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The anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we characterize gene expression patterns in distinct neural cell types of the Drosophila visual system using genetic lines to access individual cell types, the TAPIN-seq method to measure their transcriptomes, and a probabilistic method to interpret these measurements. We used these tools to build a resource of high-resolution transcriptomes for 100 driver lines covering 67 cell types, available at http://www.opticlobe.com. Combining these transcriptomes with recently reported connectomes helps characterize how information is transmitted and processed across a range of scales, from individual synapses to circuit pathways. We describe examples that include identifying neurotransmitters, including cases of apparent co-release, generating functional hypotheses based on receptor expression, as well as identifying strong commonalities between different cell types.
Pubmed ID: 31939737 RIS Download
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Software package as distribution of ImageJ and ImageJ2 together with Java, Java3D and plugins organized into coherent menu structure. Used to assist research in life sciences.
View all literature mentionsCollection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
View all literature mentionsRepository of raw sequencing data from next generation of sequencing platforms including including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. In addition to raw sequence data, SRA now stores alignment information in form of read placements on reference sequence. Data submissions are welcome. Archive of high throughput sequencing data,part of international partnership of archives (INSDC) at NCBI, European Bioinformatics Institute and DNA Database of Japan. Data submitted to any of this three organizations are shared among them.
View all literature mentionsA next-generation web-based application that aims to provide an integrated solution for both visualization and analysis of deep-sequencing data, along with simple access to public datasets.
View all literature mentionsJava toolset for working with next generation sequencing data in the BAM format.
View all literature mentionsDatabase of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.
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View all literature mentionsDrosophila melanogaster with name w[1118]; PBac{y[+mDint2] w[+mC]=fkh-GFP.FPTB}VK00037/SM5 from BDSC.
View all literature mentionsDrosophila melanogaster with name P{w[+mC]=ey3.5-FLP.B}1, y[1] w[*]; CyO/In(2LR)Gla, wg[Gla-1] PPO1[Bc] from BDSC.
View all literature mentionsDrosophila melanogaster with name w[*] P{y[+t7.7] w[+mC]=sens-FLPG5.C}attP18; wg[Sp-1]/CyO; sens[Ly-1]/TM6B, Tb[1] from BDSC.
View all literature mentionsDrosophila melanogaster with name y[1] w[*]; Mi{Trojan-GAL4.2}kn[MI15480-TG4.2]/SM6a from BDSC.
View all literature mentionsDrosophila melanogaster with name w[1118]; PBac{y[+mDint2] w[+mC]=Ets65A-GFP.FLAG}VK00037 from BDSC.
View all literature mentionsDrosophila melanogaster with name y[1] w[*]; Mi{PT-GFSTF.0}TfAP-2[MI04611-GFSTF.0]/TM6C, Sb[1] Tb[1] from BDSC.
View all literature mentionsDrosophila melanogaster with name y[1] w[67c23]; Mi{PT-GFSTF.0}Nos[MI09718-GFSTF.0]/SM6a from BDSC.
View all literature mentionsDrosophila melanogaster with name w[1118]; TI{TI}VAChT[FRT-STOP-FRT.HA]/TM6B, Tb[1] from BDSC.
View all literature mentionsDrosophila melanogaster with name y[1] w[*]; Mi{PT-GFSTF.2}GluClalpha[MI02890-GFSTF.2]/TM6C, Sb[1] Tb[1] from BDSC.
View all literature mentionsDrosophila melanogaster with name y[1] w[*]; Mi{Trojan-GAL4.1}Oamb[MI12417-TG4.1] from BDSC.
View all literature mentionsDrosophila melanogaster with name y[1] w[*] P{y[+t7.7] w[+mC]=13XLexAop2-IVS-myr::GFP}su(Hw)attP8 from BDSC.
View all literature mentionsDrosophila melanogaster with name y[1] w[*]; Mi{Trojan-GAL4.1}Lim3[MI03817-TG4.1]/SM6a from BDSC.
View all literature mentionsDrosophila melanogaster with name y[1] w[*]; Mi{PT-GFSTF.1}klg[MI02135-GFSTF.1]/TM6C, Sb[1] Tb[1] from BDSC.
View all literature mentionsDrosophila melanogaster with name w[*]; P{y[+t7.7] w[+mC]=10XUAS-IVS-myr::GFP}attP2 from BDSC.
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