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scPerturb: Information Resource for Harmonized Single-Cell Perturbation Data
Tessa Green · Stefan Peidli · Ciyue Shen · Torsten Gross · Joseph Min · Samuele Garda · Jake Taylor-King · Debora Marks · Augustin Luna · Nils Blüthgen · Chris Sander
Event URL: https://openreview.net/forum?id=rgbeZljllwu »

Recent biotechnological advances led to growing numbers of single-cell studies, which reveal molecular and phenotypic responses to large numbers of perturbations. However, analysis across diverse datasets is typically hampered by differences in format, naming conventions, data filtering and normalization. To facilitate development and benchmarking of computational methods in systems biology, we collect a set of 44 publicly available single-cell perturbation-response datasets with molecular readouts, including RNA, proteins and chromatin accessibility (Figure Panel A). We apply uniform pre-processing and quality control pipelines and harmonize feature annotations. The resulting information resource enables efficient development and testing of computational analysis methods, and facilitates direct comparison and integration across datasets. 32 RNA datasets in this resource were perturbed using CRISPR and 9 were perturbed with drugs (Figure Panel B). We also include three scATAC datasets, as well as three CITE-seq datasets with protein and RNA counts separately downloadable. For each scRNA-seq dataset we supply count matrices, where each cell has a perturbation annotation, quality control metrics including gene counts and mitochondrial read percentage. Quality control plots for each dataset are also available on scperturb.org. Notably, more than 8000 CRISPR perturbations are shared across multiple datasets. We anticipate this data resource being useful for developing machine learning models for perturbation responses across datasets and other tasks.

Author Information

Tessa Green (Harvard University)
Stefan Peidli (Humboldt Universität Berlin)
Stefan Peidli

PhD student in computational biology. Working on metric learning to make sense of high-dimensional single-cell data with applications in cancer and covid research.

Ciyue Shen (Harvard University)
Torsten Gross
Joseph Min
Samuele Garda (Department of Computer Science, Humboldt University Berlin, Humboldt Universität Berlin)
Jake Taylor-King (Relation Therapeutics)
Debora Marks (Harvard University)

Debora is a mathematician and computational biologist with a track record of using novel algorithms and statistics to successfully address unsolved biological problems. She has a passion for interpreting genetic variation in a way that impacts biomedical applications. During her PhD, she quantified the pan-genomic scope of microRNA targeting - the combinatorial regulation of protein expression and co-discovered the first microRNA in a virus.  As a postdoc she made a breakthrough in the classic, unsolved problem of ab initio 3D structure prediction of proteins using undirected graphical probability models for evolutionary sequences. She has developed this approach to determine functional interactions, biomolecular structures, including the 3D structure of RNA and RNA-protein complexes and the conformational ensembles of apparently disordered proteins. Her new lab at Harvard is interested in developing methods in deep learning to address a wide range of biological challenges including designing drug affinity libraries for large numbers of human genes, predicting epistasis in antibiotic resistance, the effects of genetic variation on human disease etiology and drug response and sequence design for biosynthetic applications.

Augustin Luna
Nils Blüthgen
Chris Sander (Harvard Medical School)

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