SRS8337564 SAMN17287745 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source longleaf pine (Pinus palustris) habitats with grassy understory, with a recent history of fire management using prescribed burns collection_date 2017-07-21 geo_loc_name USA:Florida,Bay,Tyndall Air Force Base lat_lon 30.08 N 85.58 W ref_biomaterial primary publication samp_collect_device Ticks were collected with a carbon dioxide trap and stored in 70% ethanol. samp_mat_process 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. source_material_id GTGTGGTTGT host_life_stage adult host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337565 SAMN17287677 1595979 tick metagenome presumptive positive control bioproject 691281 PRJNA691281 host Amblyomma sp. isolation_source homo sapiens blood collection_date missing geo_loc_name missing lat_lon missing ref_biomaterial primary publication samp_collect_device missing samp_mat_process missing source_material_id TATAGCACGCa host_life_stage missing host_tissue_sampled missing BioSampleModel Metagenome or environmental SRS8337566 SAMN17287746 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source longleaf pine (Pinus palustris) habitats with grassy understory, with a recent history of fire management using prescribed burns collection_date 2017-07-21 geo_loc_name USA:Florida,Bay,Tyndall Air Force Base lat_lon 30.08 N 85.58 W ref_biomaterial primary publication samp_collect_device Ticks were collected with a carbon dioxide trap and stored in 70% ethanol. samp_mat_process 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. source_material_id TGTTACGATC host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337573 SAMN17287682 1595979 tick metagenome presumptive positive control bioproject 691281 PRJNA691281 host Ixodidae isolation_source missing collection_date missing geo_loc_name missing lat_lon missing ref_biomaterial primary publication samp_collect_device missing samp_mat_process missing source_material_id CTTAGTTCGC host_life_stage missing host_tissue_sampled missing BioSampleModel Metagenome or environmental SRS8337578 SAMN17287676 1595979 tick metagenome presumptive positive control bioproject 691281 PRJNA691281 host Amblyomma sp. isolation_source homo sapiens blood collection_date missing geo_loc_name missing lat_lon missing ref_biomaterial primary publication samp_collect_device missing samp_mat_process missing source_material_id CATGATACGC host_life_stage missing host_tissue_sampled missing BioSampleModel Metagenome or environmental SRS8337582 SAMN17287751 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source longleaf pine (Pinus palustris) habitats with grassy understory, with a recent history of fire management using prescribed burns collection_date 2017-07-21 geo_loc_name USA:Florida,Bay,Tyndall Air Force Base lat_lon 30.08 N 85.58 W ref_biomaterial primary publication samp_collect_device Ticks were collected with a carbon dioxide trap and stored in 70% ethanol. samp_mat_process 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. source_material_id CAGATGTCCT host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337592 SAMN17287698 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Dermacentor variabilis isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-07 geo_loc_name USA:Illinois,Mason lat_lon 40.1603 N 89.6025 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 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. source_material_id CTGTAGTGCG host_life_stage adult host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337594 SAMN17287686 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2010-06-17 geo_loc_name USA:Missouri,Franklin/Washington,Little Indian Creek lat_lon 38.205139 N 90.934118 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 A 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. After tick homogenization in 80 µl (nymphs) or 100 µl (adults) 5% chelex, samples were incubated 20 min at 56 degrees Celsius, followed by an eight minute boil, and centrifugation at 4000xg for 7 minutes. Multiplex PCR followed by RLB was then performed as in Fredericks et al. (2016). Due to the requirement of purified DNA for Fluidigm analysis, a standard phenol-chloroform extraction with subsequent ethanol precipitation was done. 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 TGTGCTCGCA host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337593 SAMN17287699 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-07 geo_loc_name USA:Illinois,Mason lat_lon 40.1603 N 89.6025 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 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. source_material_id TCAGATGCTA host_life_stage adult host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337591 SAMN17287685 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Dermacentor variabilis isolation_source longleaf pine (Pinus palustris) habitats with grassy understory, with a recent history of fire management using prescribed burns collection_date 2012-06-29 geo_loc_name USA:Illinois,Piatte lat_lon 39.99962 N 88.56735 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 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. source_material_id GTCATGCGTC host_life_stage adult host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337590 SAMN17287697 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Dermacentor variabilis isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-07 geo_loc_name USA:Illinois,Mason lat_lon 40.1603 N 89.6025 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 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. source_material_id CTGTGTCGTC host_life_stage adult host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337589 SAMN17287684 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Dermacentor variabilis isolation_source longleaf pine (Pinus palustris) habitats with grassy understory, with a recent history of fire management using prescribed burns collection_date 2012-06-29 geo_loc_name USA:Illinois,Piatte lat_lon 39.99962 N 88.56735 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 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. source_material_id CGTATCTCGA host_life_stage adult host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337588 SAMN17287752 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source longleaf pine (Pinus palustris) habitats with grassy understory, with a recent history of fire management using prescribed burns collection_date 2017-07-21 geo_loc_name USA:Florida,Bay,Tyndall Air Force Base lat_lon 30.08 N 85.58 W ref_biomaterial primary publication samp_collect_device Ticks were collected with a carbon dioxide trap and stored in 70% ethanol. samp_mat_process 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. source_material_id TTCGATAGCA host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337587 SAMN17287704 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-07 geo_loc_name USA:Illinois,Mason lat_lon 40.1603 N 89.6025 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 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. source_material_id CTATACAGTG host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337586 SAMN17287689 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Ixodes scapularis isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-05-22 geo_loc_name USA:Illinois,Lee,Richardson Wildlife Foundation,Beaver Woods lat_lon 41.70734 N 89.186780 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 A 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. After tick homogenization in 80 µl (nymphs) or 100 µl (adults) 5% chelex, samples were incubated 20 min at 56 degrees Celsius, followed by an eight minute boil, and centrifugation at 4000xg for 7 minutes. Multiplex PCR followed by RLB was then performed as in Fredericks et al. (2016). Due to the requirement of purified DNA for Fluidigm analysis, a standard phenol-chloroform extraction with subsequent ethanol precipitation was done. 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 GCTGACAGAG host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337585 SAMN17287703 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-07 geo_loc_name USA:Illinois,Mason lat_lon 40.1603 N 89.6025 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 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. source_material_id TATGTACGTG host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337584 SAMN17287688 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2010-06-17 geo_loc_name USA:Missouri,Franklin/Washington,Little Indian Creek lat_lon 38.205139 N 90.934118 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 A 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. After tick homogenization in 80 µl (nymphs) or 100 µl (adults) 5% chelex, samples were incubated 20 min at 56 degrees Celsius, followed by an eight minute boil, and centrifugation at 4000xg for 7 minutes. Multiplex PCR followed by RLB was then performed as in Fredericks et al. (2016). Due to the requirement of purified DNA for Fluidigm analysis, a standard phenol-chloroform extraction with subsequent ethanol precipitation was done. 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 CTATGCGATC host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337605 SAMN17287744 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source longleaf pine (Pinus palustris) habitats with grassy understory, with a recent history of fire management using prescribed burns collection_date 2017-07-21 geo_loc_name USA:Florida,Bay,Tyndall Air Force Base lat_lon 30.08 N 85.58 W ref_biomaterial primary publication samp_collect_device Ticks were collected with a carbon dioxide trap and stored in 70% ethanol. samp_mat_process 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. source_material_id GTGGAGAGCT host_life_stage adult host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337583 SAMN17287687 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2010-06-17 geo_loc_name USA:Missouri,Franklin/Washington,Little Indian Creek lat_lon 38.205139 N 90.934118 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 A 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. After tick homogenization in 80 µl (nymphs) or 100 µl (adults) 5% chelex, samples were incubated 20 min at 56 degrees Celsius, followed by an eight minute boil, and centrifugation at 4000xg for 7 minutes. Multiplex PCR followed by RLB was then performed as in Fredericks et al. (2016). Due to the requirement of purified DNA for Fluidigm analysis, a standard phenol-chloroform extraction with subsequent ethanol precipitation was done. 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 GCTACTAGCG host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337581 SAMN17287750 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source longleaf pine (Pinus palustris) habitats with grassy understory, with a recent history of fire management using prescribed burns collection_date 2017-07-21 geo_loc_name USA:Florida,Bay,Tyndall Air Force Base lat_lon 30.08 N 85.58 W ref_biomaterial primary publication samp_collect_device Ticks were collected with a carbon dioxide trap and stored in 70% ethanol. samp_mat_process 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. source_material_id TAGCTTCACT host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337580 SAMN17287702 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-07 geo_loc_name USA:Illinois,Mason lat_lon 40.1603 N 89.6025 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 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. source_material_id GATGCGAGCT host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337579 SAMN17287701 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-07 geo_loc_name USA:Illinois,Mason lat_lon 40.1603 N 89.6025 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 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. source_material_id TATCAGTCTG host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337577 SAMN17287679 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Ixodes scapularis isolation_source on unidentified bird captured in eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2013-05-10 geo_loc_name USA:Illinois,Champaign lat_lon 40.116329 N 88.243523 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 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. source_material_id TCAGCGATAT host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337576 SAMN17287696 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-07 geo_loc_name USA:Illinois,Mason lat_lon 40.1603 N 89.6025 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 A 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. After tick homogenization in 80 µl (nymphs) or 100 µl (adults) 5% chelex, samples were incubated 20 min at 56 degrees Celsius, followed by an eight minute boil, and centrifugation at 4000xg for 7 minutes. Multiplex PCR followed by RLB was then performed as in Fredericks et al. (2016). Due to the requirement of purified DNA for Fluidigm analysis, a standard phenol-chloroform extraction with subsequent ethanol precipitation was done. 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 GTAATGGAGT host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337575 SAMN17287683 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Ixodes scapularis isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2013-05-25 geo_loc_name USA:Illinois,DuPage,Hidden Lake Forest Preserve lat_lon 41.82786 N 88.04059 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 A 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. After tick homogenization in 80 µl (nymphs) or 100 µl (adults) 5% chelex, samples were incubated 20 min at 56 degrees Celsius, followed by an eight minute boil, and centrifugation at 4000xg for 7 minutes. Multiplex PCR followed by RLB was then performed as in Fredericks et al. (2016). Due to the requirement of purified DNA for Fluidigm analysis, a standard phenol-chloroform extraction with subsequent ethanol precipitation was done. 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 TGTAGGTGGA host_life_stage adult host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337574 SAMN17287749 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source longleaf pine (Pinus palustris) habitats with grassy understory, with a recent history of fire management using prescribed burns collection_date 2017-07-21 geo_loc_name USA:Florida,Bay,Tyndall Air Force Base lat_lon 30.08 N 85.58 W ref_biomaterial primary publication samp_collect_device Ticks were collected with a carbon dioxide trap and stored in 70% ethanol. samp_mat_process 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. source_material_id CAGGCTCAGT host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337572 SAMN17287681 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Ixodes scapularis isolation_source on unidentified bird captured in eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2013-05-10 geo_loc_name USA:Illinois,Champaign lat_lon 40.116329 N 88.243523 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 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. source_material_id GTAGTACACA host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337571 SAMN17287675 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Ixodes scapularis isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2013-05-24 geo_loc_name USA:Illinois,DuPage,Danada Forest Preserve lat_lon 42.45951 N 89.15274 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 A 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. After tick homogenization in 80 µl (nymphs) or 100 µl (adults) 5% chelex, samples were incubated 20 min at 56 degrees Celsius, followed by an eight minute boil, and centrifugation at 4000xg for 7 minutes. Multiplex PCR followed by RLB was then performed as in Fredericks et al. (2016). Due to the requirement of purified DNA for Fluidigm analysis, a standard phenol-chloroform extraction with subsequent ethanol precipitation was done. 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 CGACGCTGAT host_life_stage adult host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337570 SAMN17287694 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-07 geo_loc_name USA:Illinois,Mason lat_lon 40.1603 N 89.6025 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 A 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. After tick homogenization in 80 µl (nymphs) or 100 µl (adults) 5% chelex, samples were incubated 20 min at 56 degrees Celsius, followed by an eight minute boil, and centrifugation at 4000xg for 7 minutes. Multiplex PCR followed by RLB was then performed as in Fredericks et al. (2016). Due to the requirement of purified DNA for Fluidigm analysis, a standard phenol-chloroform extraction with subsequent ethanol precipitation was done. 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 ATCTAGATCA host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337569 SAMN17287748 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source longleaf pine (Pinus palustris) habitats with grassy understory, with a recent history of fire management using prescribed burns collection_date 2017-07-21 geo_loc_name USA:Florida,Bay,Tyndall Air Force Base lat_lon 30.08 N 85.58 W ref_biomaterial primary publication samp_collect_device Ticks were collected with a carbon dioxide trap and stored in 70% ethanol. samp_mat_process 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. source_material_id GGTCGTGCAT host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337568 SAMN17287674 1595979 tick metagenome presumptive positive control bioproject 691281 PRJNA691281 host Ixodes sp. isolation_source cell culture collection_date missing geo_loc_name missing lat_lon missing ref_biomaterial primary publication samp_collect_device missing samp_mat_process missing source_material_id GTCGTCGTCT host_life_stage missing host_tissue_sampled missing BioSampleModel Metagenome or environmental SRS8337567 SAMN17287747 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source longleaf pine (Pinus palustris) habitats with grassy understory, with a recent history of fire management using prescribed burns collection_date 2017-07-21 geo_loc_name USA:Florida,Bay,Tyndall Air Force Base lat_lon 30.08 N 85.58 W ref_biomaterial primary publication samp_collect_device Ticks were collected with a carbon dioxide trap and stored in 70% ethanol. samp_mat_process 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. source_material_id GTCTTGGCTC host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337595 SAMN17287690 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Ixodes scapularis isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-13 geo_loc_name USA:Illinois,Lee,Richardson Wildlife Foundation,Bunting Woods lat_lon 41.70734 N 89.186780 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 A 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. After tick homogenization in 80 µl (nymphs) or 100 µl (adults) 5% chelex, samples were incubated 20 min at 56 degrees Celsius, followed by an eight minute boil, and centrifugation at 4000xg for 7 minutes. Multiplex PCR followed by RLB was then performed as in Fredericks et al. (2016). Due to the requirement of purified DNA for Fluidigm analysis, a standard phenol-chloroform extraction with subsequent ethanol precipitation was done. 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 TTAGTGGTGA host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337596 SAMN17287705 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-07 geo_loc_name USA:Illinois,Mason lat_lon 40.1603 N 89.6025 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 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. source_material_id TGATACTCTG host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337597 SAMN17287680 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Ixodes scapularis isolation_source on unidentified bird captured in eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2013-05-10 geo_loc_name USA:Illinois,Champaign lat_lon 40.116329 N 88.243523 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 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. source_material_id CTACTGATGA host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337598 SAMN17287691 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-07 geo_loc_name USA:Illinois,Mason lat_lon 40.1603 N 89.6025 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 A 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. After tick homogenization in 80 µl (nymphs) or 100 µl (adults) 5% chelex, samples were incubated 20 min at 56 degrees Celsius, followed by an eight minute boil, and centrifugation at 4000xg for 7 minutes. Multiplex PCR followed by RLB was then performed as in Fredericks et al. (2016). Due to the requirement of purified DNA for Fluidigm analysis, a standard phenol-chloroform extraction with subsequent ethanol precipitation was done. 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 GTTGATGAGT host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337599 SAMN17287753 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source longleaf pine (Pinus palustris) habitats with grassy understory, with a recent history of fire management using prescribed burns collection_date 2017-07-21 geo_loc_name USA:Florida,Bay,Tyndall Air Force Base lat_lon 30.08 N 85.58 W ref_biomaterial primary publication samp_collect_device Ticks were collected with a carbon dioxide trap and stored in 70% ethanol. samp_mat_process 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. source_material_id GTCTAGCAGG host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337600 SAMN17287692 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-07 geo_loc_name USA:Illinois,Mason lat_lon 40.1603 N 89.6025 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 A 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. After tick homogenization in 80 µl (nymphs) or 100 µl (adults) 5% chelex, samples were incubated 20 min at 56 degrees Celsius, followed by an eight minute boil, and centrifugation at 4000xg for 7 minutes. Multiplex PCR followed by RLB was then performed as in Fredericks et al. (2016). Due to the requirement of purified DNA for Fluidigm analysis, a standard phenol-chloroform extraction with subsequent ethanol precipitation was done. 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 TGTTGTGGTA host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337601 SAMN17287700 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-07 geo_loc_name USA:Illinois,Mason lat_lon 40.1603 N 89.6025 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 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. source_material_id CAGTCAGAGT host_life_stage adult host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337602 SAMN17287706 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Haemaphysalis leporispalustris isolation_source on Zonotrichia albicollis captured in eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-10-12 geo_loc_name USA:Illinois,Champaign lat_lon 40.116329 N 88.243523 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 A 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. After tick homogenization in 80 µl (nymphs) or 100 µl (adults) 5% chelex, samples were incubated 20 min at 56 degrees Celsius, followed by an eight minute boil, and centrifugation at 4000xg for 7 minutes. Multiplex PCR followed by RLB was then performed as in Fredericks et al. (2016). Due to the requirement of purified DNA for Fluidigm analysis, a standard phenol-chloroform extraction with subsequent ethanol precipitation was done. 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 TGATGTATGT host_life_stage larva host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337603 SAMN17287693 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Amblyomma americanum isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-07 geo_loc_name USA:Illinois,Mason lat_lon 40.1603 N 89.6025 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 A 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. After tick homogenization in 80 µl (nymphs) or 100 µl (adults) 5% chelex, samples were incubated 20 min at 56 degrees Celsius, followed by an eight minute boil, and centrifugation at 4000xg for 7 minutes. Multiplex PCR followed by RLB was then performed as in Fredericks et al. (2016). Due to the requirement of purified DNA for Fluidigm analysis, a standard phenol-chloroform extraction with subsequent ethanol precipitation was done. 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 GATCGTCTCT host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental SRS8337604 SAMN17287707 1595979 tick metagenome field collected tick tested for the presence of one or more pathogenic or potentially pathogenic tick-borne microorganisms bioproject 691281 PRJNA691281 host Ixodes scapularis isolation_source eastern deciduous forests usually dominated by oak and hickory with variable understory vegetation frequently including or dominated by invasive shrubs collection_date 2012-06-06 geo_loc_name USA:Illinois,Peoria lat_lon 40.694592 N 89.590363 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 A 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. After tick homogenization in 80 µl (nymphs) or 100 µl (adults) 5% chelex, samples were incubated 20 min at 56 degrees Celsius, followed by an eight minute boil, and centrifugation at 4000xg for 7 minutes. Multiplex PCR followed by RLB was then performed as in Fredericks et al. (2016). Due to the requirement of purified DNA for Fluidigm analysis, a standard phenol-chloroform extraction with subsequent ethanol precipitation was done. 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 CATAGACGTG host_life_stage nymph host_tissue_sampled whole body BioSampleModel Metagenome or environmental