title: OP34GRUN1_TACGTATAGC_L1
organism: tick metagenome
attributes.tag: strain
attributes.value: not applicable
attributes.tag: isolate
attributes.value: OP34GRUN1
attributes.tag: collection_date
attributes.value: 2015-09-24
attributes.tag: env_biome
attributes.value: savana
attributes.tag: env_feature
attributes.value: grass
attributes.tag: env_material
attributes.value: plant above surface, excluding fruit and seed
attributes.tag: geo_loc_name
attributes.value: Kenya:Laikipia,Ol Pejeta
attributes.tag: host
attributes.value: Rhipicephalus pulchellus
attributes.tag: isol_growth_condt
attributes.value: not applicable
attributes.tag: lat_lon
attributes.value: 0.020887 N 36.860287 E
attributes.tag: host_life_stage
attributes.value: nymph
attributes.tag: host_tissue_sampled
attributes.value: whole body
attributes.tag: samp_collect_device
attributes.value: Ticks were collected by dragging using a 1 m2 cloth and stored in 70% ethanol.
attributes.tag: samp_mat_process
attributes.value: DNA extraction. 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 ?l genomic digestion buffer (PureLink Pro 96 kit). DNA was extracted with Invitrogen's PureLink Pro 96 kit (Fisher Scientific, Suwanee, GA) per manufacturer's protocol and eluted in 70 ?l elution buffer. Proteinase K digestion was performed overnight. DNA was quantified on a Qubit 2.0 (Life Technologies) using High Sensitivity DNA Kit. Samples containing sufficient DNA were sent for high throughput sequencing. A total of 1081 ticks were sequenced, of which there were 857 nymphs and 224 adults. High throughput sequencing. Target regions of 31 bacterial and one protozoal gene wereamplified using the primer sets in Table S4 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.
attributes.tag: samp_store_temp
attributes.value: -20 degrees C
attributes.tag: source_material_id
attributes.value: TACGTATAGC
attributes.tag: BioSampleModel
attributes.value: MIMARKS.specimen
attributes.tag: BioSampleModel
attributes.value: MIGS/MIMS/MIMARKS.host-associated