GEO DataSets

(Submitter supplied) We used deep RNA sequencing to obtain high coverage RNA-Seq data of five C. crescentus cell cycle stages, each with three biological replicates. We found that 1,586 genes (over a third of the genome) display significant differential expression between stages. This gene list, which contains many genes previously unknown for their cell cycle regulation, includes almost half of the genes involved in primary metabolism, suggesting that these "house-keeping" genes are not constitutively transcribed during the cell cycle, as often assumed. more...

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17158

15 Samples

Download data: CSV

(Submitter supplied) Investigation of whole genome gene expression level changes in a Caulonacter crescentus NA1000 Plac::CCNA_00382 (ccrM) mutant, compared to the wild-type strain. The mutations engineered into this strain cause the CcrM DNA methyltransferase to be overexpressed and the chromosome to be constitutively methylated at the adenine at GANTC motifs. References of strains: CcrMOE: Collier, J. and Shapiro, L. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Expression profiling by array

Platform:

GPL17931

6 Samples

Download data: PAIR

(Submitter supplied) Investigation of whole genome gene expression level changes in a Caulobacter crescentus NA1000 delta-CCNA_00382 (ccrM) mutant, compared to the wild-type strain. The mutations engineered into this strain render it incapable of methylating its genome on the adenine at GANTC motifs. References for strains : WT: Marks, M.E., Castro-Rojas, C.M., Teiling, C., Du, L., Kapatral, V., Walunas, T.L. and Crosson, S. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Expression profiling by array

Platform:

GPL17931

6 Samples

Download data: PAIR

(Submitter supplied) The purpose of this experiment was to examine the differential transcriptional profiles of Caulobacter CB15N grown in M2-Glucose versus M2-Inositol.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by array

Platform:

GPL2749

2 Samples

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(Submitter supplied) We wanted to test the effect on global gene expression of depleting the essential cell cycle regulator CtrA in order to determine the genes both indirectly and directly transcriptionally regulated by CtrA Gene expression changes in S. meliloti 1,2,4 and 6 hours post CtrA depletion

Organism:

Sinorhizobium meliloti 1021; Sinorhizobium meliloti

Type:

Expression profiling by array

Platform:

GPL18182

24 Samples

Download data: TXT

(Submitter supplied) Supporting data for: Holtzendorff et. al., "Oscillating global regulators." Keywords = gcrA Keywords = global regulator Keywords: repeat sample

Organism:

Caulobacter vibrioides

Type:

Expression profiling by array

Platform:

GPL1076

13 Samples

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(Submitter supplied) RNA-based regulation of gene expression is substantially contributing to the ability of bacteria to rapidly adapt to changing environmental conditions. This study employs RNAseq to define the transcriptome of Caulobacter in response to treatment with the DNA-crosslinking agent mitomycin C. We identify a small, regulatory RNA ChvR synthesized under the control of the conserved ChvIG two-component system which represses production of a TonB-dependent receptor, ChvT, in Caulobacter crescentus. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21317

6 Samples

Download data: WIG

(Submitter supplied) CRISPR interference (CRISPRi) is a powerful new tool used in different organisms that provides a fast, specific, and reliable way to knockdown gene expression. Caulobacter crescentus is a well-studied model bacterium, and although a variety of genetic tools have been developed, it currently takes several weeks to delete or deplete individual genes, which significantly limits genetic studies. Here, we optimized a CRISPRi approach to specifically downregulate the expression of genes in C. more...

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24555

4 Samples

Download data: WIG

(Submitter supplied) In the alpha subclass of proteobacteria iron homeostasis is controlled by diverse iron responsive regulators. Caulobacter crescentus, an important freshwater α-proteobacterium, uses the ferric uptake repressor (Fur) for such purpose. However, the impact of the iron availability on the C. crescentus transcriptome and an overall perspective of the regulatory networks involved remain unknown. In this work we report the identification of iron-responsive and Fur-regulated genes in C. more...

Organism:

Caulobacter vibrioides NA1000; Caulobacter vibrioides CB15

Type:

Expression profiling by array

Platform:

GPL10469

4 Samples

Download data: TXT

(Submitter supplied) Gene transfer agents (GTA) are domesticated prophages that cannot self-multiply and be infectious but might have been co-opted to perform biological functions for the host bacteria. Recently, Caulobacter crescentus, a bacterium best known as a model organism to study bacterial cell biology and cell cycle regulation1, has been demonstrated to produce bona fide GTA particles (CcGTA). Two direct activators of the CcGTA biosynthetic gene cluster, GafY and GafZ, have been identified, however, it is unknown how GafYZ controls transcription mechanistically or how they coordinate gene expression of the CcGTA gene cluster with other accessory genes elsewhere on the genome for an ultimate CcGTA synthesis. more...

Organism:

Caulobacter vibrioides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18006 GPL32154

42 Samples

Download data: TXT

(Submitter supplied) The Caulobacter cell cycle includes sequential differentiation of the cell poles and an asymmetric cell division yielding distinct daughter cells. RNA-seq and ribosome profiling were used to measure global messenger RNA (mRNA) abundance and translation levels throughout the Caulobacter cell cycle revealing translational control in 51% of cell cycle-regulated genes. Ribosome profiling levels were temporally regulated for ten proteins encoding asymmetrically localized multi-protein assemblies that specify cell fate upon cell division, with five ORFs being regulated with a >2 fold contribution from the translation efficiency. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18276

12 Samples

Download data: TXT

(Submitter supplied) The study investigated gene expression patterns in liver tissue to understand the biological functions of genes that are potentially involved in controlling / regulating feed efficiency in Nordic dairy cattle.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19172

38 Samples

Download data: TXT

(Submitter supplied) Supporting data for Hottes et al., "DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus" The microarray component of this work monitors mRNA expression during the cell cycle of synchronized populations of Caulobacter crescentus cells. Transcription during the normal cell cycle is compared with transcription during a cell cycle where expression of dnaA, which encodes a key DNA replication initiation factor, is delayed. more...

Organism:

Caulobacter vibrioides

Type:

Expression profiling by array

Platforms:

GPL1076 GPL2748 GPL2749

83 Samples

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(Submitter supplied) The cold shock proteins belong to a family of RNA binding proteins presenting a highly conserved domain, called cold shock domain (CSD). They are involved in various cellular processes, including adaptation to low temperature, nutritional stress, cell growth and stationary phase. Here we investigate the role of CspC in C. crescentus stationary phase and the molecular mechanisms underlying gene regulation by this protein. more...

Organism:

Caulobacter vibrioides CB15; Caulobacter vibrioides NA1000

Type:

Expression profiling by array

Platform:

GPL10469

8 Samples

Download data: TXT

(Submitter supplied) The highly conserved chaperonin GroESL performs a crucial role in protein folding, however the essential cellular pathways that rely on this chaperone are underexplored. Loss of GroESL leads to severe septation defects in diverse bacteria, suggesting the folding function of GroESL may be integrated with the bacterial cell cycle at the point of cell division. Here, we describe new connections between GroESL and the bacterial cell cycle using the model organism Caulobacter crescentus. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26943

2 Samples

Download data: XLSX

(Submitter supplied) We report gene expression responses of Caulobacter crescentus to osmotic upshock (150 mM sucrose). The goal of this study is compare the transcriptional responses of wild type, sigT deletion, and gsrN overexpression (gsrN++) strains. The data provide a high resolution view of how two major regulators of the general stress response (sigT and gsrN) shape transcription upon shift to a hyperosmotic environment.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21015

31 Samples

Download data: TXT

(Submitter supplied) Coexpression of proteins in response to pathway-inducing signals is the founding paradigm of gene regulation. Yet, it remains unexplored whether the relative abundance of coregulated proteins requires precise tuning. Here we present large-scale analyses of protein stoichiometry and corresponding regulatory strategies for 21 pathways and 67-224 operons in divergent bacteria separated by 0.6-2 billion years. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168; Escherichia coli str. K-12 substr. MG1655; Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759; Caulobacter vibrioides

Type:

Other

7 related Platforms

21 Samples

Download data: WIG

(Submitter supplied) Background and methods: The effects of microbiota toward hematopoietic stem and progenitor cells (HSPCs) were very much complicated based on previous reports. In the current study, normal inbred C57BL6 (B6) mice from the Jackson Laboratory were maintained in the SPF environment for three weeks. Baseline complete blood counts were normal, and animals were then separated into two groups: 1) SPF mice stayed in the SPF facility, and 2) SPF mice being transferred to a conventional facility for co-housing (CVT). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

8 Samples

Download data: CSV

(Submitter supplied) Background and Purpose: Constitutional GATA2 deficiency caused by heterozygous germline GATA2 mutation has a broad spectrum of clinical phenotypes including systemic infections, lymphedema, cytopenias, MDS and AML. A comprehensive profiling of transcriptome of hematopoiesis in GATA2 deficiency is currently lacking. Methods: We performed single-cell RNA sequencing of sorted bone marrow CD34+ hematopoietic stem and progenitor cells (HSPCs) from eight GATA2 deficiency patients, who had various well characterized GATA2 mutations and clinically manifest myelodysplasia. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

13 Samples

Download data: CSV

(Submitter supplied) We sequenced single cells coming from three developmental stages of chicken forelimb. We identified different cell populations with distinct transcriptional profiles. The supplementary file contains processed UMI count matrices, which also include meta data of each cell, e.g. cluster.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19787

3 Samples

Download data: TXT