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

Stp1 regulated genes in Streptococcus agalactiae strain A909

ABSTRACT: Genes that showed altered expression between wild type A909 and the isogenic Stp1 mutant were identified by microarray analysis Deletion mutants were examined for changes in gene expression

ORGANISM(S): Streptococcus agalactiae

SUBMITTER: Lakshmi Rajagopal

PROVIDER: E-GEOD-21564 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RgfC/A regulated genes in Streptococcus agalactiae strain A909

Project description:Genes that showed altered expression between wild type A909 and isogenic rgfC/A mutant were identified. A strain with a deletion in RgfC/A (SAK_1917/SAK_1918) was derived and microarray analysis was performed to identify genes regulated by the RgfC/A two component system. strain comparison, global regulation, two component system Deletion mutant was compared to the wild type strain A909 for changes in gene expression

2010-04-28 | E-GEOD-21563 | biostudies-arrayexpress

Stp1 and Stk1 regulated genes during S. aureus post-exponential phase growth

Project description:Genes that showed altered expression in Stk1 and Stp1 deficient Staphylococcus aureus Newman were identified. strain comparison, global regulation Deletion mutants were examined for alterations in gene expression.

2010-04-22 | E-GEOD-21426 | biostudies-arrayexpress

The gene expression profiling array of LncRNA between tumor tissues and paired non-tumor tissues in HBV-positive hapatocellular carcinoma

Project description:Investigation of whole genome gene expression level changes of LncRNAs in tumor tissues and paired non-tumor tissues in HBV-positive hapatocellular carcinoma. The different expression genes were further analysised. The human LncRNA microarray analysis of the 10 samples (5 non-tumor tissues and 5 paired tumor tissues) were completed. Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis. Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit; 4) Array scanning using the Agilent Scanner G2505C. Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and mRNA level (*_RMA.calls) files were generated after normalization. All mRNAs level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.mRNAs that at least 3 out of 6 samples have values greater than or equal to lower cut-off: 50.0 (“All Targets Value”) were chosen for further data analysis. Differentially expressed mRNAs were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable mRNAs expression pattern among samples.

2013-08-10 | E-GEOD-49713 | biostudies-arrayexpress

Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription

Project description:To fit within the confines of the cell, bacterial chromosomes are highly condensed into a structure called the nucleoid. Despite the high degree of compaction in the nucleoid, the genome remains accessible to essential biological processes, such as replication and transcription. Here, we present the first high-resolution chromosome conformation capture-based molecular analysis of the spatial organization of the Escherichia coli nucleoid during rapid growth in rich medium and following an induced amino acid starvation that promotes the stringent response. Our analyses identify the presence of origin and terminus domains in exponentially growing cells. Moreover, we observe an increased number of interactions within the origin domain and significant clustering of SeqA-binding sequences, suggesting a role for SeqA in clustering of newly replicated chromosomes. By contrast, ‘histone-like’ protein (i.e. Fis, IHF and H-NS) binding sites did not cluster, and their role in global nucleoid organization does not manifest through the mediation of chromosomal contacts. Finally, genes that were downregulated after induction of the stringent response were spatially clustered, indicating that transcription in E. coli occurs at transcription foci. A 4 chips study of exponentially growing wild type E. coli strain MG1655 grown in LB rich media or after induction of the stringent response by serine hydroxamate for 30 min. Two technical replicates, Three biological replicates mixed prior hybridization on the chip.

2013-05-01 | E-GEOD-40304 | biostudies-arrayexpress

Comparative analysis of chrysanthemum transcriptome in response to infection of three viruses: Cucumber mosaic virus, Tomato spotted wilt virus, and Potato virus X

Project description:Gene expression analysis of chrysanthemum infected with three different viruses including Cucumber mosaic virus, Tomato spotted wilt virus, and Potato virus X have been performed using the chrysanthemum 135K microarray. Mock and each virus infected chrysanthemum plants were subjected for microarray analysis.

2015-01-01 | E-GEOD-55985 | biostudies-arrayexpress

Comprehensive transcriptional profiling analysis reveals candidate regulators in cold-stressed seedlings of Petunia hybrida

Project description:Investigation of gene expression level changes in Petunia hybrida seedlings subjected to cold at 2°C for 0.5 h, 2 h, 24 h and 5 d, compared to the CK. The custom-designed four-plex microarray with 72000 features was constructed based on the EST sequences generated in Breuillin's study together with all sequences of P.hybrida and P.axillaris available at Genbank, TIGR, and the Solanaceae genomics network SGN, which was ultimately composed by a set of 24816 non-redundant unique sequences (unigenes).The probe intensity files resulting from RNA hybridization were first read into R. Background Correction, quantile normalization and summarization were then performed using the Robust Multi-array Average (RMA) method included in Bioconductor Affy package based on the home made chip description library.

2015-01-15 | E-GEOD-64963 | biostudies-arrayexpress

Expression analysis of channel catfish anterior kidney at 48h post immersion challenge of vaccinated fish (28 days post vaccination with attenuated Edwardsiella ictaluri) with virulent E. ictaluri

Project description:To determine the global gene transcriptional changes in vaccinated channel catfish anterior kidney after immersion challenge with a virulent Edwardsiella ictaluri compared to sham vaccinated catfish control. The attenuated Edwardsiella ictaluri used for vaccination was Aquavac-ESC which was commercially available, the virulent strain of Edwardsiella ictaluri is the AL93-58 strain. A six chip study using total RNA samples including 3 controls (no vaccination, no challenge) and 3 treated groups (challenge after vaccination). Each RNA sample used for microarray was pooled fish anterior kidney samples (5 fish anterior kidney samples were pooled as one). Each chip measrues the expression level of 65,182 genes. For each sequence, 3 probes were selected. Two copies were prepared on arrays.

2011-10-04 | E-GEOD-32588 | biostudies-arrayexpress

Expression analysis of channel catfish anterior kidney at 48h post immersion vaccination with attenuated Edwardsiella ictaluri

Project description:To determine the global gene transcriptional changes in channel catfish anterior kidney after immersion vaccination with attenuated Edwardsiella ictaluri compared to sham vaccinated catfsih control. The attenuated Edwardsiella ictaluri used for vaccination was Aquavac-ESC which was commercially available. A six chip study using total RNA samples including 3 control and 3 vaccinated samples. Each RNA sample used for microarray was poold fish anterior kidney samples (5 fish anterior kidney samples were pooled as one). Each chip measrues the expression level of 65,182 genes. For each sequence, 3 probes were selected. Two copies were prepared on arrays.

2011-09-09 | E-GEOD-32046 | biostudies-arrayexpress

Expression analysis of Lactococcus lactis NIAI712 and its plasmid cured variant

Project description:L. lactis NIAI712 carries five different plasmids, including an 8.7-kb plasmid designated pAG6. In this study, genome-wide expression profiles of the pAG6-cured variant was compared to the wild-type strain. Two samples of total RNA recovered from a wild-type culture of L. lactis NIAI712 and a pAG6-cured variant were examined

2013-08-31 | E-GEOD-48143 | biostudies-arrayexpress

Expresion analyses of red2 deletion cells

Project description:Investigation of whole genome gene expression level changes in red2?, compared to the parental wild-type strain. The red2 deletion cells analyzed in this study will be described in Sugiyama and Sugioka-Sugiyama. An mRNA profiling study using total RNA recovered from vegetatively growing wild-type culture of fission yeast and red2 deletion cultures of fission yeast. Each chip measures the expression level of 4.997 genes from S.pombe with fourteen 60-mer probe pairs (PM/MM) per gene, with seven-fold technical redundancy.

2013-12-01 | E-GEOD-49006 | 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