High Molecular Weight DNA library construction:
Fosmid/ BAC libraries and 20kb-PacBio libraries are routinely constructed in the lab.
We employed short-read and long-read sequencing technologies such as Ion Torrent, Illumina, MGISEQ, and PacBio Sequel to study genetic variation. We have experience in handling large sequencing data sets for de novo genome assembly, reference mapping, gene annotation, and comparative genomics.
We used EST/cDNA/RNA/miRNA sequencing to study gene expression profiles, alternate splicing, and transcript annotation. Short-read sequencing platform such as Ion Torrent has been used to study gene expression profiles. Iso-seq using a long-read PacBio sequencing platform is used to study alternative splicing and discover new rare transcripts.
Genetic Linkage Analysis:
Genotyping-by-sequencing (GBS) techniques such as reduced representation library (RRL) sequencing, targeted enrichment sequencing or amplicon sequencing have been used to study genetic variation in populations. Linkage phase can be analyzed with phenotypic data to find a correlation between genotype and phenotype and then develop markers for genetic improvement programs.
Shotgun or amplicon sequencing of 16S, 18S, ITS fragments on Ion Torrent, 454 or PacBio have been used to study genetic diversity of interesting environmental samples such as peat swamp forests, coral reefs, lignocellulolytic composts, cow rumens, and termite guts.
Infrastructure in the Proteomics Research Laboratory is centered around state-of-the-art mass spectrometry for identification, characterization, and quantitation of target peptides or proteins or proteomes. The facility is equipped with two mass spectrometer systems: AB SCIEX TripleTOF® 6600+ and JEOL SpiralTOF™ S3000.