Data underlying the figures in the publication “Lineage recording in human cerebral organoids”, published in Nat Methods, 2022, 19, 90–99. https://doi.org/10.1038/s41592-021-01344-8 Table of contents: Supplementary Tables 1-8: Experimental data supporting the figures of the publication. Data availability Sequence data that support the findings of this study have been deposited in ArrayExpress under the accession codes E-MTAB-10973, E-MTAB-10974 (scRNA-seq data based on 10x Genomics), E-MTAB-10972 (spatial transcriptomic RNA-seq data based on 10x Visium) and E-MTAB-10971 (iTracer-perturb data). Bulk sequencing of barcode and scar library data as well as processed sequencing data have been deposited in Mendeley Data at https://doi.org/10.17632/nj3p3pxv6p. Code availability The computational code used in this study is available at GitHub (https://github.com/quadbiolab/iTracer) or upon request.