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

Transcriptomic description of a classic model of carbon catabolic repression in Streptomyces coelicolor: Glucose effect

ABSTRACT: The aim of this work was to use a high density microarray approach in Streptomyces coelicolor M145 using a represive condition (RM) (0.5%agar+0.5%glucose) and non-repressive condition (NRM) (agar 1%)

ORGANISM(S): S. coelicolor_M145_strain

SUBMITTER: alba romero

PROVIDER: E-MTAB-3603 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic description of a classic model of carbon catabolic repression in Streptomyces coelicolor:Glk effect

Project description:The aim of this work was to use a high density microarray approach in Streptomyces coelicolor M145 and a glk substituted mutant (ScoZm)derived from it, to evaluate the paradigmatic model proposed for CCR in Streptomyces

2016-04-02 | E-MTAB-3602 | biostudies-arrayexpress

S.coelicolor_Rok7B7vsM145_MM+mannitol_time_course_expression

Project description:For transcript analysis, total RNA was isolated as described (Noens et al, 2007) from surface-grown mycelia of S. coelicolor M145 and its rok7B7 null mutant, cultivated on MM agar plates with mannitol (1% w/v) as the sole carbon source (plates were covered with cellophane discs). Two independent biological replicate experiments were performed. Samples were taken at 14h (early vegetative growth), 24 h (vegetative growth), 30 h (early aerial growth), 36 h (aerial growth), 42 h (early sporulation) and 54 h (sporulation). Total RNA was purified using the Kirby-mix protocol (Kieser et al, 2000). DNaseI treatment was used to fully remove any traces of DNA. Before use, the RNA samples were checked for integrity on an Agilent 2100 Bioanalyzer (Agilent Technologies). cDNA preparation and labeling was performed as previously described (Bucca et al, 1997, Bucca et al, 2009). The filtered data sets were analyzed using rank products analysis (Breitling et al, 2004) via the Rank-ProdIt tool (Laing and Smith, 2010). Differentially expressed genes were identified as demonstrating a > 2 fold change in expression between the parental strain M145 (wild-type) and the rok7B7 mutant.

2014-01-14 | E-MTAB-1465 | biostudies-arrayexpress

Transcriptome data for Streptomyces coelicolor at 2 growth stage

Project description:Transcriptome analysis of Streptomyces coelicolor MT1110 cultures grown in SMM + 0.5% casaminoacids at 30?C up to mid exponential and stationary phase. Total RNA was extracted from both stages of growth, labelled with Cy3-dCTP and mixed with genomic DNA from S. coelicolor M145 labelled with Cy5-dCTP that was used as common reference in an indirect type of microarray experiment. Labelled Cy3/Cy5-dCTP samples were hybridized onto SCO-Chip2-v2 High Density IJISS arrays.

2020-08-01 | E-MAXD-61 | biostudies-arrayexpress

Combined transcriptome analysis and polysome profiling of Streptomyces coelicolor MT1110 in SMMS

Project description:Total RNA, low ribosome density (LRD) and polysome associated RNA were obtained from parallel S.coelicolor cultures of wild type strain MT1110 grown on solid medium SMMS up to rapid growth phase II. The abundance of each RNA in the total RNA, the LRD or polysome pool was quantified by Cydye labeling and hybridization on high density whole genome 105K S.coelicolor DNA microarrays using S.coelicolor M145 as reference.

2018-11-01 | E-MTAB-6206 | biostudies-arrayexpress

Differential expression of S. coelicolor M145 vs. tdd8 mutants in R5

Project description:Differential expression data set of S. coelicolor M145, tdd8 deletion mutant and overexpressed tdd8 mutant cultured in R5. RNA samples were collected at the visual onset Red antibiotic production following by cDNA synthesis and labeling. The hybridization was conducted using DNA 104K microarrays (Surrey) using gDNA from S. coelicolor M145 as reference.

2015-06-08 | E-MTAB-2644 | biostudies-arrayexpress

Genome-scale transcriptomic study into the role of AbsA2 in regulating antibiotic biosynthesis in Streptomyces coelicolor

Project description:Here we report the construction of a absA2 mutant strain which exhibited the classic precocious hyper-production of antibiotics and its complementation by an N-terminal triple-FLAG tagged version of AbsA2. The complemented and non-complemented absA2 mutant strains were used in large-scale time-course experiments to investigate the effect of deleting absA2 on gene expression at multiple time points and identify AbsA2 DNA binding sites in ChIP-on-chip studies using high-density microarrays.

2019-02-16 | E-MTAB-3528 | biostudies-arrayexpress

Characterization of deletions of the HBB locus by array comparative genomic hybridization

Project description:Array-CGH used to characterize HBB deletions causing beta thalassemia and HPFH Two-color experiment comparing thalssemia/HPFH subjects with normal DNA

2015-05-06 | E-GEOD-68587 | biostudies-arrayexpress

Physical mapping of bread wheat chromosome 5A: an integrated approach

Project description:The huge size, the redundancy and the great repeated portion of the bread wheat genome [Triticum aestivum (L.)], placed it among the most difficult species to be sequenced and dissected at the genetic, structural and evolutionary levels. To overcome the limitations, a strategy based on the genome compartmentalization in individual chromosomes and the subsequent production of physical maps was established within the frame of the International Wheat Genome Sequence Consortium. A total of 95,812 BAC clones of short (5AS) and long (5AL) arm-specific BAC libraries, were fingerprinted and assembled into contigs by complementary analytical approaches based on FingerPrinted Contigs and Linear Topological Contig. Combined anchoring approaches based on PCR marker screening, microarray and BlastN searches, applied to interlinked genomic tools, that is genetic maps, deletion bin map, high-density neighbor map, BAC end sequences, genome zipper and chromosome survey sequences, allowed the development of a high quality physical map, with an anchored physical coverage of 75% for 5AS and 53% for 5AL, with high portions (64 and 48%, respectively) ordered along the chromosome. The gene distribution along the wheat chromosome 5A compared with the closest related genomes showed a pattern of syntenic blocks belonging to different chromosomes of Brachypodium, rice and sorghum and regions involving translocations and inversions. The physical map presented here is currently the most comprehensive map for 5A chromosome and represents an essential resource for fine genetic mapping and map-based cloning of agronomically relevant traits, and a reference for the 5A sequencing projects. 55 DNA pools of short arm of chromsome 5A and 63 DNA pools of long arm of 5A. The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.

2015-08-13 | E-GEOD-66996 | biostudies-arrayexpress

LNGFR- and Thy-1-based prospective isolation of human mesenchymal stem cells reveals functionally distinct subpopulations.

Project description:Human multipotent mesenchymal stem cells (MSCs), isolated based on their adherence to plastic, show poor growth and differentiation and frequently contain contaminating cells, which limits to clarify their own characteristics. In this study, the identification of two cell surface markers, LNGFR and Thy-1, allowed the prospective isolation of highly purified clonogenic human MSCs. Furthermore, single cell sorting assays followed by in vitro expansion revealed three distinct MSC subpopulations: rapidly-, moderately- and slowly proliferating MSC clones (RPCs, MPCs and SPCs, respectively). While RPCs exhibited robust multilineage differentiation and self-renewal potency, MPCs and SPCs contained a majority of senescent cells and exhibited frequent genome errors. Single cell sorting assays followed by in vitro expansion revealed three distinct MSC subpopulations: rapidly-, moderately- and slowly proliferating MSC clones (RPCs, MPCs and SPCs, respectively). Sample: RPC, MPC and SPC (n=3).

2011-12-22 | E-GEOD-34484 | biostudies-arrayexpress

Acquired resistance to mutant-selective EGFR inhibitor AZD9291 is associated with increased dependence on RAS signaling

Project description:To compare gene copy number in cell populations with acquired resistance to specified EGFR inhibitors to parental cell lines. The aim of the experiment was to determine whether gain or loss of copy number of particular genes was associated with resistance to particular EGFR inhibitors. Comparing gene copy number in PC9 parental cells to gene copy number in 5 cell populations resistant to AZD9291, 2 cell populations resistant to WZ4002, 2 cell populations resistant to afatinib and 4 cell populations resistant to gefitinib.

2015-04-14 | E-GEOD-59239 | 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