“The Genomics Facility provides state-of-the-art facilities for high-throughput genomic research.”

Advice and technical support for Genomics research projects

We provide specialised advice on experimental design for genomics projects and offer full technical support. We cover a broad range of applications including ChIP-seq, RNA-seq, whole genome and exome re-sequencing, targeted re-sequencing, methylome analysis, amplicon sequencing and small RNA-seq.

High throughput sequencing
The Facility runs an NGS library prep and sequencing service with fast turnaround time and high quality data generation using two Illumina HiSeq2500 sequencers and a MiSeq personal sequencer. Training and support in experimental design and sample preparation/validation is available and data processing, sequence alignment and further analyses are performed by the LMS Bioinformatics Core team.

Single-cell Genomics
The facility has experience with single-cell analysis and provides access to a Fluidigm C1 cell capture system and the Biomark HD for digital PCR. We are developing new methodologies to enable large scale single cell projects at a reasonable cost.

shRNA Library clone picking service
The Facility hosts the GIPZ Lentiviral™ short hairpin RNA libraries for mouse and human genomes and can pick clones targeting genes of interest on demand.

Open access equipment
The Facility provides open access to specific equipment like Covaris shearing for sequencing library preparation, Bioanalyser for RNA and DNA quality assessment, Nanodrop and Qubit for nucleic acid quantification, Fluidigm AccessArray system for high throughput amplicon generation, TissueLyser for nucleic acid extraction, and real-time PCR machines (ABI 7500Fast and 7900HT).

Selected Publications

Beagrie RA, Scialdone A, Schueler M, Kraemer DC, Chotalia M, Xie SQ, Barbieri M, de Santiago I, Lavitas LM, Branco MR, Fraser J, Dostie J, Game L, Dillon N, Edwards PA, Nicodemi M, Pombo A. (2017) Complex multi-enhancer contacts captured by genome architecture mapping. Nature 534; 519-524. doi:10.1038/nature21411

Kang H, Kerloc’h A, Rotival M, Xu X, Zhang Q, D’Souza Z, Kim M, Scholz JC, Ko JH, Srivastava PK, Genzen JR, Cui W, Aitman TJ, Game L, Melvin JE, Hanidu A, Dimock J, Zheng J, Souza D, Behera AK, Nabozny G, Cook HT, Bassett JH, Williams GR, Li J, Vignery A, Petretto E, Behmoaras J. (2014) Kcnn4 is a regulator of macrophage multinucleation in bone homeostasis and inflammatory disease. Cell Reports 8(4):1210-24.

Atanur SS, Diaz AG, Maratou K, Sarkis A, Rotival M, Game L, Tschannen MR, Kaisaki PJ, Otto GW, Ma MC, Keane TM, Hummel O, Saar K, Chen W, Guryev V, Gopalakrishnan K, Garrett MR, Joe B, Citterio L, Bianchi G, McBride M, Dominiczak A, Adams DJ, Serikawa T, Flicek P, Cuppen E, Hubner N, Petretto E, Gauguier D, Kwitek A, Jacob H, Aitman TJ. (2013) Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat. Cell 154(3):691-703.