NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE108616 Query DataSets for GSE108616
Status Public on Feb 20, 2018
Title Are small RNAs involved in the regulation of nitrogen metabolism in haloarchaea?
Organism Haloferax mediterranei
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Small RNAs have been studied in detail in Bacteria and Eukarya domain, but in the case of Archaea domain the knowledge is scarce and the physiological function of the majority is still uncertain. To extend the knowledge of sRNAs in Archaea domain and its possible role in the regulation of the nitrogen assimilation metabolism in haloarchaea, Haloferax mediterranei has been used as a model microorganism. Bioinformatic approach has allowed to predict 295 putative sRNAs genes in the genome of H. mediterranei, 88 of which have been verified by means of RNA-seq. The secondary structure of putative sRNAs and its possible targets have been identified. Curiously, some of them present as possible targets genes related to the nitrogen assimilation, as glutamate dehydrogenase or regulatory nitrogen protein PII. Analysis of RNA-seq data has also revealed differences in the expression pattern of 16 sRNAs according to the nitrogen source. Consequently, RNomic and the bioinformatic approaches used in this work have allowed the identification of new sRNAs in Hfx. mediterranei, some of which show different expression pattern depending on the nitrogen source. It suggests that these sRNAs could be involved in the regulation of nitrogen assimilation, being able to constitute important gene regulatory network.
 
Overall design microRNAs were isolated from Hfx. Mediterranei cultures grown in the presence of two different nitrogen sources, nitrate and ammonium, to mid-exponential phase.
 
Contributor(s) Payá G, Bautista V, Camacho M, Castejón-Fernández N, Alcaraz LA, Bonete MJ, Esclapez JM
Citation(s) 29439418
Submission date Dec 28, 2017
Last update date Feb 20, 2018
Contact name Julia Esclapez
E-mail(s) julia.esclapez@ua.es
Phone 0034 96 590 3400
Organization name University of Alicante
Department Biochemistry
Lab María José Bonete
Street address Crta San Vicente del Raspeig s/n
City San Vicente del Raspeig
State/province Alicante
ZIP/Postal code 03690
Country Spain
 
Platforms (1)
GPL20667 Illumina HiSeq 2500 (Haloferax mediterranei)
Samples (15)
GSM2907033 Ammonium replicate 6.1
GSM2907034 Ammonium replicate 6.2
GSM2907035 Ammonium replicate 6.3
Relations
BioProject PRJNA427822
SRA SRP127683

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE108616_sRNA.gff3.gz 1021 b (ftp)(http) GFF3
GSE108616_sRNA_normCounts.txt.gz 6.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap