Julia Montague at GalSeq, Milan
- Post by: fantom
- 29 April 2025
- No Comment
Galseq Secondment
During my secondment at GalSeq, a genomics company in Milan that specializes in next-generation sequencing (NGS) technologies, I learned how to prepare and sequence RNA-seq and PCR amplicon libraries. It was a great hands-on opportunity to learn about Illumina-based NGS workflows and pick up library prep best practices. Furthermore, I developed skills in nucleic acid purification and analytical steps using automated electrophoresis. I gained a solid understanding of how high-quality sequencing data is generated, which has helped me to bridge my understanding between the wet lab side of an omics-project and the downstream computational analysis. Back in the lab at UNIMIB, I analyzed the data mostly using open-source bioinformatics tools, but also did some custom scripting for quality control and visualization. I wrote pipelines for genome alignment and read counting, and performed downstream analyses including differential gene expression (DGE), gene set enrichment (GSEA), ligand-receptor binding, gene module, and negative/positive CRISPR screening enrichment using popular tools like DESeq2, clusterProfiler, BulkSignalR, WGCNA, MAGeCK, and others. Along the way, I refined my coding abilities in R and Python. The output of this secondment will directly contribute to the progress of my FANTOM projects on drug-tolerant persister cells in ALK+ ALCL and whole-genome CRISPR knockout screening of other ALK+ malignancies.
