Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Role of YbeY in Yersinia enterocolitica O:3

ABSTRACT: In order to detect genes that are directly or indirectly affected by the inactivation of the ybeY gene the transcriptomes of the WT and ybeY bacteria grown at 22°C and 37°C were determined. The two temperatures were chosen since temperature is an important cue regulating the virulence genes. When comparing the WT and ybeY mutant strain transcriptomes of bacteria grown at 22°C we found changes in the expression of 350 genes in the ybeY bacteria, out of which 121 (34.6%) were up-regulated and 229 (65.4%) down-regulated. At 37°C 334 genes in the ybeY bacteria showed changes, out of which 48 (14.4%) were up-regulated and 286 (85.6%) down-regulated. Expression of 92 genes was changed at both temperatures, of these 92 genes, 12 were up- and 80 down-regulated.

ORGANISM(S): Yersinia enterocolitica subsp. palearctica Y11

PROVIDER: GSE62601 | GEO | 2014/10/23

SECONDARY ACCESSION(S): PRJNA264525

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Role of YbeY in Yersinia enterocolitica O:3

Project description:In order to detect genes that are directly or indirectly affected by the inactivation of the ybeY gene the transcriptomes of the WT and ybeY bacteria grown at 22Â°C and 37Â°C were determined. The two temperatures were chosen since temperature is an important cue regulating the virulence genes. When comparing the WT and ybeY mutant strain transcriptomes of bacteria grown at 22Â°C we found changes in the expression of 350 genes in the ybeY bacteria, out of which 121 (34.6%) were up-regulated and 229 (65.4%) down-regulated. At 37Â°C 334 genes in the ybeY bacteria showed changes, out of which 48 (14.4%) were up-regulated and 286 (85.6%) down-regulated. Expression of 92 genes was changed at both temperatures, of these 92 genes, 12 were up- and 80 down-regulated. Bacterial RNA profiles of wild type and ybeY- strains were generated using deep sequencing, in duplicates, under two growth temperatures (22Â°C and 37Â°C).

2014-10-23 | E-GEOD-62601 | biostudies-arrayexpress

Role of RfaH in Yersinia enterocolitica O:3

Project description:To assess the effects of rfaH mutation on gene expression, RNA sequencing was carried out using the RNA extracted from rfaH mutant and wild type bacteria cultivated at both 22?C and 37?C. Additionally, to differentiate between genes affected directly by the rfaH mutation and those affected by the O-antigen negative phenotype, the Y. enterocolitica O:3 strain YeO3-R1 missing the O-antigen was included in the RNA-sequencing study. At RT-grown bacteria altogether 77 (45 up- and 32 down-regulated) differentially expressed genes were identified. At 37ºC, on the other hand, 44 genes were differentially expressed; 14 genes up- and 30 genes down-regulated. The RNA-sequencing data of YeO3-R1 was available only for bacteria grown at 22?C and the comparison revealed that 22 of the 102 genes were similarly differentially expressed both in rfaH and YeO3-R1 mutants. To detect genes regulated directly or indirectly by Hfq, deep RNA-seq was performed with RNA isolated from Y. enterocolitica wild-type strain 6471/76 and the YeO3-hfq::Km strain. Total RNA was isolated from two biological replicas of bacteria grown in LB to logarithmic phase (OD600 = 0.6) at two different temperatures, RT and 37°C. knocking out of Hfq affected the transcription of 346 genes at RT and 541 genes at 37°C, i.e., ca. 8 and 12.5 % of the Y. enterocolitica genes, respectively. At RT, of the 346 genes 216 genes were down- and 132 up-regulated, and at 37°C, of the 541 genes, 96 were down- and 445 up-regulated. A total of 95 genes were differentially expressed both at RT and 37°C; 27 showed down- and 59 up-regulated. For 9 genes opposite changes took place depending on the growth temperature. Bacterial RNA profiles of wild type, rfaH- and hfq- strains were generated using deep sequencing, in duplicates, under two growth temperatures (22°C and 37°C). The RNA-sequencing data of YeO3-R1 was generated only from bacteria grown at 22?C.

2015-03-04 | E-GEOD-66516 | biostudies-arrayexpress

Role of RfaH in Yersinia enterocolitica O:3

Project description:To assess the effects of rfaH mutation on gene expression, RNA sequencing was carried out using the RNA extracted from rfaH mutant and wild type bacteria cultivated at both 22˚C and 37˚C. Additionally, to differentiate between genes affected directly by the rfaH mutation and those affected by the O-antigen negative phenotype, the Y. enterocolitica O:3 strain YeO3-R1 missing the O-antigen was included in the RNA-sequencing study. At RT-grown bacteria altogether 77 (45 up- and 32 down-regulated) differentially expressed genes were identified. At 37ºC, on the other hand, 44 genes were differentially expressed; 14 genes up- and 30 genes down-regulated. The RNA-sequencing data of YeO3-R1 was available only for bacteria grown at 22˚C and the comparison revealed that 22 of the 102 genes were similarly differentially expressed both in rfaH and YeO3-R1 mutants. To detect genes regulated directly or indirectly by Hfq, deep RNA-seq was performed with RNA isolated from Y. enterocolitica wild-type strain 6471/76 and the YeO3-hfq::Km strain. Total RNA was isolated from two biological replicas of bacteria grown in LB to logarithmic phase (OD600 = 0.6) at two different temperatures, RT and 37°C. knocking out of Hfq affected the transcription of 346 genes at RT and 541 genes at 37°C, i.e., ca. 8 and 12.5 % of the Y. enterocolitica genes, respectively. At RT, of the 346 genes 216 genes were down- and 132 up-regulated, and at 37°C, of the 541 genes, 96 were down- and 445 up-regulated. A total of 95 genes were differentially expressed both at RT and 37°C; 27 showed down- and 59 up-regulated. For 9 genes opposite changes took place depending on the growth temperature.

2015-03-04 | GSE66516 | GEO

Transcriptome analysis of gene expression in sec59-1∆ yeast cells

Project description:Microarray data revealed that, 1880 genes were up regulated and 1430 genes were down regulated among that 3310 genes, 92 lipidomic genes were up regulated and 17 genes were down regulated in sec59-1∆. In sec59-1∆ cells, phospholipid, neutral lipid, sphingolipid and fatty acid metabolism genes were up regulated. N-Glycosylation defect affected various organelle functions such as mitochondria, peroxisome, vacuole and ER. Finally we can conclude from the microarray data, N-glycosylation plays a crucial role in regulating the lipidome homeostasis Microarray data revealed that, 1880 genes were up regulated and 1430 genes were down regulated among that 3310 genes, 92 lipidomic genes were up regulated and 17 genes were down regulated in sec59-1∆. In sec59-1∆ cells, phospholipid, neutral lipid, sphingolipid and fatty acid metabolism genes were up regulated. N-Glycosylation defect affected various organelle functions such as mitochondria, peroxisome, vacuole and ER. Finally we can conclude from the microarray data, N-glycosylation plays a crucial role in regulating the lipidome homeostasis

2018-01-15 | GSE70809 | GEO

Genes significantly down or Up-regulated upon RNF219 knockdown

Project description:Genes significantly down or Up-regulated upon RNF219 knockdown

| PRJNA377128 | ENA

Differential expression of genes in Listeria monocytogenes under thermo-tolerance condition of heat shock

Project description:Previous studies have shown the increased thermo-tolerance of pathogenic bacteria if pre-exposed to temperatures above their optimal levels prior to a particular heat treatment. It was unclear, however, whether there was a direct relationship between the different gene expression and the induced thermo-tolerance. Microarray analysis was performed to identify the differentially expressed genes during heat stress by comparing the transcriptome of L. monocytogenes under optimal temperature (37°C), and thermo-tolerance inducing (48°C for 30 minutes. A majority of the differentially expressed genes were up-regulated at heat shock as compared to those that were down-regulated when the cells were exposed to thermo-tolerance inducing conditions. Though many of the differentially expressed genes could be tentatively classified based on the current functional classification of genes (COG) per the NCBI database, many of the gene loci could not been attributed to a specific function due to the current limited knowledge on the functional genomics of L. monocytogenes.

2020-12-31 | GSE26570 | GEO

Microarray Transcriptome Comparison Subzero Temperature and Optimal Temperature Growth in Psychrobacter arcticus 273-4

Project description:Permafrost soils are extreme environments that exert low-temperature, desiccation and starvation stress on bacteria over thousands to millions of years. To understand how Psychrobacter arcticus 273-4 survived for > 20,000 years in permafrost, transcriptome analysis was performed during growth at 22°C, 17°C, 0°C, and -6°C using a mixed effects ANOVA model. Genes for transcription, translation, energy production and most biosynthetic pathways were down-regulated at low temperatures. Evidence of isozyme exchange was detected over temperature for D-alanyl-D-alanine carboxypeptidases (dac1 and dac2), DEAD-box RNA helicases (csdA and Psyc_0943) and energy efficient substrate incorporation pathways for ammonium and acetate. Specific functions were compensated by up-regulation at low temperature including genes for the biosynthesis of proline, tryptophan, methionine, and histidine. RNases and peptidases were generally up-regulated at low temperatures. Changes in energy metabolism, amino acid metabolism, and RNase gene expression were consistent with induction of the stringent response by relA activity. In contrast to results observed in other psychrophiles and mesophiles, only clpB and hsp33 were up-regulated at low temperature with no up-regulation of other chaperones and peptidyl-prolyl isomerases. Knockout mutants of relA, csdA, and dac2 were all deficient in low temperature growth, but a mutant in dac1 was deficient in growth at 17°C. The combined data suggest that the basal biological machinery including translation, transcription and energy metabolism are well adapted to function across the -6°C to 22°C growth range of P. arcticus and temperature compensation by gene expression was employed to address specific challenges to low-temperature growth.

2008-12-10 | GSE12871 | GEO

Homo sapiens

Project description:Genes up and down regulated in LNCaP cells overexpressing MED1

| PRJNA175922 | ENA

Homo sapiens

Project description:Genes significantly down or Up-regulated upon RNF219 knockdown. [RNA-Seq]

| PRJNA377137 | ENA

Temperature-dependent regulation of gene expression in Japanese flounder Paralichthys olivaceus treated with Edwardsiella tarda formalin-killed cells (FKC)

Project description:156 genes showed more than 4-fold up or down-regulated expressions by FKC at 15 ºC and 22 ºC.

2017-01-15 | GSE70989 | GEO