Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of AdpA deficiency on S. griseus cells grown in SMM medium

ABSTRACT: Comparative hybridization of wild type versus AdpA deficient mutant grown on SMM medium 3 x dual channel slides, dye swap

ORGANISM(S): Streptomyces griseus subsp. griseus NBRC 13350

SUBMITTER: Genki Akanuma

PROVIDER: E-GEOD-14770 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Dynamic changes in the extracellular proteome caused by absence of a pleiotropic regulator AdpA in Streptomyces griseus.

Akanuma Genki G Hara Hirofumi H Ohnishi Yasuo Y Horinouchi Sueharu S

Molecular microbiology 20090804 5

In Streptomyces griseus, A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) triggers morphological development and secondary metabolism by inducing a pleiotropic transcriptional regulator AdpA. Extracellular proteome analysis of the wild-type and DeltaadpA strains grown to the end of the exponential phase in liquid minimal medium revealed that 38 secreted proteins, including many catabolic enzymes, such as protease, glycosyl hydrolase and esterase, were produced in an AdpA-dependent ...[more]

PMID: 19678896

Similar Datasets

Effect of AdpA deficient

Project description:Comparative hybridization of wild type versus AdpA deficient mutant 4 x dual channel slides, dye swap

2010-05-26 | E-GEOD-9882 | biostudies-arrayexpress

Time course effect of A-factor addition

Project description:Comparative hybridization of afsA deficient mutant versus afsA deficient mutant after A-factor addition 3 x dual channel slides, dye swap

2010-06-24 | E-GEOD-13804 | biostudies-arrayexpress

Effects of cholic acid on Rhodococcus sp. RHA1

Project description:Two cultures, one grown on cholic acid and the other on pyruvate. 3x dual-channel slides.

2011-03-29 | E-GEOD-28048 | biostudies-arrayexpress

Transcriptome analysis of the Tap efflux pump mutant in Mycobacterium bovis BCG.

Project description:We used DNA microarrays to define the physiological roles of the Tap efflux pump in M. bovis BCG during the exponential and the stationary phase of in vitro growth. For this purpose we constructed a M. bovis BCG strain in which the tap gene was inactivated by the insertion of a hygromycin resistance cassette (?-hyg). When the gene expression patterns of the tap mutant were compared to the wild-type strain, almost no differences were observed during exponential growth; only seven genes slightly increased their expression. In contrast, more that 100 genes showed a variation in their level of expression during stationary growth. More than ten representative genes were chosen from the microarray experiments and their expression was measured by quantitative RT-PCR using sigA as invariant internal control. In support to the gene expression profiling data, the mRNA levels of all selected genes was significantly different in the tap mutant strain relative to control. A functional category analysis (http://tuberculist.epfl.ch/index.html) of the genes differentially expressed revealed a high proportion belonging to the Virulence, Detoxification, Adaptation (VDA), Intermediary Metabolism and Respiration (IMR), Conserved Hypotheticals (CH), and Cell Wall and Cell Processing (CWCP) categories suggesting a major adaptation to a stress generated by inactivation of the tap efflux pump gene. We compared the global gene expression of the tap mutant versus the wild-type strain of M. bovis BCG during the exponential (one week; OD540= 0.2-0.3) and stationary (six weeks; OD540= 0.8-1.0) growth. Hybridizations were performed using RNA extracted from two different biological samples. Each sample was hybridized twice through swap labeling of the respective cDNAs.

2011-12-30 | E-GEOD-32249 | biostudies-arrayexpress

Ethanol treated vs paired control

Project description:6 ethanol treated animals with their paired controls Keywords: repeat sample Reference Design with 6 biological repeats (6 treated, 6 control, 12 reference)

2005-10-03 | E-GEOD-2718 | biostudies-arrayexpress

Profiling of gender-regulated gene transcripts in the filarial nematode Brugia malayi by oligonucleotide array analysis

Project description:Microarray technology permits high throughput comparisons of gene expression in different parasite stages or sexes. We now report the first use of this technology for analysis of gene expression in filarial worms. The slide array (comprised of 65 mer oligos representing 3569 EST clusters) was spotted with sequences selected from the extensive Brugia malayi EST database (http://nema.cap.ed.ac.uk/nematodeESTs/nembase.html#Annotation). Arrays were hybridized with male and female cDNA and developed with Cy5- and Cy3-fluorescent 3DNA capture reagents. The experimental design included both biological and technical (dye-flip) replicates.

2010-06-10 | E-GEOD-2038 | biostudies-arrayexpress

JIR1201, JIR1212, JIR1244, JIR1461, JIR1474, JIR3209, JIR3350, JIR3356 and JIR3528 genomic arrays

Project description:Comparing the genetic content of strains JIR1201, JIR1212, JIR1244, JIR1461, JIR1474, JIR3209, JIR3350, JIR3356 and JIR3528 to wild-type strain JIR3356. Comparison of JIR3356 with itself to eliminate any variation that may occur with the technique. This experiment should not produce any statistically significant expression changes. Two biological replicates were analysed per strain, which included a dye swap. Raw data was compiled using IMAGENE. Normalisation and statistical analysis was undertaken using BASE. Statistics were performed using the Wilcoxon signed ranked test.

2010-07-01 | E-GEOD-5157 | biostudies-arrayexpress

Desiccation and control transcriptomes of Rhodococcus jostii RHA1

Project description:Here we report the first transcriptomic analysis of a Gram-positive bacterium to desiccation. Filtered RHA1 cells incubated at either low relative humidity (20%), as an air drying treatment, or high relative humidity (100%), as a control, were transcriptionally profiled over a comprehensive time series. Keywords: stress response time course Three biological replicates from both the desiccation and control experiments were analyzed using two-colour microarrays. Over a time series for each experiment, Cy-labelled cDNA from treated and time-zero cells were hybridized, with a dye swap for one of the replicates.

2008-05-01 | E-GEOD-10378 | biostudies-arrayexpress

Effect of U94 in Gene Expression in PC3 Cells

Project description:Effect of U94 in Gene Expression in PC3 Cells

2010-06-10 | E-GEOD-1868 | biostudies-arrayexpress

Winter and fall gene expression in rainbow smelt liver

Project description:Rainbow smelt (Osmerus mordax) are freeze-resistant fish that accumulate glycerol and produce an antifreeze protein during winter. Quantitative reverse transcription-PCR (qPCR) and subtractive hybridization studies have revealed a few genes in smelt liver to be differentially regulated in winter in comparison with the fall when water temperatures are warmer. In order to further define the suite of processes that are regulated seasonally, we undertook a large-scale analysis of gene expression by hybridization of smelt cDNA to the salmonid 16K cGRASP cDNA microarray. These microarray experiments were conducted as a focused sieving exercise, which identified informative genes for further study in the microarray samples and over a seasonal sampling series using quantitative reverse-transcription PCR. Total RNA was obtained from livers of 3 male fish sampled on October 20th and aliquots were pooled to contain equimolar concentrations of each RNA preparation. Total RNA was prepared from 3 male fish on January 3rd and processed in the same manner. Fluorescently labeled cDNA preparations were made using the fall (October) and winter (January) pools and mixed before hybridization to the microarray. The cDNAs were hybridized to three separate microarrays in order to generate technical replicates. Differential expression was assessed in order to select genes for further study.

2010-05-15 | E-GEOD-17961 | biostudies-arrayexpress

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