Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE34919: Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (ChIP-chip) GSE34922: Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (Expression) Refer to individual Series

ORGANISM(S): Mycobacterium tuberculosis H37Rv

SUBMITTER: Ruben Hartkoorn

PROVIDER: E-GEOD-35080 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (ChIP-chip)

Project description:The genome wide ChIP-on-chip analysis to identify the DNA binding sites for the M.tuberculosis sigma factor Rv3286c (SigF) SigF binding sites were determined by microarray analysis of anti-sigF immunoprecipitated DNA from H37Rv(ΔrsbW/sigF)::pmySigF compared to H37Rv(ΔrsbW/sigF)::pMY769 (both cultured with pristinamycin for 3 days). 4 biological replicates were performed.

2012-01-20 | E-GEOD-34919 | biostudies-arrayexpress

Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (Expression)

Project description:The genome wide transcriptome analysis to identify the M.tuberculosis sigma factor Rv3286c (SigF) dependent transcripts as well as Pristimaycin induced transcripts Pristinamycin induced transcripts were identified by comparing the cDNA extracted from H37Rv::pMY769 with and without pristinamycin (3 biological replicates). SigF controlled transcripts were identified by comparing the cDNA extracted from H37Rv::pMYsigF with and without pristinamycin (4 biological replicates).

2012-01-20 | E-GEOD-34922 | biostudies-arrayexpress

Sigma38 binding sites in E. Coli

Project description:ChIP-seq to identify sigma38 binding sites in wild-type and delta ssrS (6S RNA knockout) strains of E. Coli K-12 MG1655, during stationary phase ChIP-seq using antibody against sigma38 in wild-type and ssrS deletion strain. Two replicates for wild type and one replicate for ssrS deletion.

2016-06-10 | E-GEOD-74836 | biostudies-arrayexpress

ChIP on chip data for AbrC3 binding sites in S. coelicolor M145

Project description:ChIP on chip assay of AbrC3 to determine its binding sites in S. coelicolor M145 genome using purified anti-AbrC3 polyclonal antibodies. Samples from nutrient broth (NB) cultures were collected at 36, 48 and 60 hours, cross-linked, and finally hybridized to DNA 104K microarrays designed by University of Surrey.

2014-01-04 | E-MTAB-1451 | biostudies-arrayexpress

Two human HCC cells (MHCC97H and MHCC97L): PML-siRNA transfected vs. control

Project description:We found PML was responsible for ATO resistance in HCC cells, PML knockdown cells show better sensitivity to ATO treatment. To further explore the mechanism of PML-induced ATO resistance, we performed a microarray assay to compare the differential gene expression profiles of PML-siRNA-treated (PML knockdown) and negative control siRNA-treated cells. Two-condition experiment, PML-siRNA vs. control cells. Biological replicates: two cell lines and each cell line has 1 control, 1 transfected, independently grown and harvested. One replicate per array. Comparisons were made between PML siRNA group and control group for each cell line

2015-04-04 | E-GEOD-67574 | biostudies-arrayexpress

RIP-seq identification of RNAs enriched on RNA polymerase and the primary sigma factor (sigma A) in Mycobacterium tuberculosis

Project description:6S RNA is a small RNA with specific secondary structure that associates with the complex of RNA polymerase (RNAP) and the primary sigma factor in majority of bacteria. In Mycobacterium smegmatis, Ms1 interacts with the RNAP core without the sigma factor and probably replaces 6S RNA. It is currently unknown if Ms1 homolog (MTS2823) in M. tuberculosis also binds to RNAP core. We sequenced RNAs that co-immunoprecipitated with RNAP or the primary sigma factor sigma A and total RNA isolated from the lysate (input sample). We expect that putative Ms1 or 6S RNA homologs are enriched in RNA polymerase or sigma A sample compared to the input.

2024-02-09 | E-MTAB-12350 | biostudies-arrayexpress

RIP-seq identification of RNAs enriched on RNA polymerase and the primary sigma factor (sigma A) in Mycobacterium tuberculosis

2024-02-09 | E-MTAB-13584 | biostudies-arrayexpress

Global distribution of RNA polymerase in Streptomyces coelicolor

Project description:Genome wide ChIP-chip analysis of RNA Polymerase binding sites in Streptomyces coelicolor MT1110 cultures grown in SMM + 0.5% casaminoacids at 30C up to mid exponential and stationary phase. Chromatin extracted from rifampicin and formaldehyde treated cultures was incubated with anti ? subunit of core RNA polymerase of E.coli monoclonal antibodies and the DNA purified from anti RNA Polymerase IP and mock IP samples was labelled with either Cy3 or Cy5- dCTP and hybridized in an direct type of microarray experiment onto SCO-Chip2-v2 High Density IJISS arrays

2020-08-01 | E-MAXD-60 | biostudies-arrayexpress

ChIP-seq of E. coli to identify H-NS and Fis binding at multiple time-points during growth in rich medium

Project description:Among the most important regulators of gene expression in bacteria are 'nucleoid-associated proteins'. These proteins alter the topology of the bound DNA by bending, wrapping or bridging it, thus having multiple effects, including transcriptional regulation, on the bacterial cell. Among the best-studied nucleoid proteins are H-NS and Fis, which bind to specific sequences on the DNA. H-NS is a global repressor of gene expression. Fis alters the global conformation of the DNA by introducing branched structures in it; but its effect on gene expression on a genomic scale remains largely unclear.<br><br>Several bacterial transcriptional regulators including H-NS and Fis have been studied using ChIP-chip. However, the higher resolution and dynamic range offered by ChIP-Seq have not been exploited for any bacterial species. By performing ChIP-Seq of these two proteins, we present the first such study in a bacterium. In addition to providing a proof-of-principle for the use of this technology for bacteria, we perform our study at multiple time-points during growth in rich medium, thus generating new insights into how these proteins function under different cellular conditions. Further, by analysing our data in conjunction with newly-generated gene expression and RNA polymerase-chromosome interaction data we provide new interpretation of the genome-scale patterns of the interactions of these proteins to the DNA.

2010-09-01 | E-MTAB-332 | biostudies-arrayexpress

Acquired resistance in M-line Biomphalaria glabrata vs. Sensitized (exposed to irradiated only) and Infected (exposed to viable only) E. paraensei

Project description:Transcriptional profile of snails with induced acquired resistance (exposed first to irradiated E. paraensei miricidia) after secondary challenge with viable miricidia. Compared to snails exposed to irradiated miricidia only or to viable miricidia only. Experiments were done over the course of 16 days, with 8 day intervals between sensitization and secondary challenge. Keywords: Dose response Each replicate is comprised of 5 individual snails from the specified treatment group. Three replicates of each treatment were analyzed on the Snail oligo array.

2010-08-01 | E-GEOD-21878 | 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