Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genes differentially expressed Haloferax mediterranei strains: control wild-type strain vs M-NM-^TphaA1 strain

ABSTRACT: Transcriptional profiling of Haloferax mediterranei comparing control wild-type strain with M-NM-^TphaA1 strain, in which phaA1 gene are knockouted. M-NM-^TphaA1 strain can accumulate PHB only. Goal was to explore the PHA biosynthetic pathway and to determine their impact on primary metabolism in H. mediterranei. Total RNA from the control Haloferax mediterranei and its M-NM-^TphaA1 strain were used to generate target cDNA, and then hybridized to 8*15K Haloferax mediterranei genome array genechips, representing about 3800 genes.

ORGANISM(S): Haloferax mediterranei

SUBMITTER: Jing Han

PROVIDER: E-GEOD-37420 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Genes differentially expressed Haloferax mediterranei strains: control wild-type strain vs M-NM-^TphaEC strain

Project description:Transcriptional profiling of Haloferax mediterranei comparing control wild-type strain with M-NM-^TphaEC strain, in which PHA synthase genes are knockouted. M-NM-^TphaEC strain is deficient in PHBV accumulation. Goal was to explore the PHBV biosynthetic pathway and to determine their impact on primary metabolism in H. mediterranei. Total RNA from the control Haloferax mediterranei and its M-NM-^TphaEC strain were used to generate target cDNA, and then hybridized to 8*15K Haloferax mediterranei genome array genechips, representing about 3800 genes.

2012-04-19 | E-GEOD-37421 | biostudies-arrayexpress

Genes differentially expressed in Haloferax mediterranei strains, DF50 and M-NM-^TdeoR2, with or without induction by fructose

Project description:Transcriptional profiling of Haloferax mediterranei DF50 and M-NM-^TdeoR2 with induction by fructose comparing with the strains without this induction. Goal was to explore the effect of induction by fructose on Haloferax mediterranei. Total RNA from the Haloferax mediterranei DF50 and M-NM-^TdeoR2 with or without induction by fructose were used to generate target cDNA, and then hybridized to Haloferax mediterranei genome array genechips, representing about 3800 genes.

2013-12-18 | E-GEOD-41134 | biostudies-arrayexpress

Genes differentially expressed Haloferax mediterranei strains: control wild-type strain vs ΔphaA1 strain

Project description:Transcriptional profiling of Haloferax mediterranei comparing control wild-type strain with ΔphaA1 strain, in which phaA1 gene are knockouted. ΔphaA1 strain can accumulate PHB only. Goal was to explore the PHA biosynthetic pathway and to determine their impact on primary metabolism in H. mediterranei.

2012-04-20 | GSE37420 | GEO

Genes differentially expressed Haloferax mediterranei strains: control wild-type strain vs ΔphaEC strain

Project description:Transcriptional profiling of Haloferax mediterranei comparing control wild-type strain with ΔphaEC strain, in which PHA synthase genes are knockouted. ΔphaEC strain is deficient in PHBV accumulation. Goal was to explore the PHBV biosynthetic pathway and to determine their impact on primary metabolism in H. mediterranei.

2012-04-20 | GSE37421 | GEO

Genes differentially expressed in Haloferax mediterranei strains, DF50 and ΔdeoR2, with or without induction by fructose

Project description:Transcriptional profiling of Haloferax mediterranei DF50 and ΔdeoR2 with induction by fructose comparing with the strains without this induction. Goal was to explore the effect of induction by fructose on Haloferax mediterranei.

2013-12-18 | GSE41134 | GEO

Checking the origin utilisation of Haloferax mediterranei H13 through high-throughput DNA sequencing

Project description:A potential origin that appears to stay dormant in its native host Haloferax volcanii lacking the main active origins becomes activated and competent for replication of the entire chromosome when integrated into the chromosome of the origin-deleted H. mediterranei. Measurement of replication dynamics (marker frequency analysis; MFA) for Haloferax mediterranei H13

2015-07-10 | E-GEOD-70592 | biostudies-arrayexpress

Chromosomal origin utilisation in Haloferax meiditerranei wild type and mutant strains

Project description:We have comprehensively explored the origin utilisation in Haloferax mediterranei. Here we report three active chromosomal origins by genome-wide replication profiling, and demonstrate that when these three origins are deleted, a dormant origin becomes activated. Genomic DNA was extracted from the H. mediterranei cultures at specific time points(12h,18h,24h,36h,42h and stationary phase 66h), or during the exponential phase (OD600≈0.5) and stationary phase (OD600≈4.0)for the origin deletion strains. After being lablled, Genomic DNA from exponential phase and stationary phase were hybridized to Haloferax mediterranei genome array genechips.

2015-07-08 | E-GEOD-70597 | biostudies-arrayexpress

Genes differentially expressed Haloarcula hispanica strains: PHB (M-NM-^TphaEC mutant) vs 960 (wild type)

Project description:Transcriptional profiling of Haloarcula hispanica comparing PHB with 960. PHB represents the PHA synthase genes mutant (i.e., M-NM-^TphaEC) which is deficient in PHBV accumulation when grown in MG medium. 960 represents the wild-type strain which can produce PHBV when grown in MG medium. Goal was to explore the PHBV biosynthesis and its impact on central metabolism in H. hispanica. Total RNA from PHB and 960 were used to generate target cDNA, and then hybridized to 8*15K Haloarcula hispanica genome array genechips, representing about 3800 genes.

2013-01-22 | E-GEOD-42799 | biostudies-arrayexpress

Haloarcula hispanica wild-type strain cultured in different media: MG vs 168

Project description:Transcriptional profiling of Haloarcula hispanica wild-type strain cultured in different media comparing MG medium with 168 medium. H. hispanica wild-type strain can accumulate PHBV in MG medium, while can not in 168 medium. Goal was to explore the PHA biosynthesis and its impact on central metabolism in H. hispanica. Total RNA from MG and 168 were used to generate target cDNA, and then hybridized to 8*15K Haloarcula hispanica genome array genechips, representing about 3800 genes.

2013-01-22 | E-GEOD-42798 | biostudies-arrayexpress

The effect of stpA deletion on S. Typhimurium gene expression during growth in rich medium

Project description:StpA is a paralogue of the nucleoid associated protein H-NS that is conserved in a range of enteric bacteria and had no known function in Salmonella enterica serovar Typhimurium. Here, we show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA-dependent genes of S. Typhimurium are a specific subset of the H-NS regulon that are predominantly under the positive control of sigma38 (RpoS), CRP-cAMP and PhoP. The regulatory role of StpA varied at different growth phases; StpA only controlled sigma38 levels at mid-exponential phase when it prevented inappropriate activation of sigma38 during rapid bacterial growth. In contrast, StpA only activated the CRP-cAMP regulon during late exponential phase. The effect of stpA deletion on S. Typhimurium gene expression during growth in LB was analysed at 4 different time points (early-log, mid-log, late-log, and stationary phase) where the gene expression profile of the stpA-deletion strain was compared to that of the parental strain. Between two and three biological replicates were performed for each strain and time point. For this study, we used Salmonella genomic DNA as the comparator which also acted as the control for spot quality.

2009-10-27 | E-GEOD-18424 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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