Useful resources
Tools for experimental design
- Harvard Primer Bank
- pga.mgh.harvard.edu/primerbank/
- Database of published PCR and RT-PCR primers
- pga.mgh.harvard.edu/primerbank/
- Primer design
- Primer 3 Plus: www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi
- Verification of primer specificity and amplicon size
- Primer-BLAST: www.ncbi.nlm.nih.gov/tools/primer-blast/
- Check primer criteria
- IDT: www.idtdna.com/site/account/login?returnurl=/calc/analyzer
- Check GC content, primer dimerization, etc. Requires registration and log in.
- IDT: www.idtdna.com/site/account/login?returnurl=/calc/analyzer
- Primer design for bisulfite PCR
- BiSearch: http://bisearch.enzim.hu
- Also allows in silico analysis of existing bisulfite primers.
- BiSearch: http://bisearch.enzim.hu
- IUPAC nucleotide codes
- Reverse complement of a sequence
- Antibody database
- CiteAb: www.citeab.com
- Ranks antibodies by number of citations.
- CiteAb: www.citeab.com
- Agonist/antagonist database
- Selleckchem: www.selleckchem.com
- Allows identification of agonists/antagonists and compares their specificity.
- Selleckchem: www.selleckchem.com
- Fluorophore spectra
- Fluorescence SpectraViewer: www.thermofisher.com/us/en/home/life-science/cell-analysis/labeling-chemistry/fluorescence-spectraviewer.html
- Compares excitation and emission wavelengths for fluorophores.
- Fluorescence SpectraViewer: www.thermofisher.com/us/en/home/life-science/cell-analysis/labeling-chemistry/fluorescence-spectraviewer.html
- Mouse colony management software
- MouseJ: www.mousej.org
- Requires download.
- MouseJ: www.mousej.org
Tools for gene identifier conversion
- Database to database conversion
- bioDBnet: biodbnet-abcc.ncifcrf.gov
- Allows conversion between identifiers, e.g. Ensembl ID to Entrez Gene ID. Does not allow UCSC Gene ID as an input (use BioTools).
- BioTools: www.biotools.fr
- Fewer options than bioDBnet but allows UCSC Gene ID as an input. Has resources for human and mouse (and other organisms).
- bioDBnet: biodbnet-abcc.ncifcrf.gov
- Ensembl ID history converter
- Ensembl version converter: useast.ensembl.org/Homo_sapiens/Tools/IDMapper?db=core
Gene and sequence databases
- Gene, protein and phenotype information
- MGI - Mouse Genome Informatics: www.informatics.jax.org
- Also includes information on spatial and temporal gene expression, Gene Ontology terms, mutant alleles, etc.
- MGI - Mouse Genome Informatics: www.informatics.jax.org
- Gene expression level comparison between tissues
- BioGPS: www.biogps.org
- Uses microarray data. Includes mouse, human and other organisms.
- BioGPS: www.biogps.org
- Mouse strain variation
- Mouse Genomes Project: www.sanger.ac.uk/science/data/mouse-genomes-project
- Allows identification of sequence variation between common laboratory mouse strains
- Mouse Genomes Project: www.sanger.ac.uk/science/data/mouse-genomes-project
- Mouse imprinted gene list
- MouseBook: www.mousebook.org/imprinting-gene-list
- A downloaded list of imprinted gene names from this database is available here (downloaded April 5, 2018 - check for updates before using).
- MouseBook: www.mousebook.org/imprinting-gene-list
- Human (and other organisms) imprinted gene list
- Catalogue of parent-of-origin effects: igc.otago.ac.nz/home.html
- Includes a downloadable table showing conservation of imprinting across species.
- Includes a downloadable table showing conservation of imprinting across species.
- Catalogue of parent-of-origin effects: igc.otago.ac.nz/home.html
Genome and epigenome browsers
- UCSC Genome Browser
- Ensembl Genome Browser
- WashU Epigenome Browser
- epigenomegateway.wustl.edu/browser/
- Useful for visualizing and comparing epigenetic states across multiple cell types.
- epigenomegateway.wustl.edu/browser/
- Integrative Genomics Viewer
- software.broadinstitute.org/software/igv/
- Useful for visualizing aligned WGBS and RRBS reads. Requires download.
- Useful for visualizing aligned WGBS and RRBS reads. Requires download.
- software.broadinstitute.org/software/igv/
Tools for analysis and figure construction
- Statistical analyses and data modeling
- JMP: www.jmp.com
- Does not require knowledge of coding. Available through NCSU Software Licensing. Requires download.
- JMP: www.jmp.com
- Guide to using R
- Cookbook for R: www.cookbook-r.com
- Hypergeometric calculation
- P-value calculator: systems.crump.ucla.edu/hypergeometric/
- Enables determination of enrichment of one dataset within another (e.g. 'are genes from network X over-represented among differentially expressed genes in my RNA-seq?').
- P-value calculator: systems.crump.ucla.edu/hypergeometric/
- Functional enrichment
- Enrichr: amp.pharm.mssm.edu/Enrichr/
- Bisulfite cloning and sequencing analysis
- BiQ Analyzer: https://biq-analyzer.bioinf.mpi-inf.mpg.de
- Allows high-throughput analysis of bisulfite cloning and sequencing data. Includes quality control steps such as eliminating PCR duplicates. Produces lollipop diagrams. Requires download (available on the shared laptop).
- BiQ Analyzer: https://biq-analyzer.bioinf.mpi-inf.mpg.de
- Venn diagram builders
- BioVenn: www.biovenn.nl
- Van de Peer lab: http://bioinformatics.psb.ugent.be/beg/tools/venn-diagrams
- BxToolBox: http://apps.bioinforx.com/bxaf7c/app/venn/app_overlap.php
- Heat map generator
- Heatmapper: http://heatmapper.ca
- Also see GraphBio below
- Concept maps and flow charts
- Lucidchart: https://www.lucidchart.com/pages/
- Exon/intron graphic maker
- Worm Web: wormweb.org/exonintron
- Scientific images and art
- Servier Medical Art: smart.servier.com
- Sequence alignment
- BoxShade: embnet.vital-it.ch/software/BOX_form.html
- Allows visualization of multiple alignments.
- BoxShade: embnet.vital-it.ch/software/BOX_form.html
- Omics data visualization
- GraphBio: http://www.graphbio1.com/en/
- Offers a range of tools for data visualization including heat maps, cluster analysis, survival curves, volcano plots and more
- GraphBio: http://www.graphbio1.com/en/
NCSU Core Facilities
- NCSU Lab Management System
- labs.ncsu.edu
- For project submission to:
- Toxicology Procedure Room booking
- Biological Resources Facility: brf.sciences.ncsu.edu
- Link is on the bottom right of the page.
- Biological Resources Facility: brf.sciences.ncsu.edu
- NCSU Software Licensing
- Office of Information Technology: software.ncsu.edu
- Full list of licensed software available to NCSU faculty, staff and students. Requires log in.
- Office of Information Technology: software.ncsu.edu
Cowley Lab inventory and ordering
- LabSuit: https://www.app.labsuit.com/login/
- Requires registration and log in.
Career development tools
- Science Careers Individual Development Plan: myidp.sciencecareers.org