Leggas, Markos

Leggas lab- research introduction:

Our lab mainly deals with the molecular and cellular biology techniques with the pharmacology tools like pharmacokinetics and pharmacodynamic experiment in discovering and developing drugs for clinical and cancer treatment. This proposal is for the analysis of data generated from Multi-Omics approach of clinical (Stool) and human cell line samples. The projects mainly focuses on the study of Neonatal abstinence syndrome (NAS) newborns treated with Clonidine/Morphine and study the effect of Mithramycin and its analogues on the of Prostate cancer cell lines (LNCap and VCaps) and Ewing sarcoma cell lines (PC3 and TC32).

Microbiome analysis by sequencing of 16S rRNA

This project seeks to determine the bacterial abundance and taxonomic classification between the stool samples of NAS infants treated with Clonidine and Morphine across different sampling time points. The reads were generated with Illumina Miseq platform targeting V3-V4 region.

RNA seq analysis of Prostate Cancer cell lines

This project mainly focuses on the study to analyze the effect of Mithramycin and its analogues on Prostate cancer cell lines LNCap and VCap. For RNAseq Illumina Novaseq 6000 S4 platform will be used. 40 million reads will be generated with Paired end sequencing (150 bp of each read).

RNA seq analysis of Ewing sarcoma cell lines

This project mainly focuses on the study to analyze the effect of Mithramycin and its analogues on Ewing cancer cell lines PC3 and TC32. For RNAseq Illumina Novaseq 6000 S4 platform will be used. 40 million reads will be generated with Paired end sequencing (150 bp of each read).

Participants:

PI- Dr. Markos Leggas

Post Doc- Ambika Dudhate

Software:

For RNA seq:

Computational methods: Read QC Read processing, genome assembly, read mapping, Differential expression analysis and annotation

Software: FastQC, RSEM, Bowtie, Blast, EBseq, Bioconductor-DeSeq, Bioconductor-edgeR , HTseq (Available on DLX)

For microbiome analysis:

Read QC, read Demultiplexing with barcodes specific to read, read processing, Denoising and clustering, Taxonomy assignment, Training of classifiers, Determination of alpha and beta diversity.

Softwares: Cut adapt, Qiime2, SRA tool kit (Available on DLX)