Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of the genes regulated by YvfI transcriptional factor

ABSTRACT: Genome-wide comparative transcriptome analysis of the Bacillus subtilis parent strain PY79 and its yvfI derivative with yvfI::T10::spc (TEK1) grown in PA medium Detailed description of sample preparation and microarray conditions can be also found in Irigul et al to be submitted

ORGANISM(S): Bacillus subtilis

PROVIDER: GSE34414 | GEO | 2013/12/11

SECONDARY ACCESSION(S): PRJNA149659

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification of the genes regulated by YvfI transcriptional factor

Project description:Genome-wide comparative transcriptome analysis of the Bacillus subtilis parent strain PY79 and its yvfI derivative with yvfI::T10::spc (TEK1) grown in PA medium Detailed description of sample preparation and microarray conditions can be also found in Irigul et al to be submitted One condition design comparision of treated vs non treated control including a dye swap, 3 biological replicates

2013-12-11 | E-GEOD-34414 | biostudies-arrayexpress

Attachment of Bacillus subtilis to the hyphae of Aspergillus niger results in altered metabolism and defense mechanisms in both partner

2014-09-09 | GSE46682 | GEO

Comparison of Bacillus subtilis wild type and cshA mutant at exponential versus stationary phase

2012-11-26 | GSE36877 | GEO

Comparison of Bacillus subtilis wild type and cshA mutant at exponential versus stationary phase

Project description:Comparison of Bacillus subtilis wild type and cshA mutant at exponential versus stationary phase. Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can be found in the submitted paper. Bacillus subtilis 168 wild type and its cshA derivative strain were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationary phase (OD600 ~2.2-2.4). For both time points, 4 biological replicates were used and 2 were mixed after cDNA labeling, resulting 2 slides for both exponential and stationary phase. Dye swaps are included in both experiments.

2012-11-26 | E-GEOD-36877 | biostudies-arrayexpress

The YmdB phosphodiesterase is a global regulator of biofilm-specific mRNA levels in Bacillus subtilis

Project description:Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can be found in the submitted paper. GSM956794-GSM956801: Bacillus subtilis 168 wild type and its ymdB derivative strain were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationary phase (OD600 ~2.2-2.4). For both time points, 4 biological replicates were used, resulting 4 slides for both exponential and stationary phase. Dye swaps are included in both experiments. GSM1011025-GSM1011032: Bacillus subtilis GP966 antibiotic tagged synthetic wild type and its ymdB E39Q point mutant strain GP969 were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationer phase (OD600 ~2.2-2.4). For both time points, 4 biological replicates were used, resulting 4 slides for both exponential and stationer phase. Dye swaps are included in both experiments.

2013-12-11 | E-GEOD-39142 | biostudies-arrayexpress

Attachment of Bacillus subtilis to the hyphae of Aspergillus niger results in altered metabolism and defense mechanisms in both partner

Project description:Transcriptome comparison of Bacillus subtilis NCIB3610 attached to the hyphae of Aspergillus niger CB 119.1 compared to Bacillus subtilis NCIB3610 cells in the supernatant of the same culture. Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can also be found in the submitted paper. B subtilis NCIB3610 cells were grown in the presence of Aspergillus niger CB 119.1 hyphae for 3 hours. The mycelium and the attached bacteria were separated from the non-attached B. subtilis cells via filtration through Miracloth. The mycelia and attached bacteria were briefly rinsed with TY medium, dried, and the sample was frozen in liquid nitrogen. Bacterial cells in the flow-through medium fraction were harvested by centrifugation at 10.397 g for 1 min. To extract RNA mainly from the bacterial cells, lysozyme solution and RiboLock (Thermo Scientific) was added followed by incubation at 37 C for 30 minutes. Further RNA extraction was performed with the Macaloid/Roche method as described before (van Hijum et al., 2005, KovÃ¡cs and Kuipers, 2011) but omitting the bead beater treatment and using RiboLock.

2014-09-09 | E-GEOD-46682 | biostudies-arrayexpress

Bacillus subtilis KS002 Targocil stimulon

Project description:Transcriptional response of Bacillus subtilis KS002 to targocil Strain KS002 (Bacillus subtilis PY79 M-NM-^TtagGHBs::cat, amyE::Phyperspank tarGHSa spc) is a targocil sensitive B. subtilis strain, with TarGH from Staphylococcus aureus as the only WTA exporter, IPTG dependent (Schirner, Stone and Walker, ACS Chem Bio 2011). Strain KS002 was treated with or without targocil for 30 min. Each experiment was conducted three times using three independent total RNA preparations (biological triplicates). For each paried comparison, one sample was labeled with Alexa Fluor 555 and the other was with Alexa Fluor 647. For each comparison, one replicate was performed with dyeswap with the same RNA.

2014-02-01 | E-GEOD-54577 | biostudies-arrayexpress

The YmdB phosphodiesterase is a global regulator of biofilm-specific mRNA levels in Bacillus subtilis

Project description:Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can be found in the submitted paper.

2013-12-11 | GSE39142 | GEO

Genome-wide identification of Bacillus subtilis Zur-binding sites.

Project description:The transcriptional factor Zur plays a key role in regulating zinc homeostasis in Bacillus subtilis. The genomic sites bound by Zur were mapped using a chromatine immunoprecipitation approach. This allowed the identification of 80 inter- and intragenic chromosomal sites bound by Zur. This data set contains 2 samples. Immunoprecipitated (IP) DNA from Bacillus subtilis BSAS36 strain (BSB1, a tryptophan-prototrophic derivative 168 strain expressing a SPA-tagged Zur protein) were extracted from bacterial cells in the exponential growth phase. IP and whole-cell extract DNA were hybridized on tiling array to generate ChIP-on-chip profiles. Two biological replicates were anlyzed.

2015-01-06 | E-GEOD-64671 | biostudies-arrayexpress

Sliding of Bacillus subtilis Natto

Project description:Transcriptome comparison of Bacillus subtilis Natto under sliding permissive (0.7% agar) and restrictive (1.5% agar or spo0A mutant strain) conditions. B subtilis Natto wild type cells were grown on the top of LB solid medium with 1.5% and 0.7% agar concentration (samples 1-4). B subtilis Natto wild type and spo0A derivative were grown on top of LB solid medium with 0.7% agar concentration (Sample 5-7). In first experiment, 4 biological replicates were used, while in the second experiment 3 biological replicates included. Dye swaps are included in both experiments.

2015-08-04 | E-GEOD-43840 | 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