Genomics Unit

The CRG Genomics Unit is part of the CNAG-CRG, the national genome analysis centre. The Unit aims at providing excellent, state-of-the-art services for microarray technology and next-generation sequencing. In addition to providing service, the Unit is dedicated to test, implement, and to develop new protocols for various sequencing applications to advance the analysis of genes and genomes. The Unit is equipped with two Illumina HiSeq 2500, and we have access to the HiSeq 4000 at CNAG. Additionally, the unit operates an Illumina MiSeq sequencer. Protocols for a broad range of applications like genomic sequencing, exome enrichment, amplicon sequencing, ChIP-Seq, and transcriptome characterization at the level of total RNA, small RNA, or mRNA are available for routine use. Besides the routine protocols, a constant focus of the Unit is the customization of library preparation protocols. Together with the Biomolecular Screening and Protein Technologies Unit several enzymes were produced that allow much more cost-efficient library preparation compared to commercial kits while maintaining identical properties and quality. In a collaborative project with colleagues from South Africa a custom protocol has been developed to perform targeted RNA sequencing of pathogenic bacteria in mixtures of bacterial and human RNA with very low percentages of RNA originating from the pathogenic bacteria.

• Improvement of single cell RNA-seq protocols (InDrop-seq).    
• In-house production and improvement of additional enzymes for library preparation applications (together with the Biomolecular Screening and Protein Technologies Unit)
• Modified protocols for improved targeted re-sequencing

Willis JR, González-Torres P, Pittis AA, Bejarano LA, Cozzuto L, Andreu-Somavilla N, Alloza-Trabado M, Valentín A, Ksiezopolska E, Company C, Onywera H, Montfort M, Hermoso A, Iraola-Guzmán S, Saus E, Labeeuw A, Carolis C, Hecht J, Ponomarenko J, Gabaldón T.
“Citizen science charts two major “stomatotypes” in the oral microbiome of adolescents and reveals links with habits and drinking water composition.”
Microbiome, 6(1):218, 2018.

Orgeur M, Martens M, Leonte G, Nassari S, Bonnin MA, Börno ST, Timmermann B, Hecht J, Duprez D, Stricker S.
“Genome-wide strategies identify downstream target genes of chick connective tissue-associated transcription factors.”
Development, 145(7), 2018.

Mrosk J, Bhavani GS, Shah H, Hecht J, Krüger U, Shukla A, Kornak U, Girisha KM.
“Diagnostic strategies and genotype-phenotype correlation in a large Indian cohort of osteogenesis imperfecta.”
Bone, 110:368-377, 2018.

Stadhouders R, Vidal E, Serra F, Di Stefano B, Le Dily F, Quilez J, Gomez A, Collombet S, Berenguer C, Cuartero Y, Hecht J, Filion GJ, Beato M, Marti-Renom MA, Graf T.
“Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming.”
Nat Genet, 50(2):238-249, 2018.