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 SAOUHSC_02810 deletion in S. aureus NCTC8325

ABSTRACT: To analyze function of SAOUHSC_02810, we have employed whole genome microarray expression profiling to identify genes transcription changed in mutant strain. SAOUHSC_02810 were replaced by ermB gene. Cells were grown to OD600=2.0, and the RNA level of wild type NCTC8325 and SAOUHSC_02810 mutant were compared.

ORGANISM(S): Staphylococcus aureus subsp. aureus NCTC 8325

SUBMITTER: Haipeng Sun

PROVIDER: E-GEOD-56283 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Effect of different Two-component systems system deletion in S. aureus NCTC8325

Project description:To analyze function of three Two-component systems SAOUHSC_00184-185, SAOUHSC_01313-1314, and SAOUHSC_01980-1981, we have employed whole genome microarray expression profiling to identify genes transcription changed in respective mutant strains. Target TCSs were replaced by ermB gene. Cells were grown to OD600=2.0, and the RNA level of wild type NCTC8325 and three TCSs mutant were compared.

2013-09-30 | E-GEOD-51197 | biostudies-arrayexpress

Effect of TetR family regulator SAOUHSC_02897 deletion in S. aureus NCTC8325

Project description:To analyze function of TetR family regulator SAOUHSC_02897, we have employed whole genome microarray expression profiling to identify genes transcription changed in respective mutant strains. Target SAOUHSC_02897 was replaced by ermB gene. Bacteria grown in the wells of biofilm formation at 12 hours, and the RNA level of wild type NCTC8325 and SAOUHSC-02897 mutant were compared.

2013-12-18 | E-GEOD-53432 | biostudies-arrayexpress

MicroRNA-188 regulates age-related switch between osteoblast and adipocyte differentiation

Project description:To identify microRNAs which differentially expressed in the BMSCs of aged and young mice and and investigate its influences on BMSCs differentiation with ageing. The microRNAs expressions of BMSCs from 3 aged mice and 3 young mice were measured.

2014-04-29 | E-GEOD-57127 | biostudies-arrayexpress

Expression profile of WT and IKKb(EE)IEC epithelial cells (IEC)

Project description:To investigate NF-kB-driven gene expression in IEC, we performed microarray analysis from enterocytes of mice that express a constitutively active form of IKKb in intestinal epithelial cells Total RNA was prepared from enterocytes obtained from small intestines of IKKb(EE)IEC and WT littermates. Two biological replicates were performed for each experimental condition.

2011-06-09 | E-GEOD-29701 | biostudies-arrayexpress

Effect of cajanin stilbene acid and its synthetic derivatives on MCF-7 breast cancer cells

Project description:Cajanin stilbene acid (CSA) was previously shown to induce cytotoxicity against cancer cells. We have employed microarray gene expression profiling to identify deregulated genes in MCF-7 breast cancer cells upon treatment with CSA and its synthetic derivatives (CSA6, CSA9, CSA19). TGM2 gene encoding transglutaminase 2 was commonly deregulated after treatment with all four CSA compounds. All compounds revealed strong effects on cell cycle progression and DNA damage response. Promoter motif analysis of the deregulated genes further supported the microarray results emphasizing the relevance of transcription factors regulating cell cycle and proliferation, MYC being among the most pronounced ones. Interestingly, cellular movement was among the top five affected cellular functions after treatment with the four derivatives. Gene expression profiling study with Whole Human Genome RNA chips (8M-CM-^W60K Agilent) was performed in MCF-7 breast cancer cells upon treatment with CSA and its synthetic derivatives (CSA6, CSA9, CSA19). Twelve chips were used; control (x2), CSA (x2), control (x2), CSA6 (x2), CSA9 (x2), CSA19 (x2). MCF-7 cells were treated with the compounds (IC50 concentrations) for 72 hours or left untreated (DMSO control). Two independent experiments were performed for each treatment.

2015-02-27 | E-GEOD-64430 | biostudies-arrayexpress

High-resolution, genome-wide analysis of human medulloblastoma samples by array-Comparative Genomic Hybridization (aCGH)

Project description:Medulloblastoma (MB) is the most common pediatric brain tumor and is an aggressive neoplasia arising in the cerebellum. MB includes four major histological subsets commonly subdivided in: classic, desmoplastic, anaplastic or large-cell, and nodular. The current patients risk stratification is based on the age at diagnosis (> or < 3 years at diagnosis), the extent of residual tumor mass post-operative, and disease dissemination. An average risk is assigned to patients older than 3 years of age with minimal or no tumor residual. These patients are more than 60% of overall MBs and have an overall survival between 50-70% at 5 years. It is widely accepted that tumor aggressiveness and progression depend on genetic abnormalities. We performed the genome-wide study, focused on classic MB belonging to pediatric patients at standard risk. We analyzed 31 MB samples using high resolution oligonucleotide Human Genome CGH 244K (Agilent Technologies). The present study may help to identify novel molecular prognostic markers useful to refining current criteria of patientsM-BM-4 relapse risk estimation in this subgroup of patients. We analyzed 31 samples of classic medulloblastoma from patients older than 3 years of age at diagnosis

2011-01-01 | E-GEOD-23005 | biostudies-arrayexpress

Analysis of the microRNA that involved the tuberculosis or latent TB infection II

Project description:To get to know the different levels of the microRNA among the pulmonary tuberculosis patients, latent-infected individuals and the complete healthy people, we have employed the Agilent miRNA microarray (version 2.0) as a discovery platform to identify microRNA with the potential to diagnose the TB patients and the latent infected persons. The Peripheral Blood Mononuclear Cells (PBMCs) of each group were made up of equally mixed quantity of 3 volunteers. The results showed that several microRNAs were found up- or low regulated in PBMCs of TB patients versus latent-infected individuals and similarly for latent-infected individuals versus complete healthy ones. Each group have 4 volunteers. The PBMCs of each group were made up of equally mixed volumes after being purified.each group was reated three times.

2010-11-18 | E-GEOD-25435 | biostudies-arrayexpress

Ube3a-ATS characterization with strand-speicific microarray

Project description:This strand-specific array is performed to characterize expression features of Ube3a-ATS, including its imprinting status, its exon-intron structure, its transcriptional initiation and termination site as well as its polyadenylation status. The array contains reverse-complementary probes detecting transcripts from both strands and therefore we are able to pick up signal from both Ube3a sense and antisense. By comparing wild-type with various mutants, and total RNA with polyA RNA, we concluded that Ube3a-ATS is a paternally imprinted gene covering the whole gene body of Ube3a in the antisense orientation. It does not have an obvious exon-intron structure. Its transcription initiates at Snrpn major promoter and terminates ~40kb upstream of Ube3a transcriptional start site. Total RNA from Snrpn-Ube3a maternal deletion mutant (del s-u/+), its wild-type littermate, paternal deletion mutant and its wildtype littermate were analyzed. Mutant mice with S-U maternal deletion and Snrpn promoter paternal deleiton which leads to depletion of Ube3a-ATS (del s-u/0.9 and del s-u/4.8) were also analyzed. polyA RNA was purified from the sample 2 and sample 4. All eight samples were hybridized to the custom 8X60k Agilent CGH array.

2012-05-02 | E-GEOD-29254 | biostudies-arrayexpress

In vitro transcriptomic comparison of daptomycin-resistant Staphylococcus aureus

Project description:Mutants from SG511 and NCTC8325 (wild type isolates) resistant to daptomycin were obtained following serial passage experiments in vitro. Transcriptomic experiments showed alteration in the expression of genes involved in various pathways including general metabolism, cell wall regulon and lipid metabolism. Microarray was used to evaluate alteration in the transcriptome between wild type strains SG511 and NCTC8325 and their daptomycin resistant isolates, in antibiotic-free medium.

2015-11-01 | E-GEOD-50842 | biostudies-arrayexpress

RNAPII progression through H3K27me3 enriched gene bodies require JMJD3 HDM activity

Project description:Several signaling pathways require JMJD3 binding to promoters to activate the expression of target genes. Despite the known H3K27me3 demethylase activity of JMJD3 the transcriptional coactivator mechanism remains unclear. Here we reveal that JMJD3 promotes transcription of TGFb responsive genes through regulation of RNAPII progression on gene bodies. ChIPseq experiments demonstrate that upon TGFb treatment, JMJD3 and RNAPII.ser2P colocalyze extensively along intragenic regions of TGF target genes. M-BM- According to these data, genome wide analysis shows that JMJD3 dependent TGF target genes are enriched in H3K27me3 prior to TGF signaling pathway activation. M-BM- Further molecular analysis indicate that JMJD3 removes H3K27me3 and pave the way for the RNAPII.Overall, these findingsM-BM- uncover the mechanism ofM-BM- JMJD3 function in transcriptional activation We performed chromatin immunoprecipitation followed by sequencing (ChIPseq) of H3K27me3 mark in mouse neural stem cells growing under standard conditions. We also performed ChIPseq of elongating RNAPII (Ser2P) and JMJD3 in neural stem cells stimulated with TGFb cytokine.

2012-12-31 | E-GEOD-38269 | 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