LEEARUN15_GCATAATCGC_L1
tick metagenome
strain
not applicable
isolate
LEEARUN15
collection_date
2014-07-21
env_biome
savana
env_feature
grass
env_material
plant above surface, excluding fruit and seed
geo_loc_name
Kenya:Laikipia,Lewa
host
Rhipicephalus pulchellus
isol_growth_condt
not applicable
lat_lon
0.219683 N 37.442353 E
host_life_stage
nymph
host_tissue_sampled
whole body
samp_collect_device
Ticks were collected by dragging using a 1 m2 cloth and stored in 70% ethanol.
samp_mat_process
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.
samp_store_temp
-20 degrees C
source_material_id
GCATAATCGC
BioSampleModel
MIMARKS.specimen
BioSampleModel
MIGS/MIMS/MIMARKS.host-associated