Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature

ABSTRACT: RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature

PROVIDER: PRJNA470697 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7140740.fastq.gz	Fastqsanger.gz
	SRR7140738.fastq.gz	Fastqsanger.gz
	SRR7140739.fastq.gz	Fastqsanger.gz

Items per page:

1 - 3 of 3

Similar Datasets

RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature

Project description:To generate a bona fide model to study post-stress baterial programmed cell death (PCD), we used a temperature-sensitive E. coli mutant (dnaB-Ts) since temperature stress can be rapidly reversed while other stress, such as antibotic treatment, is difficult to be rapidly and completely stopped and removed for post-stress PCD analysis. When cells were shifted from permissive (30 °C) to non-permissive temperature (42 °C), the dnaB-Ts ΔahpC double mutant maintained full surival while survival of the dnaB-Ts single mutant dropped 3 orders of magnitude; similarly, the double mutant showed much higher survival during treatments with quinolones and β-lactams at permissive temperature. The purpose of the RNA-seq analyses is to uncover molecular mechanisms underlying the increased survival of the dnaB-Ts ΔahpC double mutant by comparing its transcriptional profiles with that of the dnaB-Ts single mutant at both permissive and non-permissive temperature. The results showed that multiple antioxidative systems and stress response pathways were highly upregulated due to a deficiency of ahpC when combined with a dnaB-Ts mutation. The high expression of these genes are consistent with the lower levels of toxic reactive oxygen species (ROS) in the dnaB-Ts ΔahpC mutant than in the dnaB-Ts single mutant. Thus, the RNA-seq data supported that ROS are an important lethal factor in bacterial suicide pathways when bacterial cells are exposed to harsh stress.

2018-05-12 | GSE114262 | GEO

S. cerevisiae TAF5 and taf5 temperature conditional mutants grown at permissive and non-permissive temperature

2010-03-06 | GSE20444 | GEO

Profiling of p53-responsive genes in human breast cancer cells harboring endogenous ts-p53 E285K

2012-12-31 | GSE35006 | GEO

Profiling of p53-responsive genes in human breast cancer cells harboring endogenous ts-p53 E285K

Project description:The ts-p53 E285K protein is a rare p53 mutant with temperature-sensitive (ts) loss of function characteristics. In cancer cells, which express ts-p53 E285K intrinsically, endogenous wild type p53 activity is reconstituted by appropriate cultivation temperature (permissive condition). At non-appropriate cultivation temperature (restrictive condition) this p53 mutant is inactive. The present study took advantage of this mechanism and employed IPH-926 lobular breast cancer cells and BT-474 ductal breast cancer cells, which both harbor endogenous ts-p53 E285K, for the transcriptional profiling of p53-responsive genes. This new approach eliminated the need for genetic modification or cytotoxic stimulation to achive a p53 response in the cells being investigated . Three subseqent passages of IPH-926 lobular breast cancer cells (harboring ts-p53 E285K) were seeded into two parallel culture dishes each and were allowed to adopt to restrictive and permissive condition for 24 h before analysis on Affymetrix U133 Plus 2.0 microarrays. Subsequently, this experiment was repeated with BT-474 ductal breast cancer cells (also harboring ts-p53 E285K). To gate out non-specific temperature effects, the same experiment was also performed with MCF-7 breast cancer cells (harboring wt p53). Probe sets differentially expressed at restrictive versus permissive condition in MCF-7 were considered as non-specifically regulated. These probe sets were excluded from the final statistical analysis of IPH-926 and BT-474 expression data. response to restored p53 activity

2012-12-31 | E-GEOD-35006 | biostudies-arrayexpress

S. cerevisiae TAF5 and taf5 temperature conditional mutants grown at permissive and non-permissive temperature

Project description:Expression analysis of Saccharomyces cerevisiae TAF5 and taf5 temperature conditional mutants grown at permissive and non-permissive temperature. Investigation of whole genome gene expression level changes in Saccharomyces cerevisae taf5-17, taf5-45, taf5-408 and taf5-10.4 mutants, compared to the wild-type strain. The mutations engineered into the strains confer temperature conditional growth. The mutants analyzed in this study are further described in Layer et. al., 2010. Direct Transactivator-Transcription Factor IID (TFIID) Contacts Drive Yeast Ribosomal Protein Gene Transcription. Journal of Biological Chemistry. A twenty chip study using total RNA recovered from four separate wild-type cultures of Saccharomyces cerevisiae and four separate cultures for each of four taf5 temperature conditional mutants (16 mutant cultures). Each chip measures the expression level of 5,777 genes from Saccharomyces S288C with eight 60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

2010-05-06 | E-GEOD-20444 | biostudies-arrayexpress

Transcription profiling of thermosensitive exosome mutants from permissive temperature and various time exposure to restrictive temperature

Project description:Transcriptome analyses of thermosensitive exosome mutants from permissive temperature to various time exposure to restrictive temperature.

2006-02-28 | E-MEXP-537 | biostudies-arrayexpress

TS-seq

Project description:TS-seq

| PRJNA847608 | ENA

Transcription profiling of chinsese cabbage 7-day old seedlings exposed at permissive high temperature over a time series

Project description:In order to assess a set of gene regulations to get the acquired thermotolerance in a comprehensive scale, we conducted a transcriptome analysis. Chinese cabbage microarray (A-MEXP-115)was used to examine the gene expression of 7-day old seedlings exposed at permissive high temperature over the time course (0, 0.25, 1, 3 and 12 hr).

2006-01-12 | E-MEXP-528 | biostudies-arrayexpress

Temperature induced differentiation of piA immortalised cell line PrE2.8

Project description:The cell line PrE2.8 was cultured at a permissive growth temperature of 33oC and then half transferred to a non-permissive temperature of 39.5oC for 4days. The two sets of cells were harvested and co-hybridised to identify genes with altered expression resulting from unduced differentiation. Keywords: Induction of cellular differentiation

2006-07-28 | GSE5169 | GEO

Gene expression profiling of a temperature-sensitive strain of Neospora caninum

Project description:The gene expression profiles of a temperature-sensitive strain, ts-8, was compared agains its wild type counterpart, NC-1. Keywords: mutant comparision, two class unpaired design

2006-02-20 | GSE4042 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data