(txid10665[Organism]) AND gds_sra[filter] - GEO DataSets

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Select item 2002535131.

Anti-viral defense by an ADP-ribosyltransferase that targets mRNA to block translation (RNA-Seq)

(Submitter supplied) Host-pathogen conflicts are crucibles of molecular innovation. Selection for immunity to pathogens has driven the evolution of sophisticated immunity mechanisms throughout biology, including in bacteria that must evade their viral predators known as bacteriophages. Here, we characterize a toxin-antitoxin-chaperone system, CmdTAC, in Escherichia coli that provides robust defense against infection by T4 phage. more...

Organism:: Escherichia coli; Escherichia phage T4

Type:: Expression profiling by high throughput sequencing

Platform:: GPL34102
8 Samples

Download data: CSV

Series

Accession:: GSE253513

ID:: 200253513

Select item 2002535122.

Anti-viral defense by an ADP-ribosyltransferase that targets mRNA to block translation (RIP-Seq in vivo)

Organism:: Escherichia coli; Escherichia phage T4

Type:: Other

Platform:: GPL34101
4 Samples

Download data: CSV

Series

Accession:: GSE253512

ID:: 200253512

Select item 2002535113.

Anti-viral defense by an ADP-ribosyltransferase that targets mRNA to block translation (RIP-Seq in vitro)

Organism:: Escherichia coli; Escherichia phage T4

Type:: Other

Platform:: GPL34101
2 Samples

Download data: CSV

Series

Accession:: GSE253511

ID:: 200253511

Select item 2002259734.

Direct enzymatic sequencing of 5-methylcytosine at single-base resolution [4]

(Submitter supplied) 5-methylcytosine (5mC) is the most important DNA modification in mammalian genomes as a lineage-defining mark dynamically altered in development and disease. The ideal method for 5mC localization would be both non-destructive of DNA and direct, without requiring inference based on detection of unmodified cytosines. Here, we present Direct Methylation Sequencing (DM-Seq), a bisulfite-free method for profiling 5mC at single-base resolution, using nanogram quantities of input DNA. more...

Organism:: Escherichia phage Lambda; Cloning vector pUC19; Escherichia phage T4

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL33181
8 Samples

Download data: BAM

Series

Accession:: GSE225973

ID:: 200225973

PubMed Full text in PMC Similar studies

Select item 2002259715.

Direct enzymatic sequencing of 5-methylcytosine at single-base resolution [3]

Organism:: Escherichia phage Lambda; Cloning vector pUC19; Escherichia phage T4

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL33181
19 Samples

Download data: BAM, TXT

Series

Accession:: GSE225971

ID:: 200225971

PubMed Full text in PMC Similar studies

Select item 2001462406.

Polysomes bypass a 50 nucleotide coding gap less efficiently than monosomes due to attenuation of an unstable 5’ mRNA stem loop stimulator and enhanced drop-off

(Submitter supplied) Ribosome profiling analysis of phage T4 infected E. coli yielded protected mRNA fragments within the normal size range derived from ribosomes stalled at the take-off codon. Ribosomes at this position also yielded some 53 nucleotide fragments, 16 longer. These were due to protection of the nucleotides that form the 5’ stem loop.

Organism:: Escherichia coli; Tequatrovirus T4

Type:: Other

Platforms:: GPL14548 GPL28207
4 Samples

Download data: TXT

Series

Accession:: GSE146240

ID:: 200146240

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001134257.

The bacteriophage T4 MotB protein, a DNA-binding protein, improves phage fitness

(Submitter supplied) Purpose: To investigated the role of MotB in T4 infections Method: NapIV NS were grown to a cell density of ~4 x 10^8 cells/mL (OD600 ~0.4) then infected with either wild-type T4D+ or T4motBam at a MOI of 10. RNA was isolated at 5 post-infection using method II of (Hinton 1989). rRNA subtraction was performed with the bacterial RiboMinus Kit (Ambion) according to manufacturer instructions. cDNA was prepared using the NEBNext strand specific kit (New England BioLabs) according to manufacturer instruction for libraries with 300-450 bp insert size with the following modifications. more...

Organism:: Tequatrovirus T4

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24733
6 Samples

Download data: CSV

Series

Accession:: GSE113425

ID:: 200113425

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001118088.

The E. coli global regulator DksA attenuates transcription during T4 infection

(Submitter supplied) Purpose: We investigated how deletion of DksA or ppGpp, two E. coli global transcription regulators, affects T4 infection. Method: B606, B606 DdksA, and B606 ppGpp0 were grown at 37C to early/mid log phase (OD600 ~ 0.4) then infected with moi of 10 of either wt T4 or T4motAam and total RNA was isolated. 2.5 µg total RNA from each sample was treated with a Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria; Illumina San Diego, CA) to deplete rRNA. more...