine bacterium Ruegeria pomeroyi DSS-3

PROVIDER: PRJEB12772 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR1276340.fastq.gz	Fastqsanger.gz
	ERR1276341.fastq.gz	Fastqsanger.gz
	ERR1276342.fastq.gz	Fastqsanger.gz
	ERR1276343.fastq.gz	Fastqsanger.gz
	ERR1276344.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Ruegeria pomeroyi DSS-3

Project description:Ruegeria pomeroyi DSS-3 Mutation Accumulation

| PRJNA320454 | ENA

Experimental identification of small non-coding RNAs in the model marine bacterium Ruegeria pomeroyi DSS-3

Project description:In oligotrophic ocean waters where bacteria are often subjected to chronic nutrient limitation, community transcriptome sequencing has pointed to the presence of highly abundant small RNAs (sRNAs). The role of sRNAs in regulating response to nutrient stress was investigated in a model heterotrophic marine bacterium Ruegeria pomeroyi grown in continuous culture under carbon and nitrogen limitation. RNAseq analysis identified 98 sRNAs, of which 69 were cis-encoded and located antisense to their target genes, and 30 were trans-encoded and linked to predicted target genes through complementarity analysis. The most prevalent functional roles of target genes were transport, cell-cell interactions, signal transduction, and transcriptional regulation. Thirty-two percent of the sRNAs had been identified in a previous study of R. pomeroyi growth on organic sulfur compounds, and may be constitutively expressed, while 69% were not identified in previous studies. Eighty-six percent and were transcribed equally under both carbon and nutrient limitation, and may be involved in a general stress response; 14% were differentially regulated under carbon versus nitrogen stress, and may respond to specific nutrient limitations. A network analysis of the predicted target genes of the R. pomeroyi sRNAs indicated that they average fewer connections than typical protein-encoding genes, and appear to be more important in peripheral or niche-defining functions encoded in the pan genome rather than central metabolism encoded in the core genome.

2016-02-27 | E-MTAB-4468 | biostudies-arrayexpress

Ruegeria pomeroyi DSS-3

Project description:Ruegeria pomeroyi DSS-3 Mutation Accumulation Project

| PRJNA320442 | ENA

Ruegeria pomeroyi DSS-3 isolate:ATCC 700808

Project description:Ruegeria pomeroyi DSS-3 Transposon library T8repA_Jun other

| PRJNA444445 | ENA

Ruegeria pomeroyi DSS-3 isolate:ATCC 700808

Project description:Ruegeria pomeroyi DSS-3 Transposon library T8repC_Jun other

| PRJNA444447 | ENA

Ruegeria pomeroyi DSS-3 isolate:ATCC 700808

Project description:Ruegeria pomeroyi DSS-3 Transposon Mutagenesis - T4_LowN_C other

| PRJNA501650 | ENA

Ruegeria pomeroyi DSS-3 isolate:ATCC 700808

Project description:Ruegeria pomeroyi DSS-3 Transposon Mutagenesis - T4_LowP_B other

| PRJNA501652 | ENA

Ruegeria pomeroyi DSS-3 isolate:ATCC 700808

Project description:Ruegeria pomeroyi DSS-3 Transposon Mutagenesis - T6_LowP_B other

| PRJNA501658 | ENA

Ruegeria pomeroyi DSS-3 isolate:ATCC 700808

Project description:Ruegeria pomeroyi DSS-3 Transposon Mutagenesis - T8_LowN_A other

| PRJNA501660 | ENA

Ruegeria pomeroyi DSS-3 isolate:ATCC 700808

Project description:Ruegeria pomeroyi DSS-3 Transposon Mutagenesis - T8_LowN_B other

| PRJNA501661 | 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