Useful resources

Tools for experimental design

Tools for gene identifier conversion

Gene and sequence databases

Genome and epigenome browsers

Tools for analysis and figure construction

NC State University core facilities

Cowley Lab inventory and ordering

Career development tools

 Tools for experimental design

• Harvard Primer Bank
  • pga.mgh.harvard.edu/primerbank/ 
    • Database of published PCR and RT-PCR primers

 

• 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.

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• Primer design for bisulfite PCR
  • BiSearch: http://bisearch.enzim.hu
    • Also allows in silico analysis of existing bisulfite primers.

 

• IUPAC nucleotide codes
  • www.bioinformatics.org/sms/iupac.html 

 

• Reverse complement of a sequence
  • www.bioinformatics.org/sms/rev_comp.html 

 

• Antibody database
  • CiteAb: www.citeab.com
    • Ranks antibodies by number of citations.

 

• Agonist/antagonist database
  • Selleckchem: www.selleckchem.com
    • Allows identification of agonists/antagonists and compares their specificity.

 

• 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.

 

• ​Mouse colony management software
  • ​MouseJ: www.mousej.org
    • ​Requires download.

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).

 

• 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.

 

• Gene expression level comparison between tissues
  • ​BioGPS: www.biogps.org
    • Uses microarray data. Includes mouse, human and other organisms.

 

• 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 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).

 

• 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. 
      

Genome and epigenome browsers 

• UCSC Genome Browser
  • genome.ucsc.edu 

 

• Ensembl Genome Browser
  • www.ensembl.org/index.html 

 

• WashU Epigenome Browser
  • epigenomegateway.wustl.edu/browser/ 
    • Useful for visualizing and comparing epigenetic states across multiple cell types.

 

• Integrative Genomics Viewer
  • software.broadinstitute.org/software/igv/ 
    • ​Useful for visualizing aligned WGBS and RRBS reads. Requires download.
      

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.

 

• 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?').

 

• 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).

 

• 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

 

• 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.  

NCSU Core Facilities 

• NCSU Lab Management System
  • ​labs.ncsu.edu 
  • For project submission to:
    • Cellular and Molecular Imaging Facility 
    • Genomics Sciences Laboratory 
    • METRIC (proteomics)

 

• Toxicology Procedure Room booking
  • Biological Resources Facility: brf.sciences.ncsu.edu
    • Link is on the bottom right of the page.

 

• 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.

Cowley Lab inventory and ordering 

• Quartzy: www.quartzy.com
  • Requires registration and log in.

Career development tools

• Science Careers Individual Development Plan: myidp.sciencecareers.org