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RIL-seq of Klebsiella pneumoniae SGH10 grown in LB or DMEM medium

ABSTRACT: RIL-seq of Klebsiella pneumoniae SGH10 grown in LB or DMEM medium

PROVIDER: PRJEB65980 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR12039976_1.fastq.gz	Fastqsanger.gz
	ERR12039976_2.fastq.gz	Fastqsanger.gz
	ERR12039977_1.fastq.gz	Fastqsanger.gz
	ERR12039977_2.fastq.gz	Fastqsanger.gz
	ERR12039978_1.fastq.gz	Fastqsanger.gz

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RIL-seq of Klebsiella pneumoniae SGH10 grown in LB or DMEM medium

Project description:RIL-seq experiment allows identification of pairs of interacting RNA molecules while bound to the Hfq protein. SGH10 bacteria were grown under DMEM (Dulbecco's Modified Eagle Medium) and LB (Lysogeny broth) conditions. RIL-seq was performed as previously described in Melamed et al. 2018 with adaptation of the computational analysis to the SGH10. It was applied to three biological replicates, for each growth condition. Libraries were sequenced by paired-end sequencing using Nextseq 500 Sequencer (Illumina). sequence fragments were mapped to SGH10 which contains a chromosome NZ_CP025080.1 and a plasmid NZ_CP025081.1. RIL-seq derived sequence fragments that mapped to the same locus or to two different loci were defined as single and chimeric fragments respectively. Chimeric fragments that appeared statistically significantly more than expected at random (S-chimeras) were considered as representing putative interacting RNAs.

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RNA-seq of Klebsiella pneumoniae SGH10 grown in LB or DMEM medium

Project description:RNA-seq of Klebsiella pneumoniae SGH10 grown in LB or DMEM medium

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Project description:Gene Expression profiles of E.coli grown in LB and Minimal medium (DM) at OD 600 =1 Keywords: ordered

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RNA-seq of Klebsiella pneumoniae SGH10 grown in LB or DMEM medium

Project description:SGH10 bacteria were grown under DMEM (Dulbecco's Modified Eagle Medium) and LB(Lysogeny broth). Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (SigmaAldrich) in a final concentration of 0.9 mg/ml, and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze at 37°C and in liquid nitrogen, respectively, and RNA was extracted using Tri-Reagent (Sigma-Aldrich). RNA-seq libraries were constructed by the RNAtag-seq method. RNA-seq libraries were sequenced by single end sequencing using Nextseq 500 Sequencer (Illumina). sequence fragments were mapped to SGH10 which contains a chromosome NZ_CP025080.1 and a plasmid NZ_CP025081.1. For each growth condition, three biological repeats were done.

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Project description:Gene Expression profiles of E.coli grown in LB and Minimal medium (DM) at OD 600 =1

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Project description:E. coli ΔarcZ hfq-Flag strain was transformed with a WT arcZ, mut arcZC81G or a mut arcZC81T,T82G,G83A plasmids. Single colonies of the transformants were grown overnight in LB at 37 °C with shaking (200 r.p.m.). Cultures were diluted 100-fold in fresh LB re-grown with shaking at 37 °C to an optical density of OD600 = 1.0 and induced with IPTG (1mM, 20 min), RIL-seq experiments were preformed as described in Melamed et al 2018, each repeated three times.

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