GEO DataSets

(Submitter supplied) Pseudomonas aeruginosa bacteriophage PhiKZ is the type representative of the ‘giant’ phage genus with unusually large virions and genomes. By unraveling the transcriptional map of the 280 kb genome to single-nucleotide resolution, we show that it encodes 369 genes organized in 134 operons, 20% more than originally annotated. Early transcription is initiated from 28 highly conserved AT-rich promoters distributed over the PhiKZ genome, all located on the same strand. more...

Organism:

Phikzvirus phiKZ; Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18804 GPL18644

12 Samples

Download data: TXT

(Submitter supplied) Differential RNA-seq (dRNA-seq) was performed on Pseudomonas aeruginosa alone or shortly after iinfection with the jumbo phage phiKZ

Organism:

Pseudomonas aeruginosa PAO1; Phikzvirus phiKZ

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23999 GPL28760

8 Samples

Download data: CSV

(Submitter supplied) Time course of after infection (5 min, 20 min and 40 min) of Bacillus subtilis by phage AR9

Organism:

Bacillus subtilis; Bacillus phage AR9

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22521

4 Samples

Download data: WIG

(Submitter supplied) The global transcriptional profile of novel T7-like Pseudomonas aeruginosa phage LUZ100 was obtained using the long read RNA sequencing technique ONT-cappable-seq. Using this approach we obtained a comprehensive genome-wide map of viral transcription start sites, terminators and transcription units and gained new insights in the molecular mechanisms of transcriptional regulation of T7-like temperate phages.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL32595

4 Samples

Download data: TXT

(Submitter supplied) Explore the genome-scale phage–host interactions across different developmental infection stages

Organism:

Bruynoghevirus PaP3; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by array

Platform:

GPL20140

18 Samples

Download data: TXT

(Submitter supplied) We performed high-througput RNA sequencing of RNA samples extracted from C. baltica cells infected with phi14:2 phage at 40, 90, 140 and 190 minutes after infection. The same experiments were performed with cells treated with host RNA polymerase inhibitor in order to determine which genes rely on viral rifampicin-insensitive RNA polymerase. Using this data, we identified different time classes of phage genes and revealed genes transcribed by phage RNA polymerase.

Organism:

Cellulophaga baltica; Cellulophaga phage phi14:2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26873

8 Samples

Download data: GFF3, TSV

(Submitter supplied) Grad-seq of Pseudomonas aerugionosa PAO1 at OD 0.3 with and without infection with ΦKZ bacteriophage

Organism:

Phikzvirus phiKZ; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL28760 GPL23999

44 Samples

Download data: TDF

(Submitter supplied) RNA sequencing (RNA-seq) of phage infected bacterial cultures offers a snapshot of transcriptional events occurring during the infection process, providing insights into the phage transcriptional organization as well as the bacterial response. To better mimic real environmental contexts, we performed RNA-seq of P. aeruginosa PAO1 cultures infected with phage LUZ19 in a mammalian cell culture medium (MCCM) to better simulate a phage therapy event, and the data were compared to LB medium. more...

Organism:

Pseudomonas aeruginosa PAO1; Pseudomonas phage LUZ19

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29451 GPL29452

24 Samples

Download data: CSV, XLSX

(Submitter supplied) mRNA was sequenced in triplicate in three time points to determine the global transcriptional response of S. pneumoniae that is susceptible to the bacteriophage SpSL1. Samples were taken from mid log exponential phase in standard glucose contaiing media with an MOI of 0.2 at three time points: 10 minutes, 50 minutes, and 90 minutes post infection.

Organism:

Streptococcus pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22606

5 Samples

Download data: TXT

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

Organism:

Thermus thermophilus HB8

Type:

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

Platforms:

GPL32746 GPL32745

23 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) We performed the long-read RNA sequencing technique ONT-cappable-seq on RNA samples of T. thermophilus infected with phage P23-45 5 minutes post-infection. Using this approach, we obtained the primary transcriptome at the early infection stage and sequenced it in full-length. Based on this data, we were able to identify viral transcription start sites and termination sites and uncover distinct promoter motifs.

Organism:

Thermus thermophilus HB8

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL32746

2 Samples

Download data: TXT

(Submitter supplied) By doing ChIP-seq with antibodies against two P23-45 RNA polymerases gp64 and gp96 we showed that both RNA polymerases interact with the phage genome at the early stage of infection. Gp96 interacts with pre-early P23-45 genes, while gp64 interacts with pre-early, early and some middle-stage genes.

Organism:

Thermus thermophilus HB8

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32745

21 Samples

Download data: BEDGRAPH

(Submitter supplied) Transcription, the copying of genetic information into RNA, is accomplished by multi-subunit RNA polymerases (msRNAPs) in all living organisms. msRNAPs are highly conserved in evolution and invariantly share a ~400 kDa five-subunit catalytic core1,2. A group of hypothetical single-chain proteins of unknown function, present in various bacteria and bacteriophages, was predicted to be distantly related to msRNAPs, having diverged from them before the Last Universal Common Ancestor3. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21796

12 Samples

Download data: TXT

(Submitter supplied) Pseudomonas virus PA5oct has a large, linear, double-stranded DNA genome (286,783 bp) and is related to Escherichia phages 121Q/PBECO 4, Klebsiella phage vB_KleM-RaK2, Klebsiella phage K64-1, and Cronobacter phage vB_CsaM_GAP32. A protein-sharing network analysis highlights the conserved core genes within this clade. Combining hybrid genome sequencing, RNA-Seq and mass spectrometry analyses of its virion proteins allowed us to accurately identify genes and elucidate regulatory elements for this phage (ncRNAs, tRNAs and promoter elements). more...

Organism:

Pseudomonas aeruginosa PAO1; Pseudomonas virus PA5oct

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26557 GPL18782

13 Samples

Download data: FNA, GFF3, XLSX

(Submitter supplied) Whole-genome sequencing is an important way to understand the genetic information, gene function, biological characteristics, and living mechanisms of organisms. There is no difficulty to have mega-level genomes sequenced at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. The shotgun sequencing method failed to dissect this genome. After insisting for 10 years and going over 3 generations of sequencing techniques, we successfully dissected the PaP1 genome with 91,715 bp in length. more...

Organism:

Pseudomonas phage PaP1

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17610

1 Sample

Download data: CSV, GFF

(Submitter supplied) The global transcriptional profiles of Pseudomonas aeruginosa phages LUZ19, LUZ24, YuA, PAK_P3, 14-1 and phiKZ was obtained using the long read RNA sequencing technique ONT-cappable-seq. Using this approach we obtained a comprehensive genome-wide map of viral transcription start sites, terminators and transcription units.

Organism:

Pseudomonas aeruginosa

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL31946

12 Samples

Download data: NARROWPEAK

(Submitter supplied) We have isolated and characterized several bacteriophages infecting Pseudomonas aeruginosa distantly related to Felix O1 virus and proposed they form a new subfamily named Felixounavirinae. The infectious cycle of bacteriophages belonging to this subfamily has not been studied yet in terms of gene expression. The present study reports the RNA-Seq analysis of bacteriophage PAK_P3 infecting PAK strain of P. more...

Organism:

Pseudomonas aeruginosa; Pseudomonas phage PAK_P3

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21295 GPL18644

12 Samples

Download data: FASTA, TXT, XLS

(Submitter supplied) Large-genome bacteriophages (jumbo phages) of the Chimalliviriadae family assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and CRISPR/Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24583

8 Samples

Download data: BED, BW

(Submitter supplied) The 280-kB giant bacteriophage PHIKZ expresses hundreds of transcripts upon infection of Pseudomonas aeruginosa. To illuminate which transcripts are the very first and abundant ones, we extracted RNA after infection and sequenced the transcripts. The early expressed genes promise to be important for surpassing the host defence systems and to reprogram the host machinery towards phage replication. We discovered a number of transcripts that encode for proteins which we found in an independent study to be associated with large complexes. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23999

12 Samples

Download data: WIG

(Submitter supplied) We developed ONT-cappable-seq, a specialized long-read RNA sequencing technique that allows end-to-end sequencing of primary prokaryotic transcripts using the Nanopore sequencing platform. We applied ONT-cappable-seq to study the transcriptional landscape of Pseudomonas aeruginosa phage LUZ7, leading to a comprehensive genome-wide map of viral transcription start sites, terminators and complex operon structures that fine-regulate gene expression. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL31946

8 Samples

Download data: NARROWPEAK