Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: RNA-sequencing data from Pseudomonas putida KT2440 wild-type and Hfq-tagged strain form co-immunoprecipitation experiment      
keywords:
Transcriptome or Gene expression
ID:
PRJNA338876
description:
The RNA-chaperone Hfq is a global post-transcriptional regulator in Bacteria, important especially for the fine-tuning of the gene expression when the environmental conditions change. We looked into sRNAome during the growth of Pseudomonas putida KT2440 and compared it to a strain without Hfq protein. Numerous sRNAs were upregulated at a specific point during the growth and many were affected in the Hfq absence. Further we identified Hfq-binding RNA transcripts with co-immunoprecipitation and experimentally validated 17 sRNAs. Many novel Hfq-binding sRNAs were identified and are directly or indirectly regulated by Hfq. In addition 1870 mRNAs were found to bind to Hfq during the growth. Together, 202 antisense and 355 intergenic sRNAs have been detected in this study, several of them being 3’UTR- or 5’UTR-derived, and IS-related. Overall design: 12 samples were analyzed; two strains (wild type and Hfq-FLAG-tagged strain) were compared in 3 time points during the growth in LB medium in two replicates each
accesstypes:
download
landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA338876
authentication:
none
authorization:
none
name:
Pseudomonas putida
ncbiID:
ncbitax:303
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.