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Links from GEO DataSets

Items: 20

1.

Role of the extracytoplasmic-function sigma Factor sigmaH in Mycobacterium tuberculosis global gene expression

(Submitter supplied) Like other bacterial species, Mycobacterium tuberculosis has multiple sigma (s) factors encoded in its genome. In previously published work, we and others have shown that mutations in some of these transcriptional activators render M. tuberculosis sensitive to various environmental stresses and, in some cases, cause attenuated virulence phenotypes. In this paper, we characterize a M. tuberculosis mutant lacking the ECF s factor sigma-H. more...
Organism:
Mycobacterium tuberculosis
Type:
Expression profiling by array
Platform:
GPL2787
15 Samples
Download data: TXT
Series
Accession:
GSE8689
ID:
200008689
2.

The Mycobacterium tuberculosis ECF sigma Factor sE: role in global gene expression and survival in macrophages

(Submitter supplied) In previously published work, we identified three Mycobacterium tuberculosis sigma (s) factor genes responding to heat shock (sigB, sigE and sigH ). Two of them (sigB and sigE ) also responded to SDS exposure. As these responses to stress suggested that the s factors encoded by these genes could be involved in pathogenicity, we are studying their role in physiology and virulence. In this work, we characterize a sigE mutant of M. more...
Organism:
Mycobacterium tuberculosis
Type:
Expression profiling by array
Platform:
GPL2787
15 Samples
Download data: TXT
Series
Accession:
GSE8664
ID:
200008664
3.

The single ECF sigma factor of Xylella fastidiosa is involved in the heat shock response

(Submitter supplied) Genome sequence analysis of the bacterium Xylella fastidiosa revealed the presence of two genes, named rpoE and rseA, predicted to encode an ECF sigma factor and an anti-sigma factor, respectively. In this work, an rpoE null mutant was constructed in the citrus strain J1a12 and shown to be sensitive to exposure to heat shock and ethanol. To identify the X. fastidiosa σE regulon, global gene expression profiles were obtained by DNA microarray analysis of bacterial cells under heat shock identifying 23 sigmaE-dependent genes. more...
Organism:
Xylella fastidiosa
Type:
Expression profiling by array
Platform:
GPL2708
18 Samples
Download data
Series
Accession:
GSE4960
ID:
200004960
4.

Functional Genomics Reveals Extended Roles of the Mycobacterium tuberculosis Stress Response Factor sigmaH

(Submitter supplied) DNA Microarray based comparison of M. tuberculosis and its isogenic delta-sigmaH mutant for an extended period of time, using a diamide-stress and removal strategy (post-diamide stress or PDS) Raw data has been requested of, but not provided by, the submitter.
Organism:
Mycobacterium tuberculosis
Type:
Expression profiling by array
Platform:
GPL8382
12 Samples
Download data
Series
Accession:
GSE15608
ID:
200015608
5.

Mycobacterium tuberculosis and macrophage response

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mycobacterium tuberculosis
Type:
Expression profiling by array
Platform:
GPL4057
33 Samples
Download data: GPR
Series
Accession:
GSE7963
ID:
200007963
6.

Sigma factor E of Mycobacterium tuberculosis controls the expression of bacterial components that modulate macrophages

(Submitter supplied) Sigma factor E (SigE) controls the expression of genes that are essential for Mtb virulence. In this work, we have identified the SigE regulon during infection of macrophages Our results indicate that SigE regulates the expression of genes involved in the maintenance of Mtb cell envelope integrity and function (i.e., detoxification and secretion). Keywords: strains comparison
Organism:
Mycobacterium tuberculosis
Type:
Expression profiling by array
Platform:
GPL4057
23 Samples
Download data: GPR
Series
Accession:
GSE7962
ID:
200007962
7.

The global transcriptional profile of Mycobacterium tuberculosis during human macrophages infection

(Submitter supplied) During lung infection Mycobacterium tuberculosis (Mtb) resides in macrophages and subverts the bactericidal mechanisms of these professional phagocytes. In this work we have analyzed by DNA microarray technique the global transcription profile of Mtb infecting primary human macrophages in order to identify putative bacterial pathogenic factors that can be relevant for the intracellular survival of Mtb. more...
Organism:
Mycobacterium tuberculosis
Type:
Expression profiling by array
Platform:
GPL4057
11 Samples
Download data: GPR
Series
Accession:
GSE6209
ID:
200006209
8.

Sigma factor B (sigB) response to stress conditions (0.05% SDS and 5mM Diamide)

(Submitter supplied) The numerous sigma factors present in Mycobacterium tuberculosis (MTB) are indicative of adaptability to different environmental conditions. In this report we describe the sigma factor B (sigB) regulon and the phenotypes of a MTB sigB mutant strain exposed to different stresses like SDS and Diamide. This experiment set compares expression profiles between H37Rv wild type and H37Rv sigB null mutant as well as under different stress conditions. more...
Organism:
Mycobacterium tuberculosis
Type:
Expression profiling by array
Platform:
GPL8523
36 Samples
Download data
Series
Accession:
GSE15976
ID:
200015976
9.

RNA-seq analysis of various strains of Mycobacterium tuberculosis under normal and redox stress.

(Submitter supplied) We have performred RNA-seq analysis of WT, ∆phoP and ∆sigH Mtb H37Rv under normal and redox (Diamide) stress, to investigate the role of PhoP and SigH in maintaning the redox homoeostasis of bacterium. RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. Briefly, 25 ml of bacterial culture was grown to mid-log phase (OD600= 0.4 to 0.6) and combined with 40 ml of 5 M guanidinium thiocyanate solution containing 1% β-mercaptoethanol and 0.5% Tween 80. more...
Organism:
Mycobacterium tuberculosis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27661
12 Samples
Download data: TXT
Series
Accession:
GSE171775
ID:
200171775
10.

Genome-wide binding site profiling of NdgR in Streptomyces coelicolor

(Submitter supplied) We identified genome-wide binding regions of NdgR in Streptomyces coelicolor using chromatin immunoprecipitation sequencing (ChIP-seq). We constructed 6×myc-tagged NdgR strain using homologous recombination with myc-tagging vector. Analysis of the sequencing data aligned to Streptomyces coelicolor genome database (NC_003888).
Organism:
Streptomyces coelicolor
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18886
1 Sample
Download data: GFF
Series
Accession:
GSE59010
ID:
200059010
11.

The sigmaB regulon of B. cereus ATCC14579

(Submitter supplied) The alternative sigma factor sigmaB has an important role in the acquisition of stress-resistance in many gram-positive bacteria. In the foodborne pathogen Bacillus cereus sigmaB is activated strongly upon a heat shock and other stress conditions. Here we describe the identification of the set of sigmaB-regulated genes in B. cereus by DNA microarray analysis of the transcriptome upon a mild heat shock. more...
Organism:
Bacillus cereus ATCC 14579
Type:
Expression profiling by array
Platform:
GPL4406
7 Samples
Download data
Series
Accession:
GSE6005
ID:
200006005
12.

Transcriptional analysis of a Vibrio choleare rpoH mutant vs wild-type after a heat-shock

(Submitter supplied) Vibrio cholerae, the cause of cholera, can grow in a variety of environments outside of human hosts. During infection, the pathogen must adapt to significant environmental alterations, including the elevated temperature of the human gastrointestinal tract. σ32, an alternative sigma factor encoded by rpoH, activates transcription of genes involved in the heat-shock response in several bacterial species. more...
Organism:
Vibrio cholerae; Vibrio cholerae O1 biovar El Tor str. N16961
Type:
Expression profiling by array
Platform:
GPL3651
6 Samples
Download data: TXT
Series
Accession:
GSE6097
ID:
200006097
13.

Transcriptional profiling of Mycobacterium tuberculosis Rv3852 (hns) knockout mutant

(Submitter supplied) A handful of nucleoid-associated proteins (NAPs) regulate the vast majority of genes in a bacterial cell. H-NS, the Histone-like Nucleoid-Structuring protein, is one of these NAPs and protects Escherichia coli from foreign gene expression. Though lacking any sequence similarity with E. coli H-NS, Rv3852 was annotated as the H-NS ortholog in Mycobacterium tuberculosis, as it resembles human histone H1. more...
Organism:
Mycobacterium tuberculosis H37Rv
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17280
4 Samples
Download data: TXT
Series
Accession:
GSE95181
ID:
200095181
14.

Sigma(M) regulated genes under antibiotic stress (vancomycin)

(Submitter supplied) Abstract of associated manuscript: The Bacillus subtilis extracytoplasmic function (ECF) sigma(M) factor is activated by cell envelope stress elicited by antibiotics, and by acid, heat, ethanol and superoxide stresses. Here, we have used several complementary approaches to identify genes controlled by sigma(M). In many cases, expression is only partially dependent on sigma(M) because of both overlapping promoter recognition with other ECF sigma factors and the presence of additional promoter elements. more...
Organism:
Bacillus subtilis
Type:
Expression profiling by array
Platform:
GPL7420
14 Samples
Download data: GPR
Series
Accession:
GSE13820
ID:
200013820
15.

RNA-sequencing based analysis of Listeria monocytogenes 10403S::ΔBCHL Prha-sigH and ΔBCHL Prha

(Submitter supplied) In this study, RNA-seq was used to compare the transcriptomes of Listeria monocytogenes 10403S::ΔBCHL Prha-sigH and ΔBCHL Prha. RNA-seq was performed on ΔBCHL Prha-sigH and ΔBCHL Prha RNA samples representing three independent biological replicates at log phase in Brain Heart Infusion (BHI) broth under rhamnose induction. Indexed and purified cDNA libraries (6 libraries including 3 replicates for 2 strains) were loaded together onto an independent flow cell without any other samples; sequencing was carried out by running Hiseq 2500 (single-end, 150-bp per read). more...
Organism:
Listeria monocytogenes 10403S
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20912
6 Samples
Download data: TXT, XLSX
Series
Accession:
GSE73008
ID:
200073008
16.

Oxidative stress dependent regulon of AosR

(Submitter supplied) Analyzing differences in transcriptome profile of Rv and RvDaosR under normal and oxidized conditions
Organism:
Mycobacterium tuberculosis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17879
12 Samples
Download data: TXT
Series
Accession:
GSE161190
ID:
200161190
17.

Identification of the WhiB5 regulon in Mycobacterium tuberculosis H37Rv

(Submitter supplied) We used DNA microarrays to define the M. tuberculosis whiB5 regulon and to study the variation of the global transcription profile in response of its induction. For this purpose we constructed a M. tuberculosis strain in which whiB5 was transcribed from an pristinamycin-inducible promoter and its transcriptional profile was compared on DNA microarray with the transcriptional profile of its control strain (empty vector-containing clone). more...
Organism:
Mycobacterium tuberculosis; Mycobacterium tuberculosis H37Rv
Type:
Expression profiling by array
Platform:
GPL4057
8 Samples
Download data: TXT
Series
Accession:
GSE30299
ID:
200030299
18.

A member of the cAMP receptor protein family of transcription regulators in M. tuberculosis is required for virulence

(Submitter supplied) Deletion of gene Rv3676 in Mycobacterium tuberculosis coding for a transcription factor belonging to the cAMP receptor protein (CRP) family caused growth defects in laboratory medium, in bone marrow-derived macrophages and in a mouse model of tuberculosis. Transcript profiling of M. tuberculosis grown in vitro identified 16 genes with significantly altered expression in the mutant compared with the wild type. more...
Organism:
Mycobacterium tuberculosis
Type:
Expression profiling by array
Platform:
GPL5753
14 Samples
Download data: TXT
Series
Accession:
GSE8830
ID:
200008830
19.

Role of the Bacteroides fragilis EcfO regulon during oxidative stress.

(Submitter supplied) Genome expression study of Bacteroides fragilis strain 638R comparing an ecfO null mutant with an empty vector to a reo (anti-ecfO) null mutant containing the ecfO gene on a plasmid under the control of an IPTG inducible promoter.
Organism:
Bacteroides fragilis 638R
Type:
Expression profiling by array
Platform:
GPL15788
7 Samples
Download data: CALLS, PAIR
Series
Accession:
GSE39231
ID:
200039231
20.

Characterization of the EcfO regulon

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Bacteroides fragilis NCTC 9343; Bacteroides fragilis 638R
Type:
Expression profiling by array
Platforms:
GPL15187 GPL15188
6 Samples
Download data: CALLS, PAIR
Series
Accession:
GSE35539
ID:
200035539
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