6SM6_TTGCAGATCA
tick metagenome
field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms
host
Ixodes scapularis
isolation_source
riparian corridor of eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs
collection_date
2013-10-08
geo_loc_name
USA:Illinois,DuPage,Churchill Woods Forest Preserve,Babcock Grove
lat_lon
41.891272 N 88.045424 W
ref_biomaterial
primary publication
samp_collect_device
Ticks were collected by dragging using a 1 meter square cloth and stored in 70% ethanol.
samp_mat_process
Individual ticks were rinsed in 70% ethanol, air dried, and homogenized using a TissueLyzer II (Qiagen, Germantown, MD) in 2 ml deep-well 96-well plates at 25 Hz for 2 x 3 minutes. Each well contained a 5 ml steel bead (Qiagen) and 50 μl genomic digestion buffer. DNA was extracted with Invitrogen's PureLink Pro 96 kit (Fisher Scientific, Suwanee, GA) per manufacturer's protocol and eluted in 70 μl elution buffer. Proteinase K digestion was performed overnight. DNA was quantified on a Qubit 2.0 (Life Technologies) using High Sensitivity DNA Kit. Samples containing sufficient DNA were sent for high throughput sequencing. 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.
source_material_id
TTGCAGATCA
host_life_stage
adult
host_tissue_sampled
whole body
BioSampleModel
Metagenome or environmental