Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multiple-species sample

ABSTRACT: Suppression PCR-based selective enrichment sequencing for pathogen and antimicrobial resistance detection on cell-free DNA in sepsis

PROVIDER: PRJNA1100967 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28857900_1.fastq.gz	Fastqsanger.gz
	SRR28857901_1.fastq.gz	Fastqsanger.gz
	SRR28857902_1.fastq.gz	Fastqsanger.gz
	SRR28857903_1.fastq.gz	Fastqsanger.gz
	SRR28857904_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 21

Similar Datasets

Investigating PCR bias in TnSeq

Project description:As transposon sequencing (TnSeq) assays have become prolific in the microbiology field, it is of interest to scrutinize their potential drawbacks. TnSeq results are determined by counting transposon insertions following the PCR-based enrichment and subsequent deep sequencing of transposon insertions. Here we explore the possibility that PCR amplification of transposon insertions in a TnSeq library skews the results by introducing bias into the detection and/or enumeration of insertions. We compared the detection and frequency of mapped insertions when altering the number of PCR cycles in the enrichment step. In addition, we devised and validated a novel, PCR-free TnSeq method where the insertions are enriched via CRISPR/Cas9-targeted transposon cleavage and subsequent Oxford Nanopore sequencing. These PCR-based and PCR-free experiments demonstrate that, overall, PCR amplification does not significantly bias the results of the TnSeq assay insofar as insertions in the majority of genes represented in our library were similarly detected regardless of PCR cycle number and whether or not PCR amplification was employed. However, the detection of a small subset of genes which had been previously described as essential is indeed sensitive to the number of PCR cycles. We conclude that PCR-based enrichment of transposon insertions in a TnSeq assay is reliable but researchers interested in profiling essential genes should carefully weigh the number of amplification cycles employed in their library preparation protocols. In addition, we present a PCR-free TnSeq alternative that is comparable to traditional PCR-based methods although the latter remain superior owing to their accessibility and high sequencing depth.

2020-12-21 | GSE162988 | GEO

Bisulfite-free, nano-scale analysis of 5-hydroxymethylcytosine at single base resolution

Project description:High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites of small-scale samples represents a continuous challenge. Here, we present CATCH-seq, a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. CATCH-seq is based on selective 5hmC oxidation, labeling and subsequent C-to-T transition during PCR. Applications of CATCH-seq to nano-scale DNA samples reveal previously underappreciated non-CG 5hmCs in the hESC genome and base-resolution hydroxymethylome in human cell-free DNA.

2018-10-09 | GSE112048 | GEO

Integrated host-microbe metagenomics of cell-free nucleic acid for sepsis diagnosis in critically ill adults [plasma]

Project description:Here we developed a new approach to sepsis diagnosis that integrates host transcriptional profiling with metagenomic broad-range pathogen detection from cell-free plasma RNA and DNA.

2022-08-03 | GSE189401 | GEO

Integrated host-microbe metagenomics of cell-free nucleic acid for sepsis diagnosis in critically ill adults [paxgene]

2022-08-03 | GSE189400 | GEO

Deep subsurface sample

Project description:Bicarbonate metabolising microorganisms from deep granitic subsurface through selective enrichment

| PRJNA643233 | ENA

Deep subsurface sample

Project description:Methane metabolising microorganisms from deep granitic subsurface through selective enrichment

| PRJNA643974 | ENA

Activation of Thousands of Genes in the Lungs and Kidneys by Sepsis is Countered by the Selective Nuclear Blockade

Project description:The steady rise of sepsis globally has reached almost 49 million cases in 2017, and 11 million sepsis-related deaths. The genomic response to sepsis comprising multi-system stage of raging microbial inflammation has been reported in the whole blood, while effective treatment is lacking besides anti-microbial therapy and supportive measures. Here we show that, astoundingly, 6,237 significantly expressed genes in sepsis are increased or decreased in the lungs, the site of acute respiratory distress syndrome (ARDS). Moreover, 5,483 significantly expressed genes in sepsis are increased or decreased in the kidneys, the site of acute injury (AKI). This massive genomic response to polymicrobial sepsis is countered by the selective nuclear blockade with the cell-penetrating Nuclear Transport Checkpoint Inhibitor (NTCI). It controlled 3,735 sepsis-induced genes in the lungs and 1,951 sepsis-induced genes in the kidneys. The NTCI also reduced without antimicrobial therapy the bacterial dissemination: 18-fold in the blood, 11-fold in the lungs, and 9-fold in the spleen. This enhancement of bacterial clearance was not significant in the kidneys. Cumulatively, identification of the sepsis-responsive host’s genes and their control by the selective nuclear blockade advances a better understanding of the multi-system mechanism of sepsis. Moreover, it spurs much-needed new diagnostic, therapeutic, and preventive approaches.

2023-08-14 | GSE239388 | GEO

Deep subsurface sample

Project description:Organic carbon metabolising microorganisms from deep granitic subsurface through selective enrichment

| PRJNA644301 | ENA

Deep subsurface sample

Project description:Organic carbon metabolising microorganisms from deep granitic subsurface through selective enrichment

| PRJNA644302 | ENA

Deep subsurface sample

Project description:Polymeric carbon compound metabolizing microorganisms from deep granitic subsurface through selective enrichment

| PRJNA644915 | ENA