Multiple genetic variants of piscine Cryptosporidium spp. were charac... - SRA

SRX1961439: Multiple genetic variants of piscine Cryptosporidium spp. were characterized by next-generation-sequencing, starting from total genomic preparations of fish gastrointestinal scrapings.
1 ION_TORRENT (Ion Torrent PGM) run: 45,653 spots, 10.7M bases, 7.4Mb downloads

Design: Template emulsion PCR and enrichment were performed according to the manufacturers recommendations on the One-Touch 2 and One-Touch ES instruments (Life Technologies, USA). Sequencing was performed on an Ion Torrent PGM (Life Technologies, USA) using the Ion PGM Sequencing 400 Kit and 316-V2 semiconductor chips, following the manufacturers recommendations. Fusion primers (IDT, USA) were based on the secondary primers 18SiF and 18SiR [11] and ActinallF2 and ActinallR1, and included unique sample-specific barcodes (MID tags) and P1 and A adaptors. All PCR amplicons were double purified using the Agencourt AMPure XP Bead PCR purification protocol (Beckman Coulter Genomics, USA), pooled in roughly equimolar ratios after Qubit fluorometric quantitations (Thermo Fisher Scientific, USA) and sequenced. Multiple genetic variants of piscine Cryptosporidium spp. were characterized by next-generation-sequencing, starting from total genomic preparations of fish gastrointestinal scrapings. Targeted locus: Actin. Sequencing approach: Amplicon sequencing.

Submitted by: Murdoch University

Study: Multiple genetic variants of piscine Cryptosporidium spp. were characterized by next-generation-sequencing, starting from total genomic preparations of fish gastrointestinal scrapings. Targeted loci

PRJNA326557 • SRP078383 • All experiments • All runs

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Multiple genetic variants of piscine Cryptosporidium spp. were characterized by next-generation-sequencing, starting from total genomic preparations of fish gastrointestinal scrapings. Molecular taxonomic identifications from NGS data were achieved by BLAST searches using public (NCBI GenBank) and in-house (curated) databases. NGS-based taxonomic identifications were also compared to more conventional analyses based on PCR-Sanger sequencing.The objective was to compare the two approaches to resolve the systematics of piscine Cryptosporidium spp. and to resolve multiple infections.

Sample:

SAMN05383671 • SRS1571352 • All experiments • All runs

Organism: Paracanthurus hepatus

Library:

Name: CT_IT_Lib08

Instrument: Ion Torrent PGM

Strategy: AMPLICON

Source: GENOMIC

Selection: PCR

Layout: PAIRED

Runs: 1 run, 45,653 spots, 10.7M bases, 7.4Mb

Run	# of Spots	# of Bases	Size	Published
SRR3932024	45,653	10.7M	7.4Mb	2016-07-22

ID:: 2823043

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