Databases and other resources

Online Databases

Databases on aging:

• Human Ageing Genomic Resources
• Lifespan observation database
• Age related databases (JenAge)
• Digital Ageing Atlas​

Genome browsers:

• UCSC Genome Browser
• ENSEMBL Genome Browser
• NCBI Genome
• African Turquoise Killifish Genome Browser
• Mouse Genome Informatics at JAX

Interaction and network databases:

• BioGriD project
• STRING
• Histome
• GeneMania

Pathway informations:

• Gene Ontology Consortium
• KEGG
• Wikipathways
• GSEA/MSigDB
• REACTOME
• Biocarta
• Panther
• ConnectivityMap
• GTEX
• OMIM​

Transcription factors, target genes and motifs:

• Transcription Factor Encyclopedia
• JASPAR (TF motifs)
• TRANSFAC (TF motifs)
• STAMP (motif clustering and alignement)
• ChEA (Curated TF binding from ChIP-X experiments)
• ReMap2018 (Curated TF binding from ChIP-X experiments)​

Epigenomics resources:

• ENCODE
• NIH Roadmap
• WashU Epigenome Browser
• ModEncode

Genomic data repositories:

• GEO Datasets
• ArrayExpress
• CistromeMap
• SRA

Other Important Resources

Transgenic mouse ordering:

• JAX mouse search
• UC Davis Knock-Out Mouse Project (KOMP)
• International Mouse Strain Resource

Literature resources:

• Norris Medical Library
• Pubmed
• MouseMine
• Mouse Genetics (Lee M. Silver) at MGI
• Statistics for biologists (Nature Methods)
• PubCrawler (Alert Service for PubMed and GenBank)
• Commonly misidentified cell lines

Protocol resources:

• Worthington tissue dissociation guide
• 10xGenomics protocol resources

Plasmid databases/ordering:

• Addgene
• Sigma Mission shRNA search tool

Antibody validation databases:

• The Antibody Validation Database
• ENCODE validated antibodies

Validated qPCR primer repositories:

• PrimerBank
• RTPrimerDB
• Mouse qPCR primer depot (in silico)

Molecular cloning resources:

• NEBCutter2.0
• NEB traditional cloning guide
• SnapGene Viewer (Plasmid map annotation)

Online Protocol resources:

• Morimoto Lab protocols