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Primary nucleotide sequence databases (next-generation sequencing)

Next-generation sequencing experiments have generated large amounts of data that are collected in public archives (primary databases). Secondary data extracted from these primary databases are available in the gene expression and disease/disorder…
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ENA
Dataset

ENA European Nucleotide Archive

Offers a repository for related with nucleotide sequencing workflows. ENA…

Offers a repository for related with nucleotide sequencing workflows. ENA provides data model containing input information, output machine data and interpreted information. The database gathers a…

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ArrayExpress
Dataset

ArrayExpress

A database of functional genomics experiments that can be queried and the data…

A database of functional genomics experiments that can be queried and the data downloaded. ArrayExpress includes data generated by sequencing or array-based technologies. Data are submitted by users…

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SRA
Dataset

SRA Sequence Read Archive

Stores raw sequence data from next-generation sequencing (NGS) technologies.…

Stores raw sequence data from next-generation sequencing (NGS) technologies. SRA is a database which works as a core infrastructure for sharing of pre-publication sequence data, with the aim to make…

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GEO
Dataset

GEO Gene Expression Omnibus

An international public repository for high-throughput microarray and…

An international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw…

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BioSD
Dataset

BioSD BioSamples Database

A database at EBI that stores information about biological samples used in…

A database at EBI that stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. The goals of the BioSample Database include: (i)…

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TIARA
Dataset

TIARA Total Integrated Archive of short-Read and Array

Gathers information about raw-level personal genomic data from whole genome…

Gathers information about raw-level personal genomic data from whole genome next generation sequencing (NGS) and ultra-high-resolution comparative genomic hybridization (CGH) arrays. TIARA enables…

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NCBI BioSample
Dataset

NCBI BioSample

Contains descriptions of biological source materials used in experimental…

Contains descriptions of biological source materials used in experimental assays.

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compendiumdb
Desktop

compendiumdb

Provides an environment for downloading functional genomics data from Gene…

Provides an environment for downloading functional genomics data from Gene Expression Omnibus (GEO), parsing the information into a local or remote database, and interacting with the database using…

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DOR
Dataset

DOR DDBJ Omics Archive

A public functional genomics data repository supporting MIAME and…

A public functional genomics data repository supporting MIAME and MINSEQE-compliant data submissions. Array- and sequence-based data are accepted in the MAGE-TAB format.

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RNASeq-er
Web

RNASeq-er

Accesses the results of a systematically and continually updated and…

Accesses the results of a systematically and continually updated and continually growing analysis of public RNA-seq data in European Nucleotide Archive (ENA). RNASeq-er enables ontology-powered…

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SRAdb
Desktop

SRAdb

Helps to make queries of the metadata associated with SRA submission, study,…

Helps to make queries of the metadata associated with SRA submission, study, sample, experiment and to run more robust and precise, and to make access to sequencing data in the SRA easier. All the…

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GSA
Dataset

GSA Genome Sequence Archive

Provides a data repository for archiving raw sequence data. GSA is built based…

Provides a data repository for archiving raw sequence data. GSA is built based on INSDC data standards, structures and provides data archival services for scientific communities. This resource…

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SeqDepot
Dataset

SeqDepot

Enables users to retrieve and process with minimal effort both primary and…

Enables users to retrieve and process with minimal effort both primary and intrinsic feature data for existing sequences. SeqDepot is a database that assimilates known primary sequences with…

CODEX
Dataset

CODEX

Provides access to processed and curated NGS experiments, including ChIP-Seq…

Provides access to processed and curated NGS experiments, including ChIP-Seq (transcription factors and histones), RNA-Seq and DNase-Seq. The current focus of this database is to unify NGS data for…

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VaProS
Web

VaProS VAriation effect on PROtein Structure and function

Integrates information in structural biology with genome, transcriptome,…

Integrates information in structural biology with genome, transcriptome, interactome and other information and provides seamless environment to scientists for analyzing these different types of…

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NCBI Trace…
Dataset

NCBI Trace Archive

A permanent repository of DNA sequence chromatograms (traces), base calls, and…

A permanent repository of DNA sequence chromatograms (traces), base calls, and quality estimates for single-pass reads from various large-scale sequencing projects.

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RNASeqMetaDB
Dataset

RNASeqMetaDB

Permits efficient searching of its database containing comprehensive…

Permits efficient searching of its database containing comprehensive information for all public RNA-seq data sets on mice with genotype as a factor. RNASeqMetaDB contains metadata for a total of 306…

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GEN3VA
Dataset

GEN3VA GENE Expression and Enrichment Vector Analyzer

Enables the integrative analysis of aggregated collections of tagged gene…

Enables the integrative analysis of aggregated collections of tagged gene expression signatures identified and extracted from GEO. GEN3VA can be used to identify, aggregate, and analyze themed…

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NCBI BioProject
Dataset

NCBI BioProject

Established to facilitate organization and classification of project data…

Established to facilitate organization and classification of project data submitted to NCBI, EBI and DDBJ databases.

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MetaSRA
Desktop

MetaSRA Meta Sequence Read Archive

A database of normalized sequence read archive (SRA) sample-specific metadata…

A database of normalized sequence read archive (SRA) sample-specific metadata following a schema inspired by the metadata organization of the ENCODE project. MetaSRA involves mapping samples to terms…

ModelDB
Dataset

ModelDB

Congregates computational neuroscience models in any simulator format or…

Congregates computational neuroscience models in any simulator format or programming language. ModelDB provides a free platform, both public and private, which allows users to submit the source code…

CGHub
Dataset

CGHub Cancer Genomics Hub

A secure repository for storing, cataloging, and accessing cancer genome…

A secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects.

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NCBI SRA…
Desktop

NCBI SRA Toolkit

Enables reading of sequencing files from the SRA database and writing files…

Enables reading of sequencing files from the SRA database and writing files into the same format. The NCBI SRA Toolkit is provided in the form of the SRA SDK, and can be compiled with GCC. It allows…

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Illumina Data…
Dataset

Illumina Data Sets

View sequencing data generated on Illumina sequencers and analyzed in…

View sequencing data generated on Illumina sequencers and analyzed in BaseSpace, the Illumina genomics computing environment. See how BaseSpace makes it easy to analyze your sequencing data and…

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DRA
Dataset

DRA DDBJ Sequence Read Archive

An archive database for output data generated by next-generation sequencing…

An archive database for output data generated by next-generation sequencing machines including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, and others.

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