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Series GSE85581 Query DataSets for GSE85581
Status Public on Jan 01, 2017
Title RNA-sequencing data from Pseudomonas putida KT2440 wild-type and Hfq-tagged strain form co-immunoprecipitation experiment
Organism Pseudomonas putida
Experiment type Expression profiling by high throughput sequencing
Summary 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
Contributor(s) Bojanovič K, Long KS
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Submission date Aug 14, 2016
Last update date May 15, 2019
Contact name Klara Bojanovic
Phone 004524653766
Organization name Technical University of Denmark
Department Novo Nordisk Foundation Center for Biosustainability
Street address Building 220, Kemitorvet
City Kgs. Lyngby
ZIP/Postal code 2800
Country Denmark
Platforms (1)
GPL22319 Illumina NextSeq 500 (Pseudomonas putida)
Samples (12)
GSM2278534 Wt1_Ex
GSM2278535 Wt2_Ex
GSM2278536 Wt1_Tr
BioProject PRJNA338876
SRA SRP082120

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Supplementary file Size Download File type/resource
GSE85581_KBojanovic_Processed_data_KB4.xlsx 11.2 Mb (ftp)(http) XLSX
GSE85581_KBojanovic_Processed_data_KB4_coIP.ptt.txt.gz 148.2 Kb (ftp)(http) TXT
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Processed data are available on Series record

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