KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Deposited data | ||
| PsychENCODE human brain RNAseq | Li etal.18 | https://psychencode.synapse.org; http://resource.psychencode.org/ |
| GTEx v8 human brain RNAseq | GTEx Consortium89 | https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000424.v8.p2 Accession ID: 26317 |
| ROSMAP human RNAseq | De Jager et al.90 | https://www.radc.rush.edu; https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage/StudyDetails?Study=syn3219045 |
| BrainSpan human brain developmental RNAseq | Miller et al.26 | https://www.brainspan.org |
| Allen Human Brain Atlas | Hawrylycz et al.28 and Arnatkeviciute et al.91 | https://figshare.com/articles/dataset/AHBAdata/6852911 |
| PsychENCODE non-human primate brain RNAseq | Zhuetal.19 | http://evolution.psychencode.org |
| Developmental macaque RNA-seq atlas | Yin et al.43 | GEO: GSE128537 |
| UK Biobank (neuroimaging+genetics) | Warrieretal.10 | Application 20904 |
| Neuroimaging GWAS summary statistics | Warrieretal.10 | https://portal.ide-cam.org.uk/overview/483 |
| Neuroimaging lifespan models | Bethlehem et al4 | https://github.com/brainchart/Lifespan |
| Evolution, development, and cross-subject “population” allometric scaling maps | Hill et al.29 and Reardon et al.30 | https://github.com/netneurolab/neuromaps |
| Neurotransmitter/receptor maps | Hansen et al.37 | https://github.com/netneurolab/hansen_receptors |
| Venous density maps (VENAT) | Huck et al.92 | https://figshare.com/articles/dataset/VENAT_Probability_map_nii_gz/7205960 |
| Diffusion MRI fiber length profiling | Bajada et al.93 | https://balsa.wustl.edu/study/1K3l |
| Cognitive function map | Assem et al.33 | https://balsa.wustl.edu/study/B4nkg |
| Alzheimer disease PET maps | Vogel et al.34 | https://neurovault.org/collections/12296/ |
| ENIGMA cross-disorder cortical thickness map | Larivière et al.36 | https://enigma-toolbox.readthedocs.io/en/latest/pages/04.crossdisorder/index.html |
| Glioblastoma and low grade glioma tumor map | Mandal et al.35 | https://neurovault.org/images/785830/ |
| BigBrain | Amunts et al.38 | https://bigbrain.loris.ca/main.php |
| LiBD Spatial RNA-seq | Die cytoarchitektonik der hirnrinde des erwachsenen menschen Google Books.40 | http://research.libd.org/spatialLIBD/ |
| PsychENCODE WGCNA modules | Gandal et al.58 | http://resource.psychencode.org |
| Mutational constraint datasets (gnomAD v2.1.1) | Chen et al.62 | https://gnomad.broadinstitute.org |
| Mutational constraint datasets (DECIPHER) | Firth et al.61, Collins et al.63 | https://www.deciphergenomics.org |
| Meta-analytic multi-ancestry quantitative trait loci | Zeng et al.71 | https://github.com/jxzb1988/MMQTL |
| MGB Biobank | Zeng et al.75 | https://www.massgeneralbrigham.org/en/research-and-innovation/participate-in-research/biobank |
| Software and algorithms | ||
| RStudio (“Ghost Orchid” for macOS) with R (v.4.1.2) | Team, R.S. RStudio: integrated development for R | https://www.rstudio.com |
| RNA-seq preprocessing for PsychENCODE and GTEx | Kim et al.94 | https://github.com/gandallab/C4A-network |
| ToppGene | Chen et al.56 | https://toppgene.cchmc.org |
| MAGMA | de Leeuw et al.65 | https://ctg.cncr.nl/software/magma |
| FUSION | Gusev et al.95 | https://github.com/gusevlab/fusion_twas |
| Genomic quality control | Peterson et al.96 | https://github.com/getian107/MGBB-QC; https://github.com/Annefeng/PBK-QC-pipeline |
| FreeSurfer (v6.0.1) | Fischl et al.97 | https://afni.nimh.nih.gov/ |
| AFNI | Cox et al.98,99 | https://surfer.nmr.mgh.harvard.edu/ |
| ENIGMA toolbox | Larivière et al.36 | https://enigma-toolbox.readthedocs.io/en/latest/ |
| neuromaps | Markello et al.100 | https://github.com/netneurolab/neuromaps |
| Lifespan brain charts | Bethlehem et al.4 | https://github.com/brainchart/Lifespan |