Imperial College : C. gattii Illumina resequencing project - WM276 - SRA

SRX213993: Imperial College : C. gattii Illumina resequencing project - WM276
1 ILLUMINA (Illumina HiSeq 2000) run: 11M spots, 2.2G bases, 1.3Gb downloads

Design: Genomic DNA from all 23 Cryptococcus gattii strains was isolated with the EpiCentre MasterPureTM Yeast DNA Purification Kit according to a modified version of the instruction manual. Briefly, the strains were grown in liquid YPD media for 24 h at 25°C rotating at 20 rpm. Cells from 3 ml of culture were harvested by centrifugation at 17,000 x g for 5 minutes. Cells were lysed in 300ul of Yeast Cell Lysis solution by mechanical disruption with 0.1 mm silica spheres (FastPrepTM Lysing Matrix, MP Biomedicals) twice for 30 seconds at 6,800 rpm in a Precellys®24 and incubation at 65°C for 15 minutes. Samples were cooled down on ice for 5 minutes and proteins removed by vortexing with 150ul of MPC Protein Precipitation Reagent and following centrifugation for 10 minutes at 17,000 x g. DNA was recovered with 500ul isopropanol and centrifugation at 17,000 x g for 10 minutes. DNA was purified by RNase A treatment for 60 minutes at 37C followed by phenol:chloroform extraction and ethanol precipitation. DNA yield and quality was determined by spectrophotometry. 2ug of genomic DNA were used for library preparation: DNA was fragmented to 150-500 bp using Covaris shearing and processed with the TruSeqTM DNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions. Purification steps were performed with Agencourt AMPureXP magnetic particles (Beckham Coulter) on a magnetic stand (AmBio). Whole genomes were sequenced on an Illumina HiSeq2000 at the MRC Clinical Science Centre, Imperial College London (UK).

Submitted by: IMPERIAL COLLEGE

Study: DNAseq of Cryptococcus gattii VGI, VGII, VGIII and VGIV (Farrer et al 2016)

PRJNA183619 • SRP017762 • All experiments • All runs

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To decipher the regulation of cryptococcal hypervirulence, we combined comparative whole genome sequencing with extensive phenotypic testing of both outbreak and non-outbreak strains.

Sample: Generic sample from C. gattii

SAMN01830690 • SRS383007 • All experiments • All runs

Organism: Cryptococcus gattii WM276

Library:

Instrument: Illumina HiSeq 2000

Strategy: WGS

Source: GENOMIC

Selection: RANDOM

Layout: PAIRED

Spot descriptor:

1 forward101 reverse

Runs: 1 run, 11M spots, 2.2G bases, 1.3Gb

Run	# of Spots	# of Bases	Size	Published
SRR643918	10,956,792	2.2G	1.3Gb	2013-12-20

ID:: 293191

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Sequence Read Archive

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