| Attributes |
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collection_date
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2017-06-16
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ref_biomaterial
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primary publication
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source_material_id
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ATCGCATAGA
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host
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Amblyomma americanum
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geo_loc_name
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USA:Florida,Clay,Camp Blanding Army Base
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samp_mat_process
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Individual ticks were rinsed in 70% ethanol and air dried. Ticks were homogenized in 2 ml microcentrifuge tubes for 2 minutes in 30 ��l 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 ��l digestion buffer, samples were incubated over night at 56 degrees Celsius for protein digestion. DNA was extracted in 600 ��l, 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 ��l 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.
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host_life_stage
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nymph
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lat_lon
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29.95 N 81.98 W
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host_tissue_sampled
|
whole body
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samp_collect_device
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Ticks were collected with a carbon dioxide trap and stored in 70% ethanol.
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isolation_source
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longleaf pine (Pinus palustris) habitats with grassy understory, with a recent history of fire management using prescribed burns
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