Genomic sequencing reads from the Plasmodium knowlesi H(AW) reference... - SRA

SRX1175910: Genomic sequencing reads from the Plasmodium knowlesi H(AW) reference strain
1 ILLUMINA (Illumina HiSeq 2500) run: 11.6M spots, 2.3G bases, 1.5Gb downloads

Design: Clonal parasites were grown in Rhesus blood that was washed and layered on Lymphoprep (TM) to remove white blood cells. DNA was prepared using the Qiagen DNeasy blood and tissue kit following the manufacturer's instructions. Library construction and sequencing were preformed at the Broad Institute, Cambridge, MA, USA. Illumina fragment libraries were generated as previously described (PMID: 18987734) with the following modifications. For each sample, 100 ng of genomic DNA was sheared to 200 bp in size using a Covaris LE220 instrument (Covaris, MA) with the following parameters: temperature: 7–9 °C; duty cycle: 20%; intensity: 5; cycles per burst: 200; time: 90 s; shearing tubes: Crimp Cap microTUBES with AFA fibers Covaris, MA). DNA fragments were end repaired, 3’ adenylated, ligated with indexed Illumina sequencing adapter, and PCR enriched, as previously described (PMID: 21205303). The resulting Illumina fragment sequencing libraries were normalized and were size selected to contain inserts of 180 bp ± 3% in length using a Pippen Prep system (Sage Science, MA) following the manufacturer’s recommendations. Illumina sequencing libraries were quantified using quantitative PCR (KAPA Biosystems, MA) following the manufacturer’s recommendations. Libraries were normalized to 2 nM and denatured using 0.1 N NaOH. Sequencing Flowcell cluster amplification was performed according to the manufacturer’s recommendations using the V3 TruSeq PE Cluster Kit and V3 TruSeq Flowcells (Illumina, CA). Flowcells were sequenced with 101 base paired end reads on a Illumina HiSeq2500 instrument, using V3 TruSeq Sequencing by synthesis kits and analyzed with the Illumina RTA v1.12 pipeline (Illumina, CA).

Submitted by: Harvard T.H.Chan School of Public Health

Study: Plasmodium knowlesi Raw sequence reads

PRJNA294104 • SRP063014 • All experiments • All runs

show Abstracthide Abstract

The Apicomplexan Plasmodium knowlesi is the causative agent of malaria-like disease in macaques, and passes through a mosquito vector. Human beings bit by infected mosquitos may on occassion be infected with Plasmodium knowlesi and become severely ill. Four Plasmodium strains and the reference strain have been sequenced to establish a background for understanding transmission of the parasite to humans.

Sample: Plasmodium knowlesi H(AW) substrain of the reference strain Plasmodium knowlesi H

SAMN04018698 • SRS1050839 • All experiments • All runs

Organism: Plasmodium knowlesi

Library:

Name: H(AW)

Instrument: Illumina HiSeq 2500

Strategy: WGS

Source: GENOMIC

Selection: RANDOM

Layout: PAIRED

Spot descriptor:

1 forward102 reverse

Links:

NCBI link: NCBI Entrez (PUBMED)

Runs: 1 run, 11.6M spots, 2.3G bases, 1.5Gb

Run	# of Spots	# of Bases	Size	Published
SRR2222335	11,568,000	2.3G	1.5Gb	2015-10-05

ID:: 1707064

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