Project description:The utility of RADseq in an experimental setting is also demonstrated, based on our chasacterisation of an APOBEC mutation signature in an APOBEC3A transfected mouse cell line. 0D5 cells, derived from SSM3 cells, were co-transfected with a mixture containing pcDNA3.1 vectors expressing either APOBEC3A or APOBEC3B (kindly donated by Vincent Caval), pcDNA3.1 construct expressing deaminase null APOBEC3A linked to a uracil deglycosylase construct and a plasmid encoding mutant GFP and WT mCherry that is a reporter for APOBEC mutagenesis. Cells were grown, and gDNA extracted, prior to preparation of RADseq libraries using a PstI- MspI double-digest. Libraries underwent a Pippin Prep to select fragments in the size range of 220-520 bp (genomic sequence plus 148 bp of adapters). Single-end sequencing (1x101bp) was performed on an Illumina NovaSeq6000 utilizing v1.5 chemistry. Reads were aligned to mm10 using bwa mem and variants called using the GATK4 pipeline.
Project description:Illumina technology was used to generate mRNA profiles of galls from root-knot nematodes infected and corresponding uninfected roots from Poplar CAD and WT lines. RNA was extracted from 3 replicates.TruSeq mRNA Stranded libraries were constructed and after pooling and normalization of libraries, sequencing was done on a NextSeq500 Sequencing System. Raw reads were trimmed for quality and mapped to the substituted genome sequence of P. tremula x P. alba 717-1B4 using CLC Genomics Workbench v9.5.2 and the primary transcripts only.
