Genome-Scale CRISPRi Atlas Maps Function of Nearly 11,700 Genes in Human Stem Cells

The open-access dataset provides a searchable reference that researchers can use to build hypotheses, train computational models, and speed preclinical discovery.

Overview

In July 2026 the UC San Diego team published a genome-scale CRISPRi perturbation atlas in Nature Biotechnology that links gene perturbations to whole-transcriptome outcomes in human induced pluripotent stem cells.
The project systematically repressed 11,692 expressed genes and measured effects in more than 2.5 million single cells to create a high-resolution genotype–phenotype map.
Researchers combined CRISPR interference with single-cell RNA sequencing to cluster perturbation-driven transcriptional signatures and reconstruct regulatory modules that underlie pluripotency and metabolism.
Experimental follow-up validated new regulators identified by the atlas, including ZBTB41 and RNF7, and showed that DBR1 strongly influences adenosine-to-inosine RNA editing.
The open dataset, supported by NIH programs such as Bridge2AI and NHGRI, is meant as a community resource for hypothesis generation, AI model training, virtual disease modeling, and target discovery though further validation will be needed before clinical translation.