Difference between revisions of "FlyBase:Drosophila Online Resources"

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=Cell Lines and Cell Culture=
 
=Cell Lines and Cell Culture=
* '''Cellosaurus'''<br />A thesaurus of cell lines which attempts to list all cell lines used in biomedical research. [http://web.expasy.org/cellosaurus/ '''Cellosaurus''']
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* <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>Drosophila Genomics Resource Center (DGRC) Cell Line Catalog</b>:<br />[https://dgrc.bio.indiana.edu/cells/Catalog DGRC Cell lines, Indiana University, Bloomington, IN, USA]
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* <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 Cell line protocols, Indiana University, Bloomington, IN, USA]
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* <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 Cell line FAQs, Indiana University, Bloomington, IN, USA]
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* <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 Feeder Cells, Indiana University, Bloomington, IN, USA]
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* <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 Fly Extract, Indiana University, Bloomington, IN, USA]
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* <b>DGRC: Fly Extract</b>:<br />[https://dgrc.bio.indiana.edu/cells/FlyExtract Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
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* <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]
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* <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]
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* <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=
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* <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]
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* <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]
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* <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]
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* <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>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]
  
=Drosophila Genomes Data and Metadata=
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=DNA Reagents=
* <b>Drosophila Genomics Resource Center (DGRC) DNA Clones Catalog</b>:<br />[https://dgrc.bio.indiana.edu/clones/Catalog DGRC Clones, Indiana University, Bloomington, IN, USA]
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* <b>Addgene Highly requested Drosophila plasmids</b>: <br />[https://www.addgene.org/search/catalog/pooled-libraries/?q=Drosophila Addgene, Watertown, MA, USA]
* <b>Drosophila Genomics Resource Center (DGRC) DNA Clone Collections</b>:<br />[https://dgrc.bio.indiana.edu/clones/BulkCollections DGRC Clone Collections, Indiana University, Bloomington, IN, USA]
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* <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]
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* <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]
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* <b>DGRC DNA Clones Catalog</b>:<br />[https://dgrc.bio.indiana.edu/clones/Catalog Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
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* <b>DGRC DNA Clone Collections</b>:<br />[https://dgrc.bio.indiana.edu/clones/BulkCollections  Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
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* <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]
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* <b>DGRC DNA Clone Protocols</b>:<br />[https://dgrc.bio.indiana.edu/Protocols?tab=clones Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
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* <b>DGRC DNA Vectors Catalog</b>:<br />[https://dgrc.bio.indiana.edu/vectors/Catalog Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
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* <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]
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* <b>DGRC DNA Vectors Protocols</b>:<br />[https://dgrc.bio.indiana.edu/Protocols?tab=vectors Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
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* <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]
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* <b>TRiP: Plasmid cloning protocols</b>:<br />[https://fgr.hms.harvard.edu/cloning-and-sequencing TRiP, Harvard Medical School, Boston, MA, USA]
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* <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=

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