SAMN18586823
External Id
University of Illinois at Urbana-Champaign
INSDC center name
2022-04-01T00:57:15.397Z
INSDC first public
2022-04-01T00:57:15.397Z
INSDC last update
SRS8662564
INSDC secondary accession
live
INSDC status
Metagenome or environmental
NCBI submission model
Metagenome.environmental.1.0
NCBI submission package
SRS8662564
SRA accession
2018-08-23
collection date
field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms
description
USA:Georgia,Richmond,Fort Gordon
geo loc name
Amblyomma americanum
host
nymph
host life stage
whole body
http://purl.obolibrary.org/obo/BTO_0001489
host_tissue_sampled
longleaf pine (Pinus palustris) habitats with grassy understory, with a recent history of fire management using prescribed burns
isolation source
33.3591 N 82.2254 W
lat lon
tick metagenome
http://purl.obolibrary.org/obo/NCBITaxon_1595979
organism
primary publication
ref_biomaterial
Individual ticks were rinsed in 70% ethanol and air dried. Ticks were homogenized in 2 ml microcentrifuge tubes for 2 minutes in 30 μl digestion buffer (10 mM Tris HCl, ph 8; 5 mM EDTA; 100 mM NaCl; 0.2% SDS; 2 mg/ml protease K) followed by a quick centrifugation, and another 3 minute homogenization. After addition of 170 μl digestion buffer, samples were incubated over night at 56 degrees Celsius for protein digestion. DNA was extracted in 600 μl, after addition of 10 mM Tris buffer, using a standard phenol-chloroform protocol with the phenol-chloroform-isoamyl alcohol buffered for DNA. After ethanol precipitation (glycogen, but no additional salt added), samples were re-suspended in 30 μl elution buffer and stored at -20 degrees Celsius. DNA samples were quantified on a Qubit 2.0 (Life Technologies) using the Qubit dsDNA HS Assay Kit. Gene target regions were amplified using Fluidigm and sequenced using Illumina® HiSeq Rapid sequencing kit version 2 on a HiSeq 2500 sequencer (Illumina®, San Diego, CA, USA) at the W. M. Keck Center for Comparative and Functional Genomics at the University of Illinois at Urbana-Champaign as described previously (Muturi et al., 2016; doi:10.1186/s13071-016-1299-6). Briefly, sample DNA was amplified on the Fluidigm® microfluidics PCR platform with appropriate linkers and sample barcodes. The final Fluidigm® products were pooled in equimolar ratio for sequencing and spiked with 10% non-indexed PhiX control library (Illumina®) and sequenced by 2 x 250 nt paired-end sequencing on the Illumina® HiSeq® Rapid system. Fastq files were generated with the bcl2fastq v2.17.1.14 Conversion Software (Illumina®). Finally, the raw reads were demultiplexed by primer and by sample with the Fluidigm® demultiplexing pipeline v 2.0.
samp mat process
Ticks were collected with a carbon dioxide trap and stored in 70% ethanol.
samp_collect_device
TAGAGTCTGT
source_material_id
GW1DTAN13_TAGAGTCTGT
title