GEO DataSets

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

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platform:

GPL19545

6 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of Mycobacterium tuberculosis H37Rv::pTetInt-dcas9 comparing 100ng/ml ATc treated cells with Atc-untreated cells after 7 days of treatment with shaking at 200rpm at 37°C.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platform:

GPL19545

3 Samples

Download data: GPR, TXT

(Submitter supplied) Transcriptional profiling of Mycobacterium tuberculosis H37Rv::pTetInt-dcas9 comparing 100ng/ml ATc treated cells with Atc-untreated cells after 4 days of treatment with shaking at 200rpm at 37°C.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platform:

GPL19545

3 Samples

Download data: GPR, 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) RNA-seq was utilized to compare the transcriptomes of S. mutans strains that had or hadn't experienced CRISPR interference of a green fluorescent protein gene

Organism:

Streptococcus mutans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21130

9 Samples

Download data: TXT

(Submitter supplied) Progression through the Caulobacter cell cycle is driven by the master regulator CtrA, an essential two-component signaling protein that regulates the expression of nearly 100 genes. CtrA is abundant throughout the cell cycle except immediately prior to DNA replication. However, the expression of CtrA-activated genes is generally restricted to S-phase. We identify the conserved protein SciP (small CtrA inhibitory protein) and show that it accumulates during G1 where it inhibits CtrA from activating target genes. more...

Organism:

Caulobacter vibrioides CB15

Type:

Expression profiling by array

Platform:

GPL10469

4 Samples

Download data: TXT

(Submitter supplied) Cell cycle progression in most organisms requires tightly regulated programs of gene expression. The transcription factors involved typically stimulate gene expression by binding specific DNA sequences in promoters and recruiting RNA polymerase. Here, we find that the essential cell cycle regulator GcrA in Caulobacter crescentus activates the transcription of target genes in a fundamentally different manner. more...

Organism:

Caulobacter vibrioides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21016 GPL21015

10 Samples

Download data: WIG

(Submitter supplied) We sought to define the transcriptional regulon of the ChvI response regulator in Caulobacter crescentus. This study compares gene expression between ∆chvI cells and cells overexpressing the constitutively-active chvI(D52E) mutant. Our work provides a global view of the genes directly and indirectly regulated by the ChvGI two-component system in C. crescentus.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24555

12 Samples

Download data: TXT

(Submitter supplied) The Mobile CRISPRi system with and without mRFP-targeting sgRNA was engineered into Pseudomonas aeruginosa PA14 strain with chromosomally encoded mRFP. RNA was isolated from these strains, and the corresponding cDNA library was synthesized and sequenced in 150 bp paired-end reads. Approximately 1,000,000 reads were collected for each of the two samples, with ~94% alignment to PA14 WT by Bowtie254, and transcripts were counted with HTSeq55. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20881

2 Samples

Download data: GTF, TXT

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

Organism:

Brevundimonas subvibrioides

Type:

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

Platforms:

GPL27605 GPL27606

15 Samples

Download data: BW

(Submitter supplied) Transcriptional rewiring is the regulation of different targets genes by orthologous regulators in different organisms. While this phenomenon has been observed, it has not been extensively studied, particularly in core regulatory systems. Several global cell cycle regulators are conserved in the Alphaproteobacteria, providing an excellent model to study this phenomenon. First characterized in Caulobacter crescentus, GcrA and CcrM compose a DNA methylation-based regulatory system that helps coordinate the complex life cycle of this organism. more...

Organism:

Brevundimonas subvibrioides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27606

6 Samples

Download data: BED, BW, TXT

(Submitter supplied) Transcriptional rewiring is the regulation of different targets genes by orthologous regulators in different organisms. While this phenomenon has been observed, it has not been extensively studied, particularly in core regulatory systems. Several global cell cycle regulators are conserved in the Alphaproteobacteria, providing an excellent model to study this phenomenon. First characterized in Caulobacter crescentus, GcrA and CcrM compose a DNA methylation-based regulatory system that helps coordinate the complex life cycle of this organism. more...

Organism:

Brevundimonas subvibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27605

9 Samples

Download data: TXT, XLSX

(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) 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) Genome-wide screens have discovered a large set of essential genes in the human pathogen Streptococcus pneumoniae. However, the function of many essential genes is still unknown, hampering vaccine and drug development programs. Based on results from transposon-sequencing (Tn-Seq), we refined the list of essential genes in S. pneumoniae serotype 2 strain D39. Next, we created a knockdown library targeting all 391 potentially essential genes using CRISPR interference (CRISPRi). more...

Organism:

Streptococcus pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18183

6 Samples

Download data: TXT

(Submitter supplied) CRISPR/Cas9-based functional genomics have transformed our ability to elucidate mammalian cell biology. Most previous CRISPR-based screens were implemented in cancer cell lines, rather than healthy, differentiated cells. Here, we describe a CRISPR interference (CRISPRi)-based platform for genetic screens in human neurons derived from induced pluripotent stem cells (iPSCs). We demonstrate robust and durable knockdown of endogenous genes in such neurons, and present results from three complementary genetic screens. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL20301

14 Samples

Download data: MTX, TSV, TXT

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

Organism:

Caulobacter vibrioides CB15

Type:

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

Platform:

GPL32211

63 Samples

Download data

(Submitter supplied) During infection, transcriptional changes in both the phage and its host bacterium influence the outcome of infection. The xenobiotic response element (XRE) family of transcription factors (TFs), which are commonly encoded by bacteria and phages, regulate diverse aspects of bacterial cell physiology and can impact phage infection dynamics. Through a pangenome analysis of Caulobacter species isolated from soil and aquatic ecosystems, we uncovered an apparent radiation of an XRE TF gene cluster, several of which have established functions in the regulation of holdfast adhesin development and biofilm formation in C. more...

Organism:

Caulobacter vibrioides CB15

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32211

33 Samples

Download data: CSV