Data for "Genetic and methylomic interrogation of brain cell-type shifts in autism, schizophrenia, and Alzheimer’s disease" (Yap et al. 2023). Source data from ROSMAP, LIBD and UCLA_ASD post-mortem brain datasets. This data repository contains 3 files: 220819_Supplementary_Tables.xlsx Supplementary Tables for the manuscript: Supplementary Table 1: Comparison of CTP deconvolution methods in the ROSMAP dataset. mcc* denotes methylCC deconvolution; sSV* denotes smartSVA; h* indicates Houseman using array reference data; hseq* indicates Houseman with sequencing reference data; celfie* indicates CelFIE (and includes an output titled "unknown1"); VAEe* indicates variational autoencoder embeddings. Supplementary Table 2: Comparison of CTP deconvolution methods in the LIBD dataset. mcc* denotes methylCC deconvolution; sSV* denotes smartSVA; h* indicates Houseman using array reference data; hseq* indicates Houseman with sequencing reference data; celfie* indicates CelFIE (and includes an output titled "unknown1"); VAEe* indicates variational autoencoder embeddings. Supplementary Table 3: Comparison of CTP deconvolution methods in the UCLA_ASD dataset. mcc* denotes methylCC deconvolution; sSV* denotes smartSVA; h* indicates Houseman using array reference data; hseq* indicates Houseman with sequencing reference data; celfie* indicates CelFIE (and includes an output titled "unknown1"); VAEe* indicates variational autoencoder embeddings. Supplementary Table 4: Deconvolved brain CTPs (raw), with covariates. Supplementary Table 5: Deconvolved brain CTPs (clr-transform, offset 1e-3), with covariates and raw PGS for all ancestries. Comp* indicates compositionally-aware principal components of the CTP data; *pgs_raw indicates PGS calculated for using genotyping across all ancestries. This table has a total of n=1,098 across all ancestries, including n=885 EUR. After applying a rel<0.05 threshold on the n=885 EUR, there were n=878 EUR which were used in the PGS analysis so that population stratification PCs did not simply capture family structure. Supplementary Table 6: Deconvolved brain CTPs (clr-transform, offset 1e-3), with covariates and standardised PGS for n=878 Europeans. *pgs_raw indicates unstandardised PGS, PC* indicates genotyping PCs within the European dataset, *_PGS indicates standardised PGS within the European subset. Supplementary Table 7: Deconvolved brain CTPs (clr-transform, offset 1e-3), adjusted for oligodendrocyte proportions, with covariates. Supplementary Table 8: Deconvolved brain CTPs (raw), adjusted for oligodendrocyte proportions, with covariates. 20220108_maf05_gwas_ctp.tar.gz GWAS summary statistics for the 7 brainCTPs (clr-transformed): Exc, Inh, Astro, Endo, Micro, Oligo, OPC METAL output format: MarkerName: SNP Allele1 Allele2 Freq1: Allele1 frequency FreqSE: frequency standard error MinFreq: minimum Allele1 frequency in meta-analysis MaxFreq: maximum Allele1 frequency in meta-analysis Effect: effect size StdErr: standard error of effect size P-value: calculated in inverse variance weighted meta-analysis Direction: directions of effects across the 3 datasets HetISq: heterozygosity I-squared HetChiSq: heterozygosity chi-squared HetDf: heterozygosity degress of freedom HetPVal: heterozygosity test p-value 20220108_maf05_gwas_ctp_pc.tar.gz GWAS summary statistics for the 5 CTP_PCs METAL output format (see above) Source data: ROSMAP: Raw methylation .idat files were obtained from Synapse accession syn7357283. Whole genome sequencing .vcf files (variants jointly called with MSBB and Mayo studies) were obtained from Synapse accession syn11707420. LIBD: Raw methylation .idat files were obtained from GEO accession GSE74193. SNP genotypes were downloaded from dbGaP accession phs000417.v2.p1. UCLA-ASD: The processed methylation beta matrix was downloaded from Synapse accession syn8263588. SNP genotypes were downloaded from Synapse accession syn10537134. GWAS summary statistics are available at: 10.5281/zenodo.7604231 Code is available on GitHub: gandallab/brain_CTP_deconv