GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mycolicibacterium smegmatis MC2 155; Mycobacterium tuberculosis H37Rv

Type:

Other

Platforms:

GPL14824 GPL15323

87 Samples

Download data: PAIR

(Submitter supplied) After induction of DosR from a tet regulated promoter (uninduced controls were treated with an equivalent ammount of the solvent, DMSO), transcription was arrested using 50 ug/ul of rifampin leaving RNA degradation as the sole vector responsible for mRNA abundance. mRNA half-lives were calculated from the decay of signal intensity from T0.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Other

Platform:

GPL14824

30 Samples

Download data: PAIR

(Submitter supplied) Transcription was arrested using 50 ug/ul of rifampin leaving RNA degradation as the sole vector responsible for mRNA abundance at 20C (cold) or in 0.2%O2 (hypoxia). mRNA half-lives were calculated from the decay of signal intensity from T0.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Other

Platform:

GPL14824

24 Samples

Download data: PAIR

(Submitter supplied) Transcription was arrested using 50 ug/ul of rifampin leaving RNA degradation as the sole vector responsible for mRNA abundance. mRNA half-lives were calculated from the decay of signal intensity from T0.

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Other

Platform:

GPL15323

9 Samples

Download data: PAIR

(Submitter supplied) Transcription was arrested using 50 ug/ul of rifampin leaving RNA degradation as the sole vector responsible for mRNA abundance. mRNA half-lives were calculated from the decay of signal intensity from T0.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Other

Platform:

GPL14824

24 Samples

Download data: PAIR

(Submitter supplied) Control of mRNA half-life is a powerful strategy to adjust individual mRNA levels to various stress conditions, because the mRNA degradation rate controls not only the steady-state mRNA level but also the transition speed of mRNA levels. Here, we analyzed mRNA half-life changes in response to cold stress in Arabidopsis cells using genome-wide analysis, in which mRNA half-life measurements and transcriptome analysis were combined. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

21 Samples

Download data: CEL

(Submitter supplied) Mycobacterium tuberculosis (Mtb) is a bacterial pathogen that causes tuberculosis (TB), an infectious disease that inflicts major health and economic costs around the world. Mtb encounters diverse environments during its lifecycle and responds to these changes by reprogramming its transcriptional output. However, the mechanisms and regulation of Mtb transcription remains poorly understood. In this work, we simultaneously determine the 5' and 3' ends of individual RNA molecules in Mtb cells using the SEnd-seq method, which enables us to profile the Mtb transcriptome at high resolution. more...

Organism:

Mycobacterium tuberculosis; Mycolicibacterium smegmatis

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL27507 GPL28556 GPL22688

69 Samples

Download data: WIG

(Submitter supplied) RNA-Seq results accompanying submission of a manuscript: "Cholesterol-dependent transcriptome remodeling reveals new insight into the contribution of cholesterol to Mycobacterium tuberculosis pathogenesis" describing the role of cholesterol and vitamin B12 in shaping the transcriptome of the Mycobacterium tuberculosis H37Rv and M. tuberculosis ∆prpR - propionate regulator (PrpR) mutant. Next generation sequencing results are provided in three independent biological replicates for each strain growing in three different media - minimal medium with glycerol or cholesterol as the sole carbon source and standard 7H9/10% OADC medium. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26169

21 Samples

Download data: FNA, GFF, TXT

(Submitter supplied) Dormant Mycobacterium tuberculosis bacilli play important role in latent tuberculosis infection. Previously we have demonstrated that cultivation of M. tuberculosis in potassium-deficient media resulted in the generation of dormant ‘non-culturable’ cells. Addition of a moderate concentration of rifampicin enabled to kill a minor subpopulation of actively replicating bacilli and obtain a homogeneous ‘zero-CFU’ population of dormant cells characterized by total inability to produce colonies on solid media and by high potential to reactivate after reintroducing of potassium. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18768

12 Samples

Download data: TXT, XLS

(Submitter supplied) Transcriptional profiling of M.tuberculosis to 10 mM vitamin C at 8 h. This was compared to gene expression profile of untreated M. tuberculosis culture.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platform:

GPL18055

7 Samples

Download data: TXT

(Submitter supplied) Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control. However, the extent to which their genes are regulated post-transcriptionally remains unresolved. To gain insight into role of de novo transcription in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed RNA in Karenia brevis. These isolated fractions were then used for analysis of global de novo transcription by hybridization to a K. more...

Organism:

Karenia brevis

Type:

Expression profiling by array

Platform:

GPL13364

9 Samples

Download data: TXT

(Submitter supplied) Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control. However, the extent to which their genes are regulated post-transcriptionally remains unresolved. To gain insight into the role of differential mRNA stability in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed and pre-existing RNA pools in Karenia brevis. more...

Organism:

Karenia brevis

Type:

Expression profiling by array

Platform:

GPL13364

18 Samples

Download data: TXT

(Submitter supplied) The human pathogen, Mycobacterium tuberculosis, develops a dormant infection, in which organisms survive within the body. We established a unique in vitro dormancy model based on the characterization of drug-resistance to INH and rifampin. M. tuberculosis cells were maintained in controlled and defined multiple stress conditions with low oxygen (5% dissolved oxygen tension), acid (pH 5.) along with glycerol-deprived medium conditions. more...

Organism:

Mycobacterium tuberculosis; Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platforms:

GPL4388 GPL4369

75 Samples

Download data: TXT

(Submitter supplied) Mycobacterium tuberculosis (Mtb) infects alveolar macrophages (AMs) causing pulmonary tuberculosis (PTB), the more frequent form of the disease. Less frequently, Mtb disseminates to many other organs and tissues resulting in different extrapulmonary forms of TB. Nevertheless, very few studies have addressed the global mRNA response of human AMs, in particular from humans with the active form of the disease. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

43 Samples

Download data: TXT

(Submitter supplied) We measure the stability of mRNAs in rapidly dividing yeast by metabolic labeling with thiouracil and determine the effects on mRNA stability in the presence of various inhibitors of translation elongation and initiation.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

67 Samples

Download data: FPKM_TRACKING

(Submitter supplied) In-vivo Gene Signatures of Mycobacterium tuberculosis In C3HeB/FeJ Mice

Organism:

Mycobacterium tuberculosis CDC1551; Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platform:

GPL18320

12 Samples

Download data: GPR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15138

13 Samples

Download data: BEDGRAPH

(Submitter supplied) To construct a regulatory map of the genome of the human pathogen, Mycobacterium tuberculosis, we applied two complementary high-resolution approaches, strand-specific RNA-seq and ChIP-seq, to survey the global transcriptome and monitor genome-wide dynamics of RNA polymerase (RNAP) and NusA. ChIP-seq revealed that RNAP and the antiterminator, NusA, occurred ubiquitously with the NusA profile mirroring RNAP distribution in both the exponential and stationary phases of growth. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15138

3 Samples

Download data: BEDGRAPH

(Submitter supplied) To construct a regulatory map of the genome of the human pathogen, Mycobacterium tuberculosis, we applied two complementary high-resolution approaches, strand-specific RNA-seq and ChIP-seq, to survey the global transcriptome and monitor genome-wide dynamics of RNA polymerase (RNAP) and NusA. ChIP-seq revealed that RNAP and the antiterminator, NusA, occurred ubiquitously with the NusA profile mirroring RNAP distribution in both the exponential and stationary phases of growth. more...

Organism:

Mycobacterium tuberculosis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15138

10 Samples

Download data: BEDGRAPH

(Submitter supplied) Plants possess a cold acclimation system to acquire freezing tolerance through pre-exposure to non-freezing low temperatures. The transcriptional cascade of C-repeat binding factors (CBFs)/dehydration response element-binding factors (DREBs) is considered a major transcriptional regulatory pathway during cold acclimation. However, little is known regarding the functional significance of mRNA stability regulation in the response of gene expression to cold stress. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

20 Samples

Download data: CEL, CHP