Datasets

Title	Bacteria differently regulate mRNA abundance to specifically respond to various stresses
Organism
Number of Samples	5
Release Date	2015/05/11 00:00
Sequencing Types
Protocol Details

Title
Authors	Bartholomäus A, Fedyunin I, Feist P, Sin C, Zhang G, Valleriani A, Ignatova Z
Journal	Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
Publication Date	2016 Mar 13
Abstract	Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities to maximize cell survival. We present a global analysis of the response of Escherichia coli to acute heat and osmotic stress. We combine deep sequencing of total mRNA and ribosome-protected fragments to provide a genome-wide map of the stress response at transcriptional and translational levels. For each type of stress, we observe a unique subset of genes that shape the stress-specific response. Upon temperature upshift, mRNAs with reduced folding stability up- and downstream of the start codon, and thus with more accessible initiation regions, are translationally favoured. Conversely, osmotic upshift causes a global reduction of highly translated transcripts with high copy numbers, allowing reallocation of translation resources to not degraded and newly synthesized mRNAs. © 2016 The Author(s).
PMC
PMID	26857681
DOI

Run Accession	Study Accession	Scientific Name	Cell Line	Library Type	Treatment	GWIPS-viz	Trips-Viz	Reads	BAM	BigWig (F)	BigWig (R)
SRR2016457	PRJNA283800	Escherichia coli	0.0	Ribo-Seq	0.0
SRR2016459	PRJNA283800	Escherichia coli	0.0	Ribo-Seq	0.0
SRR2016461	PRJNA283800	Escherichia coli	0.0	Ribo-Seq	0.0
SRR2016463	PRJNA283800	Escherichia coli	0.0	Ribo-Seq	0.0
SRR2016465	PRJNA283800	Escherichia coli	0.0	Ribo-Seq	0.0
Run Accession	Study Accession	Scientific Name	Cell Line	Library Type	Treatment	GWIPS-viz	Trips-Viz	Reads	BAM	BigWig (F)	BigWig (R)

Bartholomäus et al. 2015 (PRJNA283800)