Genome sequencing of Escherichia coli O121 str. RM8352 - SRA

SRX4679023: Genome sequencing of Escherichia coli O121 str. RM8352
1 ILLUMINA (Illumina MiSeq) run: 772,778 spots, 387M bases, 237.1Mb downloads

Design: Illumina libraries were prepared for all strains using the KAPA Low-Throughput Library Preparation Kit with Standard PCR Amplification Module (Kapa Biosystems, Wilmington, MA), following manufacturer's instructions except for the following changes: 750 ng DNA was sheared at 30 psi for 40 s and size selected to 700-770 bp following Illumina protocols. Standard desalting TruSeq LT and PCR Primers were ordered from Integrated DNA Technologies (Coralville, IA) and used at 0.375 and 0.5 M final concentrations, respectively. PCR was reduced to 3-5 cycles. Libraries were quantified using the KAPA Library Quantification Kit (Kapa), except with 10 l volume and 90-s annealing/extension PCR, then pooled and normalized to 4 nM. Pooled libraries were requantified by ddPCR on a QX200 system (Bio-Rad), using the Illumina TruSeq ddPCR Library Quantification Kit and following manufacturer's protocols, except with an extended 2-min annealing/extension time. The libraries were sequenced 2 250 bp paired end v2 on a MiSeq instrument (Illumina) at 13.5 pM, following manufacturer's protocols.

Submitted by: United States Department of Agriculture, Agricultural Research Service

Study: Escherichia coli O121 str. RM8352 genome sequencing

PRJNA69933 • SRP161717 • All experiments • All runs

show Abstracthide Abstract

The rise in foodborne-related outbreaks of non O157 shiga-toxin producing E. coli (STECs) emphasizes the importance of developing improved methods to rapidly detect and characterize STECs. The major serovars of STEC associated with illness have been O26, O111, O103, O121, O45, and O145, accounting for 25-50% of human illness caused by STECs and, in some cases, severe illness comparable to illness caused by E. coli O157:H7. Sequencing of STECs from the agriculturally important region of the California central coast will address the diversity of genomic content and physiology of STECs compared to E. coli O157.

Sample: Pathogen: environmental/food/other sample from Escherichia coli

SAMN08724618 • SRS3772816 • All experiments • All runs

Organism: Escherichia coli O121 str. RM8352

Library:

Name: Ec08352_S12_L001

Instrument: Illumina MiSeq

Strategy: WGS

Source: GENOMIC

Selection: RANDOM

Layout: PAIRED

Runs: 1 run, 772,778 spots, 387M bases, 237.1Mb

Run	# of Spots	# of Bases	Size	Published
SRR7828054	772,778	387M	237.1Mb	2018-09-13

ID:: 6338396

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Sequence Read Archive

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