KEY RESOURCE TABLE
| Resource Type | Specific Reagent or Resource | Source or Reference | Identifiers | Additional Information |
|---|---|---|---|---|
| Add additional rows as needed for each resource type | Include species and sex when applicable. | Include name of manufacturer, company, repository, individual, or research lab. Include PMID or DOI for references; use “this paper” if new. | Include catalog numbers, stock numbers, database IDs or accession numbers, and/or RRIDs. RRIDs are highly encouraged; search for RRIDs at https://scicrunch.org/resources. | Include any additional information or notes if necessary. |
| Deposited Data; Public Database | human | database of Genotypes and Phenotypes (dbGaP): https://dbgap.ncbi.nlm.nih.gov/ | dbGaP accession numbers phs000021.v2.p1 (GAIN), phs000167.v1.p1 (MGS_nonGAIN), phs000017.v1.p1 | |
| Deposited Data; Public Database | human | Genotype Tissue Expresssion Project (GTEx): http://www.gtexportal.org; GTEx Consortium. (2015). Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science, 348(6235), 648-660. doi:10.1126/science.1262110. PMCID: 4547484 | ||
| Deposited Data; Public Database | human | Human Brain Transcriptome Project (HBT): http://hbatlas.org; Kang, H. J., Kawasawa, Y. I., Cheng, F., Zhu, Y., Xu, X., Li, M., … Sestan, N. (2011). Spatio-temporal transcriptome of the human brain. Nature, 478(7370), 483-489. doi:10.1038/nature10523. PMCID: 3566780 | NCBI GEO DataSets GSE25219-GPL5175 | |
| Deposited Data; Public Database | human | Allen Brain Atlas: http://human.brain-map.org; Sunkin, S. M., Ng, L., Lau, C., Dolbeare, T., Gilbert, T. L., Thompson, C. L., … Dang, C. (2013). Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system. Nucleic Acids Research, 41(Database issue), D996-D1008. doi:10.1093/nar/gks1042. PMCID: 3531093 | ||
| Deposited Data; Public Database | mouse | Stanford Brain RNA-Seq database: http://web.stanford.edu/group/barres_lab/brain_rnaseq.html; Cahoy, J. D., Emery, B., Kaushal, A., Foo, L. C., Zamanian, J. L., Christopherson, K. S., … Barres, B. A. (2008). A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci, 28(1), 264-278. doi:10.1523/JNEUROSCI.4178-07.2008. PMCID: PMC6671143 | ||
| Deposited Data; Public Database | human | PsychENCODE: https://www.synapse.org/pec ; http://resource.psychencode.org; Wang, D., Liu, S., Warrell, J., Won, H., Shi, X., Navarro, F. C. P., … Gerstein, M. B. (2018). Comprehensive functional genomic resource and integrative model for the human brain. Science, 362(6420). doi:10.1126/science.aat8464. PMCID: PMC6413328 | ||
| Deposited Data; Public Database | human | CommonMind Consortium: https://www.synapse.org/cmc; Hoffman, G. E., Bendl, J., Voloudakis, G., Montgomery, K. S., Sloofman, L., Wang, Y. C., … Roussos, P. (2019). CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder. Sci Data, 6(1), 180. doi:10.1038/s41597-019-0183-6. PMCID: PMC6760149 | Sage Synapse accession syn5650509 | |
| Deposited Data; Public Database | human | Lieber Institute for Brain Development (LIBD): http://eqtl.brainseq.org/; Jaffe, A. E., Straub, R. E., Shin, J. H., Tao, R., Gao, Y., Collado-Torres, L., … Weinberger, D. R. (2018). Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis. Nature Neuroscience, 21(8), 1117-1125. doi:10.1038/s41593-018-0197-y. PMCID: PMC6438700 | ||
| Deposited Data; Public Database | human | 1000 Genomes Project (1KGP): Clarke, L., Zheng-Bradley, X., Smith, R., Kulesha, E., Xiao, C., Toneva, I., … 1000 Genomes Project Consortium. (2012). The 1000 Genomes Project: data management and community access. Nat Methods, 9(5), 459-462. doi:10.1038/nmeth.1974. PMCID: PMC3340611 | ||
| Deposited Data; Public Database | n/a | Molecular Signatues Database (MSigDB) v.6.2: http://software.broadinstitute.org/gsea/msigdb/genesets.jsp; Liberzon, A., Birger, C., Thorvaldsdottir, H., Ghandi, M., Mesirov, J. P., & Tamayo, P. (2015). The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Systems, 1(6), 417-425. doi:10.1016/j.cels.2015.12.004. PMCID: 4707969 | ||
| Deposited Data; Public Database | human | NHGRI-EBI GWAS Catalog: Buniello, A., MacArthur, J. A. L., Cerezo, M., Harris, L. W., Hayhurst, J., Malangone, C., … Parkinson, H. (2019). The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Research, 47(D1), D1005-D1012. doi:10.1093/nar/gky1120. PMCID: PMC6323933 | ||
| Software; Algorithm | Rapid Imputation for COnsortias PIpeLIne (RICOPILI) | Lam, M., Awasthi, S., Watson, H. J., Goldstein, J., Panagiotaropoulou, G., Trubetskoy, V., … Ripke, S. (2020). RICOPILI: Rapid Imputation for COnsortias PIpeLIne. Bioinformatics, 36(3), 930-933. doi:10.1093/bioinformatics/btz633. PMCID: | ||
| Software; Algorithm | R v.3.5.1-intel-2019b | https://www.r-project.org/ | ||
| Software; Algorithm | PLINK v.1.9b | Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience, 4, 7. doi:10.1186/s13742-015-0047-8. PMCID: PMC4342193 | ||
| Software; Algorithm | LDSC v.1.0.1 | Bulik-Sullivan, B. K., Loh, P. R., Finucane, H. K., Ripke, S., Yang, J., Schizophrenia Working Group of the Psychiatric Genomics Consortium, … Neale, B. M. (2015). LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nature Genetics, 47(3), 291-295. doi:10.1038/ng.3211. PMCID: 4495769 | ||
| Software; Algorithm | METAL v.2011-03-25 | Willer, C. J., Li, Y., & Abecasis, G. R. (2010). METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics, 26(17), 2190-2191. doi:10.1093/bioinformatics/btq340. PMCID: 2922887 | ||
| Software; Algorithm | ASSET R package v.2.8.0 | Bhattacharjee, S., Rajaraman, P., Jacobs, K. B., Wheeler, W. A., Melin, B. S., Hartge, P., … Chatterjee, N. (2012). A subset-based approach improves power and interpretation for the combined analysis of genetic association studies of heterogeneous traits. American Journal of Human Genetics, 90(5), 821-835. doi:10.1016/j.ajhg.2012.03.015. PMCID: PMC3376551 | ||
| Software; Algorithm | LocusZoom v.1.4 | Pruim, R. J., Welch, R. P., Sanna, S., Teslovich, T. M., Chines, P. S., Gliedt, T. P., … Willer, C. J. (2010). LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics, 26(18), 2336-2337. doi:10.1093/bioinformatics/btq419. PMCID: PMC2935401 | ||
| Software; Algorithm | MAGMA v.2.3.0-intel-2019b | de Leeuw, C. A., Mooij, J. M., Heskes, T., & Posthuma, D. (2015). MAGMA: generalized gene-set analysis of GWAS data. PLoS Comput Biol, 11(4), e1004219. doi:10.1371/journal.pcbi.1004219. PMCID: 4401657 | ||
| Software; Algorithm | CAVIAR v.2.2 | Hormozdiari, F., Kostem, E., Kang, E. Y., Pasaniuc, B., & Eskin, E. (2014). Identifying causal variants at loci with multiple signals of association. Genetics, 198(2), 497-508. doi:10.1534/genetics.114.167908. PMCID: 4196608 | ||
| Software; Algorithm | FINEMAP v.1.4 | Benner, C., Spencer, C. C., Havulinna, A. S., Salomaa, V., Ripatti, S., & Pirinen, M. (2016). FINEMAP: efficient variable selection using summary data from genome-wide association studies. Bioinformatics, 32(10), 1493-1501. doi:10.1093/bioinformatics/btw018. PMCID: 4866522 |