Difference between revisions of "FlyBase:Drosophila Online Resources"

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* <b>PeptideAtlas</b>, a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments: <br />[http://www.peptideatlas.org/ Seattle Proteome Center, Seattle, Washington, USA]
 
* <b>PeptideAtlas</b>, a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments: <br />[http://www.peptideatlas.org/ Seattle Proteome Center, Seattle, Washington, USA]
 
* <b>Virtual Fly Brain</b> - A 3D brain browser with point and click searches for neurons, transgenes and phenotypes:<br />[http://www.virtualflybrain.org Virtual Fly Brain, Edinburgh and Cambridge, UK]
 
* <b>Virtual Fly Brain</b> - A 3D brain browser with point and click searches for neurons, transgenes and phenotypes:<br />[http://www.virtualflybrain.org Virtual Fly Brain, Edinburgh and Cambridge, UK]
 +
 +
=Cell Lines and Cell Culture=
 +
* <b>Cellosaurus</b>: A thesaurus of cell lines which attempts to list all cell lines used in biomedical research.<br /> [http://web.expasy.org/cellosaurus/ Swiss Institute of Bioinformatics, Geneva, Switzerland]
 +
* <b>DGRC: Cell Line Catalog</b>: <br /> [https://dgrc.bio.indiana.edu/ Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC: Cell Culture Protocols</b>: <br />[https://dgrc.bio.indiana.edu/Protocols?tab=cells Drosophila Genomics Resource Center, Indiana University,  Bloomington, IN, USA]
 +
* <b>DGRC: Cell Culture FAQ Page</b>: <br />[https://dgrc.bio.indiana.edu/FAQs?tab=cells Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC: Feeder Cells</b>: <br />[https://dgrc.bio.indiana.edu/cells/FeederCells Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC: Fly Extract</b>:<br />[https://dgrc.bio.indiana.edu/cells/FlyExtract Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DRSC: General information about cell lines</b>: <br />[https://fgr.hms.harvard.edu/drosophila-cultured-cell-lines DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>DSRC: Resource information about CRISPR modified cell lines</b>: <br />[https://fgr.hms.harvard.edu/crispr-modified-cell-lines DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>DRSC: Protocol information about CRISPR modification of cell lines</b>: <br />[https://fgr.hms.harvard.edu/cell-based-crispr DRSC, Harvard Medical School, Boston, MA, USA]
  
 
=CRISPRs and TALENs=
 
=CRISPRs and TALENs=
 +
* <b>Addgene sgRNA Libraries</b>: Pooled sgRNA libraries for pooled CRISPR cell screening <br />[https://www.addgene.org/search/catalog/pooled-libraries/?q=Drosophila Addgene, Watertown, MA, USA]
 
* <b>CCTop</b> CRISPR/Cas9 optimum target finder:<br />[http://crispr.cos.uni-heidelberg.de/ Center for Organismal Studies, Heidelberg University, Heidelberg, DE]
 
* <b>CCTop</b> CRISPR/Cas9 optimum target finder:<br />[http://crispr.cos.uni-heidelberg.de/ Center for Organismal Studies, Heidelberg University, Heidelberg, DE]
 
* <b>CHOPCHOP</b> CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:<br />[https://chopchop.cbu.uib.no/ University of Bergen, Bergen, Norway]
 
* <b>CHOPCHOP</b> CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:<br />[https://chopchop.cbu.uib.no/ University of Bergen, Bergen, Norway]
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* <b>CRISPResso2 </b> CRISPR Design Tool:<br />[https://crispresso.pinellolab.partners.org/submission Broad Institute, Cambridge, MA, Harvard Medical School, Boston, MA, Massachusetts General Hospital, Boston, MA, Dana Farber Cancer Center, Boston, MA, Children's Hospital, Boston, MA]
 
* <b>CRISPResso2 </b> CRISPR Design Tool:<br />[https://crispresso.pinellolab.partners.org/submission Broad Institute, Cambridge, MA, Harvard Medical School, Boston, MA, Massachusetts General Hospital, Boston, MA, Dana Farber Cancer Center, Boston, MA, Children's Hospital, Boston, MA]
 
* <b>CRISPRscan</b> Novel scoring algorithm for selecting sgRNAs<br />[http://www.crisprscan.org// Giraldez Lab, Yale University, New Haven, CT, USA]
 
* <b>CRISPRscan</b> Novel scoring algorithm for selecting sgRNAs<br />[http://www.crisprscan.org// Giraldez Lab, Yale University, New Haven, CT, USA]
 +
* <b>DGRC Cell lines and vector reagents for CRISPR</b>:<br />[https://dgrc.bio.indiana.edu/Search?category=&query=crispr Drosophila Genomics Resource Center (DGRC), Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC sgRNA libraries</b>:<br />[https://dgrc.bio.indiana.edu/gRNA Drosophila Genomics Resource Center (DGRC), Indiana University, Bloomington, IN, USA]
 
* <b>DRSC CRISPR Efficiency Tool for Assessment of Designs</b>:<br />[http://www.flyrnai.org/evaluateCrispr/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 
* <b>DRSC CRISPR Efficiency Tool for Assessment of Designs</b>:<br />[http://www.flyrnai.org/evaluateCrispr/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 
* <b>DRSC Find CRISPRs</b>, Drosophila CRISPR gRNA design search tool:<br />[http://www.flyrnai.org/crispr2/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 
* <b>DRSC Find CRISPRs</b>, Drosophila CRISPR gRNA design search tool:<br />[http://www.flyrnai.org/crispr2/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
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* <b>SIFTED</b>, Specificity Inference for TAL Effector Design:<br />[https://galaxyproject.org/use/sifted/ Bulyk Lab, Harvard Medical School, Boston, MA, USA]
 
* <b>SIFTED</b>, Specificity Inference for TAL Effector Design:<br />[https://galaxyproject.org/use/sifted/ Bulyk Lab, Harvard Medical School, Boston, MA, USA]
 
* <b>TALengineering.org</b>, A Comprehensive Resource for Engineered TAL Effector Technology:<br />[http://talengineering.org/ Ekker lab, Joung Lab, MGH, Boston, USA]
 
* <b>TALengineering.org</b>, A Comprehensive Resource for Engineered TAL Effector Technology:<br />[http://talengineering.org/ Ekker lab, Joung Lab, MGH, Boston, USA]
 +
* <b>TRiP: Overview of sgRNA vectors</b>:<br />[https://fgr.hms.harvard.edu/sgrna-vectors TRiP, Harvard Medical School, Boston, MA, USA]
  
 
=Data Repositories=
 
=Data Repositories=
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* <b>SRA</b>, Sequence Read Archive:<br />[http://www.ncbi.nlm.nih.gov/sra SRA, NCBI, Bethesda, MD, USA]
 
* <b>SRA</b>, Sequence Read Archive:<br />[http://www.ncbi.nlm.nih.gov/sra SRA, NCBI, Bethesda, MD, USA]
 
* <b>UCSC Genome Browser Gateway</b> - D. melanogaster:<br />[http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser, UC Santa Cruz, Santa Cruz, USA]
 
* <b>UCSC Genome Browser Gateway</b> - D. melanogaster:<br />[http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser, UC Santa Cruz, Santa Cruz, USA]
 +
 +
=DNA Reagents=
 +
* <b>Addgene Highly requested Drosophila plasmids</b>: <br />[https://www.addgene.org/search/catalog/pooled-libraries/?q=Drosophila Addgene, Watertown, MA, USA]
 +
* <b>Addgene sgRNA Libraries</b>: Pooled sgRNA libraries for pooled CRISPR cell screening <br />[https://www.addgene.org/search/catalog/pooled-libraries/?q=Drosophila Addgene, Watertown, MA, USA]
 +
* <b>DNASU Drosophila plasmids</b>: <br />[https://dnasu.org/DNASU/AdvancedSearchOptions.do?species=Drosophila%20melanogaster&psi=0 DNASU Plasmid Repository, Arizona State University, Tempe, AZ, USA]
 +
* <b>DGRC DNA Clones Catalog</b>:<br />[https://dgrc.bio.indiana.edu/clones/Catalog Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC DNA Clone Collections</b>:<br />[https://dgrc.bio.indiana.edu/clones/BulkCollections  Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC DNA Clone FAQ Page</b>:<br />[https://dgrc.bio.indiana.edu/FAQs?tab=clones Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC DNA Clone Protocols</b>:<br />[https://dgrc.bio.indiana.edu/Protocols?tab=clones Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC DNA Vectors Catalog</b>:<br />[https://dgrc.bio.indiana.edu/vectors/Catalog Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC DNA Vectors FAQs Page</b>:<br />[https://dgrc.bio.indiana.edu/FAQs?tab=vectors Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC DNA Vectors Protocols</b>:<br />[https://dgrc.bio.indiana.edu/Protocols?tab=vectors Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>TRiP: VALIUM and WALIUM plasmid vector sets</b>:<br />[https://fgr.hms.harvard.edu/trip-plasmid-vector-sets TRiP, Harvard Medical School, Boston, MA, USA]
 +
* <b>TRiP: Plasmid cloning protocols</b>:<br />[https://fgr.hms.harvard.edu/cloning-and-sequencing TRiP, Harvard Medical School, Boston, MA, USA]
 +
* <b>TRiP: Overview of sgRNA vectors</b>:<br />[https://fgr.hms.harvard.edu/sgrna-vectors TRiP, Harvard Medical School, Boston, MA, USA]
  
 
=Drosophila Genomes Data and Metadata=
 
=Drosophila Genomes Data and Metadata=
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=Laboratory Resources=
 
=Laboratory Resources=
 
* <b>Laboratory Manual of Drosophila</b>: <br />[http://darwin.bio.uci.edu/~mueller/pdf/Lab_manual.pdf PDF, Chippindale, A. ''et al''., Department of Ecology & Evolutionary Biology, University of California, Irvine, USA]
 
* <b>Laboratory Manual of Drosophila</b>: <br />[http://darwin.bio.uci.edu/~mueller/pdf/Lab_manual.pdf PDF, Chippindale, A. ''et al''., Department of Ecology & Evolutionary Biology, University of California, Irvine, USA]
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 +
=Metabolomics=
 +
* <b>FlyMet</b>, A Tissue- and Sex-Specific Metabolomic Atlas and Database :<br />[http://www.flymet.org/ FlyMet, University of Glasgow, Glasgow, Scotland]
  
 
=Miscellaneous=
 
=Miscellaneous=
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* <b>droso4schools</b>, An online resource for school lessons using the fruit fly Drosophila:<br />[https://droso4schools.wordpress.com/ Manchester Fly Facility, University of Manchester, UK]
 
* <b>droso4schools</b>, An online resource for school lessons using the fruit fly Drosophila:<br />[https://droso4schools.wordpress.com/ Manchester Fly Facility, University of Manchester, UK]
 
* <b>''Drosophila'' & Computer Programming Game</b>, A scratch computer game based on the Drosophila life cycle: <br /> [https://poppi62.wordpress.com/2015/08/28/school-flies/#ICT Manchester Fly Facility, University of Manchester, UK]
 
* <b>''Drosophila'' & Computer Programming Game</b>, A scratch computer game based on the Drosophila life cycle: <br /> [https://poppi62.wordpress.com/2015/08/28/school-flies/#ICT Manchester Fly Facility, University of Manchester, UK]
 +
* <b>Experiments with Drosophila for Biology Courses</b>, An e-resource book for laboratory experiments at under- and post-graduate levels and for research projects in Biology courses :<br />[https://www.ias.ac.in/Publications/e-Books/Experiments_with_Drosophila_for_Biology_Courses Indian Academy of Sciences, India] [http://ftp.flybase.org/flybase/associated_files/Experiments_with_Drosophila_for_Biology_Courses.pdf pdf here ]
 
* <b>Fly on the Wall</b>, a blog by Bethany Christmann regarding fruit flies and research:<br />[http://blogs.brandeis.edu/flyonthewall/ Griffith Lab, Brandeis University, Waltham, MA, USA]
 
* <b>Fly on the Wall</b>, a blog by Bethany Christmann regarding fruit flies and research:<br />[http://blogs.brandeis.edu/flyonthewall/ Griffith Lab, Brandeis University, Waltham, MA, USA]
 
* <b>FlyMove</b>, an Image, Movie and Interactive Shockwave Resource:<br />[http://flymove.uni-muenster.de/ FlyMove, Muenster, Germany]
 
* <b>FlyMove</b>, an Image, Movie and Interactive Shockwave Resource:<br />[http://flymove.uni-muenster.de/ FlyMove, Muenster, Germany]
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=Single Cell RNA-seq=
 
=Single Cell RNA-seq=
 
* <b>ASAP</b> Automated Single-cell Analysis Pipeline: <br />[https://asap.epfl.ch/ ASAP, EPFL, Lausanne, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland]
 
* <b>ASAP</b> Automated Single-cell Analysis Pipeline: <br />[https://asap.epfl.ch/ ASAP, EPFL, Lausanne, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland]
 +
 
* <b>cisTopic</b> Probabilistic modelling of cis-regulatory topics from single cell epigenomics data: <br />[https://github.com/aertslab/cisTopic/ cisTopic, VIB Center for Brain & Disease Research, Leuven, Belgium, Department of Human Genetics, KU Leuven, Leuven, Belgium]
 
* <b>cisTopic</b> Probabilistic modelling of cis-regulatory topics from single cell epigenomics data: <br />[https://github.com/aertslab/cisTopic/ cisTopic, VIB Center for Brain & Disease Research, Leuven, Belgium, Department of Human Genetics, KU Leuven, Leuven, Belgium]
 +
 +
* <b>DeepCMC</b> A Neural Networks (NN) based approach for identifying genes that contain spatial information: <br />[https://github.com/TJU-CMC-Org/SingleCell-DREAM DeepCMC, Thomas Jefferson University, Philadelphia, PA, USA]
 +
 +
* <b>Distmap</b> To spatially map single cell RNA sequencing data by using an existing reference database of in situs: <br />[https://github.com/rajewsky-lab/distmap Distmap, BIMSB and MDC, Berlin, Germany]
 +
 
* <b>DRscDB</b> DRSC scRNA-seq DataBase: <br />[https://www.flyrnai.org/tools/single_cell/ DRscDB, DRSC, Harvard Medical School, Boston, USA]
 
* <b>DRscDB</b> DRSC scRNA-seq DataBase: <br />[https://www.flyrnai.org/tools/single_cell/ DRscDB, DRSC, Harvard Medical School, Boston, USA]
 +
 +
* <b>DVEX</b> Drosophila Virtual Expression eXplorer: <br />[https://shiny.mdc-berlin.de/DVEX/ DVEX, BIMSB and MDC, Berlin, Germany]
 +
 +
* <b>Fly Cell Atlas</b> A consortium of Drosophila researchers interested in single-cell genomics, transcriptomics, and epigenomics: <br />[https://asap.epfl.ch/ Fly Cell Atlas, Founders - Stein Aerts, Leuven, Belgium, Bart Deplancke, Lausanne, Switzerland, Robert Zinzen, Berlin, Germany]
 +
 +
* <b>Lasso.TopX</b> An approach using the Lasso and ranking statistics for identifying genes that contain spatial information: <br />[https://github.com/TJU-CMC-Org/SingleCell-DREAM/ Lasso.TopX, Thomas Jefferson University, Philadelphia, PA, USA]
 +
 +
* <b>novoSpaRc</b> Predicts locations of single cells in space by solely using single-cell RNA sequencing data.: <br />[https://github.com/rajewsky-lab/novosparc novoSpaRc, Harvard and Broad Institute, Cambridge, MA, USA, Max Delbrück Center, Berlin, Germany]
 +
 
* <b>SCEA</b> Single Cell Expression Atlas - Single Cell Gene Expression Across Species: <br />[https://www.ebi.ac.uk/gxa/sc SCEA, EMBL-EBI, Hinxton, UK, Sanger Institute, Wellcome Genome Campus, Hinxton, UK, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK]
 
* <b>SCEA</b> Single Cell Expression Atlas - Single Cell Gene Expression Across Species: <br />[https://www.ebi.ac.uk/gxa/sc SCEA, EMBL-EBI, Hinxton, UK, Sanger Institute, Wellcome Genome Campus, Hinxton, UK, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK]
 +
 
* <b>SCENIC</b> Single-Cell Regulatory Network Inference and Clustering <br />[https://github.com/aertslab/SCENIC SCENIC, Center for Brain & Disease Research, Leuven, Belgium, KU Leuven, Leuven, Belgium, University of Liege, Liege, Belgium, VIB Center for Cancer Biology, Leuven, Belgium]
 
* <b>SCENIC</b> Single-Cell Regulatory Network Inference and Clustering <br />[https://github.com/aertslab/SCENIC SCENIC, Center for Brain & Disease Research, Leuven, Belgium, KU Leuven, Leuven, Belgium, University of Liege, Liege, Belgium, VIB Center for Cancer Biology, Leuven, Belgium]
 +
 
* <b>SCope</b> Fast Visualization Tool for Large-Scale and High Dimensional Single-Cell Data <br />[https://github.com/aertslab/SCope SCope, VIB KU Leuven, Leuven, Belgium]
 
* <b>SCope</b> Fast Visualization Tool for Large-Scale and High Dimensional Single-Cell Data <br />[https://github.com/aertslab/SCope SCope, VIB KU Leuven, Leuven, Belgium]
 +
 +
* <b>Seurat</b> An R package designed for QC, analysis, and exploration of single-cell RNA-seq data.: <br />[https://satijalab.org/seurat/ Seurat, NYU, NY, NY, USA]
 +
 
* <b>VSN</b> A Repository of Pipelines for Single-Cell Data Analysis in Nextflow DSL2:  <br />[https://github.com/vib-singlecell-nf/vsn-pipelines VSN-Pipelines]
 
* <b>VSN</b> A Repository of Pipelines for Single-Cell Data Analysis in Nextflow DSL2:  <br />[https://github.com/vib-singlecell-nf/vsn-pipelines VSN-Pipelines]
  
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* <b>CIS-BP</b>, The online library of transcription factors and their DNA binding motifs:<br />[http://cisbp.ccbr.utoronto.ca/ CIS-BP, Hughes Lab, University of Toronto, Toronto, Canada and Weirauch lab, Cincinnati Children's Hospital, Cincinnati, OH, USA]
 
* <b>CIS-BP</b>, The online library of transcription factors and their DNA binding motifs:<br />[http://cisbp.ccbr.utoronto.ca/ CIS-BP, Hughes Lab, University of Toronto, Toronto, Canada and Weirauch lab, Cincinnati Children's Hospital, Cincinnati, OH, USA]
 
* <b>CORE</b>, A database utilizing the ElemeNT algorithm (see below) to annotate individual Drosophila observed TSS (using either CAGE or RNAseq data) for the presence of the various core promoter elements: <br />[http://lifefaculty.biu.ac.il/gershon-tamar/index.php/core-description Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel]
 
* <b>CORE</b>, A database utilizing the ElemeNT algorithm (see below) to annotate individual Drosophila observed TSS (using either CAGE or RNAseq data) for the presence of the various core promoter elements: <br />[http://lifefaculty.biu.ac.il/gershon-tamar/index.php/core-description Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel]
* <b>DBD</b>, Transcription factor prediction database: <br />[http://www.transcriptionfactor.org/index.cgi?Home DBD, MRC, Cambridge, UK]
 
 
* <b>ElemeNT</b>, An interactive tool for rapid and convenient detection of core promoter elements within a given sequence, implemented in Perl programming language: <br />[http://lifefaculty.biu.ac.il/gershon-tamar/index.php/element-description Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel]
 
* <b>ElemeNT</b>, An interactive tool for rapid and convenient detection of core promoter elements within a given sequence, implemented in Perl programming language: <br />[http://lifefaculty.biu.ac.il/gershon-tamar/index.php/element-description Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel]
 
* <b>EPD</b>, the Eukaryotic Promoter Database:<br />[http://epd.vital-it.ch/drosophila/drosophila_database.php/ EPD, Epalinges s/Lausanne, Switzerland]
 
* <b>EPD</b>, the Eukaryotic Promoter Database:<br />[http://epd.vital-it.ch/drosophila/drosophila_database.php/ EPD, Epalinges s/Lausanne, Switzerland]

Latest revision as of 19:40, 10 June 2021

Atlases, Images and Videos

Cell Lines and Cell Culture

CRISPRs and TALENs

Data Repositories

DNA Reagents

Drosophila Genomes Data and Metadata

Gene Expression Databases and Tools

Gene Groups

General Bioinformatics Tools

Genome Sequencing Projects

Human Disease: Drosophila Models and Orthologous Genes

Interaction and Pathway Databases

Laboratory Resources

Metabolomics

Miscellaneous

Non-coding (ncRNA) Databases and Tools

General

lncRNA

miRNA

General

NOTE - mirBase Release 21 (June 2014) uses old reference genome assemblies for D. melanogaster (Dmel_Release_5), D. simulans (Dsim_Release_1) and D. pseudoobscura (Dpse_Release_2). Linkouts from D. melanogaster miRNA genes to the Ensembl Genome browser (which displays Dmel_Release_6) will point to the old "Release_5" coordinates, which will be off the mark for many genes, especially those on X, 2R, 3R and 4 chromosomes.

miRNA Target Prediction

Validated miRNA Targets

Comparative miRNA Analysis

rRNA

tRNA

snoRNA

SRP RNA

Ontology Resources

Orthology Predictions

Phylogenetic Comparison Tools

Population Biology and Polymorphism Resources

Protein Analysis and Modification

Public Education

RNAi

Sequence Analysis

Single Cell RNA-seq

  • VSN A Repository of Pipelines for Single-Cell Data Analysis in Nextflow DSL2:
    VSN-Pipelines

Taxonomy

Transcription Regulation Databases and Tools

Suggest a tool or resource