Sitemap

Category	Database	Description
Gene Expression Databases	GTEx	RNA expression across multiple human tissues.
	Expression Atlas	Provides gene expression patterns across different species and conditions, including diseases.
	GEO	Repository of high-throughput gene expression data, including RNA-seq and microarray data.
	ArrayExpress	Contains a wide array of gene expression data similar to GEO.
	Human Protein Atlas	Includes RNA and protein expression data in various tissues and organs.
Genomic Variation - population genetics	1000 Genomes Project	Catalog of human genetic variation, including common SNPs and structural variants.
	Human Genome Diversity Project (HGDP)	Focused on genetic diversity across global populations, including rare and indigenous groups.
	European Variation Archive (EVA)	Open-access repository for genomic variation data across species.
Genomic Variation - variant interpretation	gnomAD	Aggregates exome/genome sequencing data; focuses on population allele frequencies and rare variants.
	dbSNP	Database for single nucleotide polymorphisms (SNPs) and other genetic variations.
	ClinVar	Clinical significance of genetic variants linked to human health and diseases.
Genomic Variation - Large-Scale Cohorts	UK Biobank	Large-scale biomedical database with genetic, lifestyle, and health information.
	GWAS Catalog	Focuses on genetic variants associated with traits/diseases from published GWAS studies.
	TOPMed	Focuses on diseases related to heart, lung, blood, and sleep disorders.
Genomic Variation - cancer focused	cBioPortal	Interactive platform for visualizing and analyzing multi-omics cancer data with clinical outcomes.
	TCGA / GDC	Comprehensive multi-omics data for various cancer types.
	COSMIC	Catalogue of somatic mutations in cancer, including driver mutations.
	dbGaP	Contains datasets exploring the genetic basis of various diseases.
	ICGC	International repository for cancer genome data, covering rare and global cancers.
Epigenomics and Regulatory	ENCODE	Identifies all functional elements in the human genome.
	Roadmap Epigenomics Project	Provides data on the epigenomic landscape of different tissues and cell types.
	BluePrint Epigenome	Focuses on epigenomic data of blood cells in health and disease.
Integrated and Multi-Omics	Ensembl	Comprehensive resource for genomic data, including annotations and variants.
	UCSC Genome Browser	Integrates data from various genomic resources with visualization tools.
	FANTOM	Contains data on gene expression and regulatory elements, focusing on non-coding RNAs.
	Reactome	Pathway database for exploring molecular interactions and biological processes.
Single-Cell Databases	Human Cell Atlas	Provides single-cell RNA-seq data from various human tissues and organs.
	Tabula Sapiens	A single-cell transcriptomic atlas of human tissues.
Metagenomics Databases	MG-RAST	Offers analysis and archiving for metagenomic data.
	Human Microbiome Project (HMP)	Focuses on the microbial communities found in and on the human body.

NGS

Layer / Goal	Widely used method(s)	Paired newer method(s)	Why the newer one is superior	Main purpose
DNA: genome & SVs	Short-read WGS (Illumina)	Long-read WGS (PacBio HiFi, ONT Q20+); hybrid assemblies	Resolves repeats & SVs; phasing/haplotypes; fewer mapping ambiguities	Detect SNVs, indels, SVs, CNVs, haplotypes
DNA: methylation	WGBS / RRBS	EM-seq / TAPS; ONT direct 5mC calling	Less DNA damage, GC bias; direct multi-base detection	Base-level 5mC/5hmC methylome and allele-specific methylation
Chromatin accessibility	ATAC-seq / scATAC	Multiome (ATAC+RNA); long-read ATAC	Joint regulatory info; better peak-to-gene linkage	Identify open chromatin regions, TF footprints
Protein–DNA binding	ChIP-seq	CUT&Tag / CUT&RUN	Higher signal-to-noise, lower input, fewer artifacts	Map TF or histone mark binding sites
3D genome	Hi-C (in situ)	Micro-C; HiChIP; single-cell Hi-C	Nucleosome resolution, mark-anchored loops, single-cell structure	Reveal chromatin loops, domains, and genome folding
RNA: expression	RNA-seq (ribo-minus, stranded)	Long-read RNA-seq (Iso-Seq, ONT); UMI-based high-throughput	Full-length isoforms, better quant accuracy	Quantify transcript abundance and differential expression
RNA: isoforms & splicing	Junction-aware short-read RNA-seq	Long-read RNA/cDNA sequencing	Unambiguous isoforms, fusion/splice variant resolution	Study alternative splicing, fusions, and isoform diversity
Nascent transcription / kinetics	PRO-seq / GRO-seq	TT-seq; SLAM-seq / TimeLapse-seq	Time-resolved labeling; synthesis/decay rates	Measure transcriptional dynamics, initiation, and elongation
RNA–protein binding	eCLIP / iCLIP	iCLIP2 / irCLIP / RNP-MaP	Higher positional accuracy, captures weak interactions	Identify RNA-binding protein targets and motifs
RNA modifications (post-RNA)	MeRIP-seq (m6A-IP)	miCLIP2; direct RNA nanopore sequencing	Base-level m⁶A/ψ/m⁵C detection; antibody-free	Map chemical RNA modifications (m⁶A, m⁵C, ψ)
Translation	Ribo-seq	QTI/GTI-seq; disome-seq	Detects initiation, ribosome collisions	Measure translation efficiency, start-site mapping
Proteome quantification	DDA LC-MS/MS	DIA/SWATH; PASEF-DIA; single-cell proteomics	Fewer missing values, reproducible quantification	Identify and quantify proteins in bulk or single cells
Protein post-translational modification (PTM)	Phospho-enrichment + DDA	DIA phospho-proteomics; FAIMS/tims ion-mobility	Higher PTM coverage, multiplexing, improved quant	Identify and quantify phospho/acetyl/ubiquitin sites
Protein interactions / proximity	AP-MS / Co-IP-MS	BioID / TurboID / APEX	Captures transient and weak interactors; spatial context	Detect protein–protein interactions and local neighborhoods
Spatial multi-omics	Visium (10x)	Slide-seqV2; MERFISH / CosMx / Xenium	Higher plex & subcellular resolution; multi-modal	Map RNA/protein distribution within tissue context
Single-cell multi-omics	Separate scRNA/scATAC	Same-cell multiome (ATAC+RNA), SHARE-seq, Paired-Tag	Links regulatory chromatin to RNA output directly	Integrate regulatory and expression layers per cell