Sequencing read counts per sample before and after contaminant removal for 16S rRNA V1-V2 microbiome profiling of Amblyomma gemma and Rhipicephalus pulchellus tick tissues and cattle blood from Kajiado County, Kenya
Description
This dataset contains per-sample sequencing read counts before and after contaminant removal using the decontam prevalence-based method for 16S rRNA V1-V2 amplicon sequencing of tick tissues and bovine blood. Samples include haemolymph, midgut, salivary glands, and gonads (ovaries/testes) dissected from individual Amblyomma gemma (n = 25) and Rhipicephalus pulchellus (n = 8) ticks, along with blood from their cattle hosts (n = 12), collected in Kajiado County, Kenya, in April 2024. Sequencing was performed on an Illumina MiSeq platform (2 × 300 bp, V3 chemistry) and reads were processed using DADA2 v1.30.0. Columns include SampleID, reads before decontamination, reads after decontamination, and reads removed.
Files
Steps to reproduce
Partially engorged adult Amblyomma gemma and Rhipicephalus pulchellus ticks were collected from naturally infested cattle in Kajiado County, Kenya. Ticks were surface sterilised and dissected to isolate haemolymph, midgut, salivary glands, and gonads. Bovine blood was collected from the same cattle. Genomic DNA was extracted using the ISOLATE II Genomic DNA Kit (Bioline). The V1-V2 region of the 16S rRNA gene was amplified using primers 27F and 388R and sequenced on an Illumina MiSeq platform (2 × 300 bp, V3 chemistry). Raw reads were processed using DADA2 v1.30.0 in R v4.3.3. Contaminant identification and removal were performed using the prevalence-based method in the decontam R package, with four DNA extraction blanks and two PCR blanks as negative controls. Read counts before and after contaminant removal were tabulated per sample to produce this dataset.
Institutions
- International Centre of Insect Physiology and EcologyNairobi County, Nairobi