Shared Genomics Tools

Our mission

At the Shared Genomic Technologies core facility, we provide the scientific community with access to selected molecular biology tools, with a strong focus on minimizing financial costs and ensuring rapid delivery.

Our vision

In the future, we also aim to expand into the custom preparation of genetically modified research models, such as tailored cell lines. Currently, we focus on tools designed to regulate gene expression in mechanistic and functional studies. Our next step is to broaden our portfolio by adding arrayed libraries based on CRISPR and ORF vectors.

The Largest and Most Validated shRNA Collection from The RNAi Consortium

Lentivirus technology is widely used to deliver shRNAs to target cells because it can provide long-term gene silencing with high delivery efficiency. The RNAi Consortium or TRC (Broad Institute) designed and created the short hairpin RNA (shRNA) library to enable the use of RNA interference (RNAi) technology to determine the function of human annotated genes. The shRNAs were cloned into lentiviral pLKO-puro vectors. The collection was developed in 2 phases, thus the sublibraries are also designated as TRC 1/1.5 (pLKO.1) and TRC 2 (pLKO.5).

Our facility houses the entire TRC collection as TRC 1/1.5  and TRC 2 sublibraries including 127 911 clones targeting 20,000+ human genes with multiple clones per gene for replicates and transcript-specific targeting.

Libraries are for now available as bacterial LB stocks for pick-up.

TRC1 and TRC1.5 libraries share the same vector backbone, meaning their overall vector architecture and functional components are essentially identical. In contrast, the TRC2 library includes an additional WPRE (Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element) in its vector design. This element can enhance transgene expression by improving mRNA stability and nuclear export, which often results in higher marker gene expression. In practice, the presence of WPRE in TRC2 may also lead to improved viral titer compared to TRC1/1.5, making transduction more efficient under some conditions.

Key Highlights

• Pre-cloned in lentiviral vectors, pLKO.1 and pLKO.5

• U6-driven shRNA with puromycin selection of transduced cells

• Quick turn-around time

Our story

The Shared Genomics Tools core facility was established in response to the growing need for a centralized and shared infrastructure for genomic analyses. Its creation has been made possible through the support and collaboration of many colleagues and institutions, to whom we would like to express our sincere gratitude. In particular, we are deeply grateful to prof. RNDr. Ondřej Slabý, Ph.D., prof. MUDr. Tomáš Kašpárek, Ph.D. and doc. MUDr. Regina Demlová, Ph.D., whose expert guidance, encouragement, and continuous support were crucial in the establishment of this facility. We also gratefully acknowledge the Faculty of Medicine of Masaryk University for its institutional support, without which the Shared Genomics Tools core facility would not have been possible.