Whole genome sequencing of S. Typhimurium: stools - SRA

SRX1741516: Whole genome sequencing of S. Typhimurium: stools
1 ILLUMINA (Illumina HiSeq 1000) run: 2M spots, 395.7M bases, 144.4Mb downloads

Design: A 100 bp paired-end library (200 cycles) was prepared for each purified DNA sample using the NexteraXT kit (Illumina). Each of the DNA samples was indexed using the Nextera XT index kit v2 Set A (Illumina) then pooled and sequenced on the HiSeq platform (Illumina, Inc, San Diego, CA, USA) using a single lane of a HiSeq flow cell. Quality control of the libraries was performed by assessing library size distribution on an Agilent 2200 Tapestation (fragment sizes typically range between 250 – 1000 bp) and libraries were quantified by real time PCR using the KAPA library quantification kit according to the manufacturer’s protocol (Kapa Biosystems).

Submitted by: CIDM-Public Health, Institute of Clinical Pathology and Medical Research, Pathology West, NSW Health Pathology, Australia (CIDM-Public Health, Institute of Clinical Patholog)

Study: Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014

PRJNA320449 • SRP074336 • All experiments • All runs

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This study was to examine the utility of whole genome sequencing in discriminating sporadic and outbreak-linked Salmonella Typhimurium infections within the same endemic MLVA type. This has the potential to improve the accuracy of cluster definitions and timeliness of outbreak response.

Sample:

SAMN04939488 • SRS1421078 • All experiments • All runs

Organism: Salmonella enterica subsp. enterica serovar Typhimurium

Library:

Name: 54_N4956

Instrument: Illumina HiSeq 1000

Strategy: WGS

Source: GENOMIC

Selection: RANDOM

Layout: PAIRED

Runs: 1 run, 2M spots, 395.7M bases, 144.4Mb

Run	# of Spots	# of Bases	Size	Published
SRR3476832	1,978,516	395.7M	144.4Mb	2016-05-10

ID:: 2497322

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