SAMN10180895
External Id
University of Illinois
INSDC center name
2018-10-14T00:00:00Z
INSDC first public
2021-02-28T06:24:53.743Z
INSDC last update
SRS3928152
INSDC secondary accession
live
INSDC status
MIMARKS.specimen.host-associated.5.0
NCBI submission package
SRS3928152
SRA accession
2015-07-20
collection date
Keywords: GSC:MIxS;MIMARKS:5.0
description
savana
env biome
grass
http://www.ebi.ac.uk/efo/EFO_0003956
env feature
plant above surface, excluding fruit and seed
env_material
Kenya:Laikipia,Lewa
geo loc name
Rhipicephalus pulchellus
host
nymph
host life stage
whole body
http://purl.obolibrary.org/obo/BTO_0001489
host_tissue_sampled
LEEPRUN1
isolate
0.219683 N 37.442353 E
lat lon
tick metagenome
http://purl.obolibrary.org/obo/NCBITaxon_1595979
organism
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 mat process
Ticks were collected by dragging using a 1 m2 cloth and stored in 70% ethanol.
samp_collect_device
-20 degrees C
samp_store_temp
CGTAATGAGC
source_material_id
LEEPRUN1_CGTAATGAGC_L1
title