What is the Genome Targeting Catalogue (GTC)?

The Genome Targeting Catalogue is a public repository of experiments using CRISPR/Cas enzymes, manually curated from published literature. It comprises the creation of insertions and deletions, homology directed repair, CRISPR activation and inhibition, and imaging experiments. This resource aims to bring together the broadest range of experiments possible, encompassing both targeted and genome-wide studies in 47 species.

Publications are taken from English-language, peer-reviewed sources, and must include the results of an experiment undertaken using a CRISPR/Cas enzyme. To ensure that data is useful, and comparable across experiments and species, there are minimum requirements for accession to the database.

Curation is carried out at EMBL-EBI; Data can be submitted for the database in the form of an Excel spreadsheet, with metadata related to the publication and the experiments contained within it, we will also consider data submitted in the correct format by authors. Details of the requirements and curation process can be found in the Curation Documentation section of the website.

Data can be accessed in tabular form or through an application programming interface (API).

Definitions

Acronym / Term Definition
AAV Adeno-associated virus
Assay Assay is used here as a descriptor of the desired method of action of the CRISPR associated protein and the experimental output
Base editing Proteins which convert DNA bases from cytidine to uridine or adenosine to inosine are individually complexed to the Cas protein and act on genomic regions proximal to the target site.
Cas CRISPR-associated protein
CRISPR Clustered regularly interspaced short palindromic repeats
dsODN Double-stranded donor oligonucleotides
Dual sgRNA-directed deletion The use of two sgRNAs concurrently, with the aim of creating a deletion that encompasses the sequence between the two targets.
Genome-wide or arrayed study A large-scale study in which hundreds or thousands of guides are used to edit a large number of cells. These can be carried out in a pooled or arrayed format.
HDR Homology directed repair
HITI Homology-independent targeted insertion
lsODN Long Single-stranded donor oligonucleotides
MMEJ Microhomology mediated end joining
Multiplexed The introduction of more than one single guide RNA to the cells or tissue, targeting the same gene or genomic region, with the aim that they will act in the same cell.
Multitarget The use of a single guide strand or multiple strands designed to target multiple genes concurrently.
NHEJ Non-homologous end joining
PMID PubMed ID
RNAi RNA interference
RNP A ribonucleoprotein is a complex of a protein, in this case a CRISPR/Cas protein, and a ribonucleic acid, in this case a guide RNA strand.
sgRNA Single-guide RNA
sgRNA library A group of sgRNAs designed to target a selection of genes or genomic regions. They can number from a few hundred to hundreds of thousands
shRNA Short hairpin RNA
siRNA Short interfering RNA
ssODN Single-stranded donor oligonucleotides
Study An experiment which could theoretically be carried out in a single test tube. A publication may contain multiple studies.
T7E1 T7 endonuclease 1 is an enzyme which can be used in a DNA mismatch assay.
TALENs Transcription activator-like effector nucleases
Targeted study A publication with 100 or fewer targets, with information given about the efficiencies of individual guides.
TIDE Tracking of indels by decomposition
Transcriptional activation A protein which increases transcription of a gene or group of genes is complexed to the Cas protein and acts on genomic regions proximal to the target site.
Transcriptional inhibition A protein which decreases transcription of a gene or group of genes is complexed to the Cas protein and acts on genomic regions proximal to the target site.
Off-target effects Binding events at locations other than the target site, potentially causing confounding effects within an experiment.
ZFNs Zinc finger nucleases