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ArrayExpress update – from bulk to single-cell expression data

Awais Athar, Anja Füllgrabe, Nancy George, Haider Iqbal, Laura Huerta, Ahmed Ali, Catherine Snow, Nuno A Fonseca, Robert Petryszak, Irene Papatheodorou, Ugis Sarkans, Alvis Brazma
2018 Nucleic Acids Research  
Additionally, there is a significant increase in experiments investigating single cells, rather than bulk samples, known as single-cell RNA-seq.  ...  ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data from a variety of technologies assaying functional modalities of a genome, such as gene expression or promoter  ...  ACKNOWLEDGEMENTS The authors would like to thank Juan Antonio Vicziano. FUNDING  ... 
doi:10.1093/nar/gky964 pmid:30357387 pmcid:PMC6323929 fatcat:p2n5pu6dgffvtf3jp5ypftowxu

Expression Atlas update: from tissues to single cells

2019 Nucleic Acids Research  
Single Cell Expression Atlas was launched in 2018 and currently includes 123 single cell RNA-Seq studies from 12 species.  ...  With the increased availability of single cell RNA-Seq datasets in the public archives, we have now extended Expression Atlas with a new added-value service to display gene expression in single cells.  ...  We would like to thank our collaborators from  ... 
doi:10.1093/nar/gkz947 pmid:31665515 pmcid:PMC7145605 fatcat:vp5gbm3mqbhjbhbucprqwyaggq

The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data

Robert Petryszak, Nuno A Fonseca, Anja Füllgrabe, Laura Huerta, Maria Keays, Y Amy Tang, Alvis Brazma, Bonnie Berger
2017 Bioinformatics  
We present a Web service to access the results of a systematically and continually updated standardized alignment as well as gene and exon expression quantification of all public bulk (and in the near  ...  future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer.  ...  and Ontologies Team for the provision of tools for retrieval of the sequencing metadata from BioSamples database and of an up-to-date annotation of sequencing meta-data to ontologies.  ... 
doi:10.1093/bioinformatics/btx143 pmid:28369191 pmcid:PMC5870697 fatcat:ild6vn5ll5hcfj4alj5kksj234

Cell-level metadata are indispensable for documenting single-cell sequencing datasets

Sidhant Puntambekar, Jay R Hesselberth, Kent A Riemondy, Rui Fu
2021 PLoS Biology  
Single-cell RNA sequencing (scRNA-seq) provides an unprecedented view of cellular diversity of biological systems.  ...  We encourage investigators, reviewers, journals, and data repositories to improve their standards and ensure proper documentation of these valuable datasets.  ...  For GEO, this would be accomplished by updating the "Processed data files" requirements to outline required data types for single-cell sequencing submissions (Fig 1A) .  ... 
doi:10.1371/journal.pbio.3001077 pmid:33945522 pmcid:PMC8121533 fatcat:y4ndrqnb7zf2xjlls5ix2v2xvi

ArrayExpress--a public database of microarray experiments and gene expression profiles

H. Parkinson, M. Kapushesky, M. Shojatalab, N. Abeygunawardena, R. Coulson, A. Farne, E. Holloway, N. Kolesnykov, P. Lilja, M. Lukk, R. Mani, T. Rayner (+4 others)
2007 Nucleic Acids Research  
Funding to pay the Open Access publication charges for this article was provided by the FELICS grant from the European Commission.  ...  ACKNOWLEDGEMENTS The authors would like to acknowledge Patrick Kemmeren, Susanna-Assunta Sansone, Philippe Rocca-Serra, Catherine Brooksbank, Petteri Jokkinen and the EBI systems group and the ArrayExpress  ...  BULK DOWNLOADS The ArrayExpress data can be downloaded from ftp://ftp.ebi. ac.uk/pub/databases/microarray/data/.  ... 
doi:10.1093/nar/gkl995 pmid:17132828 pmcid:PMC1716725 fatcat:yrtu55lvzzci5j57beyijo2hhe

EndoDB: a database of endothelial cell transcriptomics data

Shawez Khan, Federico Taverna, Katerina Rohlenova, Lucas Treps, Vincent Geldhof, Laura de Rooij, Liliana Sokol, Andreas Pircher, Lena-Christin Conradi, Joanna Kalucka, Luc Schoonjans, Guy Eelen (+5 others)
2018 Nucleic Acids Research  
collected from 360 datasets comprising a total of 4741 bulk and 5847 single cell endothelial transcriptomes from six different organisms.  ...  The increasing use of high-throughput technologies such as gene expression microarrays and (single cell) RNA sequencing generated a wealth of data on the molecular basis of EC (dys-)function.  ...  Interestingly, all three genes marked a specific subset of TECs suggesting that the observed upregulation of cell cycle-related genes in bulk transcriptomics data results from increased expression in a  ... 
doi:10.1093/nar/gky997 pmid:30357379 pmcid:PMC6324065 fatcat:pymanotqtrdmnfnw4ltd3vsxoe

Expression Atlas update: gene and protein expression in multiple species

Pablo Moreno, Silvie Fexova, Nancy George, Jonathan R Manning, Zhichiao Miao, Suhaib Mohammed, Alfonso Muñoz-Pomer, Anja Fullgrabe, Yalan Bi, Natassja Bush, Haider Iqbal, Upendra Kumbham (+22 others)
2021 Nucleic Acids Research  
Expression Atlas contains data from differential studies (microarray and bulk RNA-Seq) and baseline studies (bulk RNA-Seq and proteomics), whereas Single Cell Expression Atlas is currently dedicated to  ...  Expression Atlas is currently divided into Bulk Expression Atlas and Single Cell Expression Atlas.  ...  We would like to thank the data wranglers of the Human Cell Atlas Data Coordination Platform for their assistance collating HCA data for the Single Cell Expression Atlas.  ... 
doi:10.1093/nar/gkab1030 pmid:34850121 pmcid:PMC8728300 fatcat:w4ochry6hreqhjcqkaezuperpe

Guidelines for reporting single-cell RNA-Seq experiments [article]

Anja Füllgrabe, Nancy George, Matthew Green, Parisa Nejad, Bruce Aronow, Laura Clarke, Silvie Korena Fexova, Clay Fischer, Mallory Ann Freeberg, Laura Huerta, Norman Morrison, Richard H. Scheuermann (+6 others)
2019 arXiv   pre-print
Single-cell RNA-Sequencing (scRNA-Seq) has undergone major technological advances in recent years, enabling the conception of various organism-level cell atlassing projects.  ...  Here, we describe guidelines for a minimum set of metadata to sufficiently describe scRNA-Seq experiments, ensuring reproducibility of data analyses.  ...  Data generators producing data from new cellular-resolution technologies can request updates to the HCA metadata standard in order to better capture information about new data types, for example 10x sequencingspecific  ... 
arXiv:1910.14623v1 fatcat:thmk5zfofrbkhfpv33znev2cym

The European Bioinformatics Institute's data resources

C. Brooksbank
2003 Nucleic Acids Research  
(ArrayExpress).  ...  As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner.  ...  Gene expression data submissions MIAMExpress MIAME-compliant microarray data submissions to the ArrayExpress database. signatures in the entry.  ... 
doi:10.1093/nar/gkg066 pmid:12519944 pmcid:PMC165513 fatcat:46gy4lg2v5ak7mdns47kaelgpu

Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata

J. J. Faith, M. E. Driscoll, V. A. Fusaro, E. J. Cosgrove, B. Hayete, F. S. Juhn, S. J. Schneider, T. S. Gardner
2007 Nucleic Acids Research  
facilitate the analysis and visualization of expression data in compendia compiled from multiple laboratories.  ...  The expression data is uniformly normalized to make the data generated by different laboratories and researchers more comparable.  ...  UPDATE AND DATA SUBMISSION PROCEDURES Raw CEL files are periodically collected from the ArrayExpress and GEO microarray databases.  ... 
doi:10.1093/nar/gkm815 pmid:17932051 pmcid:PMC2238822 fatcat:jtpkocvbufacxkpb6q7p3cs6fu

GRNdb: decoding the gene regulatory networks in diverse human and mouse conditions

Li Fang, Yunjin Li, Lu Ma, Qiyue Xu, Fei Tan, Geng Chen
2020 Nucleic Acids Research  
Based on the known TF-target relationships and the large-scale single-cell RNA-seq data collected from public databases as well as the bulk data of The Cancer Genome Atlas and the Genotype-Tissue Expression  ...  Overall, GRNdb provides a valuable and timely resource to the scientific community to elucidate the functions and mechanisms of gene expression regulation in various conditions.  ...  DATA COLLECTION AND PROCESSING Single-cell and bulk RNA-seq data collection and processing We collected the scRNA-seq datasets of diverse human and mouse conditions from public databases of Gene Expression  ... 
doi:10.1093/nar/gkaa995 pmid:33151298 fatcat:izbtliptjvbn5cknbhqlb3rhge

Toward a Public Toxicogenomics Capability for Supporting Predictive Toxicology: Survey of Current Resources and Chemical Indexing of Experiments in GEO and ArrayExpress

ClarLynda R. Williams-Devane, Maritja A. Wolf, Ann M. Richard
2009 Toxicological Sciences  
To begin to address these inadequacies, we focus chemical annotation efforts on experimental content contained in the two primary public genomic resources: ArrayExpress and Gene Expression Omnibus.  ...  A publicly available toxicogenomics capability for supporting predictive toxicology and meta-analysis depends on availability of gene expression data for chemical treatment scenarios, the ability to locate  ...  ACKNOWLEDGMENTS We would like to thank Drs Jennifer Fostel (CEBS), Chihae Yang (FDA Center for Food Safety and Nutrition), David Dix (EPA), and William Ward (EPA) for helpful comments and suggestions in  ... 
doi:10.1093/toxsci/kfp061 pmid:19332651 fatcat:xe3pftgstfhufpemlwnlbgnhda

Simulation based benchmarking of isoform quantification in single-cell RNA-seq [article]

Jennifer Westoby, Marcela Sjoberg, Anne Ferguson-Smith, Martin Hemberg
2018 biorxiv/medrxiv   pre-print
An important biological insight comes from our analysis of real data which showed that genes that express two isoforms in bulk RNA-seq predominantly express one or neither isoform in individual cells.  ...  Single-cell RNA-seq has the potential to facilitate isoform quantification as the confounding factor of a mixed population of cells is eliminated.  ...  ES cell data was accessed from the ArrayExpress database (http://www.ebi.ac.uk/arrayexpress) using the accession number E-MTAB-2600, as described in the Kolodziejczyk et al. paper [40, 55] .  ... 
doi:10.1101/248716 fatcat:ph7jb4kvmjbkbkfsqnfmwibylu

Transcriptomics and Epigenomics in head and neck cancer: available repositories and molecular signatures

Mara S. Serafini, Laura Lopez-Perez, Giuseppe Fico, Lisa Licitra, Loris De Cecco, Carlo Resteghini
2020 Cancers of the Head & Neck  
For many years, head and neck squamous cell carcinoma (HNSCC) has been considered as a single entity. However, in the last decades HNSCC complexity and heterogeneity have been recognized.  ...  To contextualize the selected data, our literature survey includes a short summary of the main characteristics of omics data repositories and web-tools for data analyses.  ...  The ArrayExpress archive is one of the ELIXIR Core Data Resources and stores data derived from array-and sequence-based experiments.  ... 
doi:10.1186/s41199-020-0047-y pmid:31988797 pmcid:PMC6971871 fatcat:wydnloqnyff4pd2k62566viibe

Bioinformatics mining for gene expression data

AnYuan GUO
2020 Scientia Sinica Vitae  
ArrayExpress update-From bulk to single-cell expression data. Nucleic Acids Res, 2019, 47: D711- 基因表达研究基础而重要, 转录组测序作为最常 见的高通量表达技术, 其数据分析和挖掘也逐渐成 熟、深入和延展.  ...  GEDS: A gene expression display server for mRNAs, miRNAs and proteins. Cells, 2019, 8: 675 11 Ghosh S, Chan C K. Analysis of RNA-seq data using TopHat and Cufflinks. In: Edwards D, ed.  ...  sequencing and analysis methods. transcriptome, bioinformatics, data mining, regulatory network, big data, tumor immunology, single cell RNA sequencing, analysis tool doi: 10.1360/SSV-2020-0260  ... 
doi:10.1360/ssv-2020-0260 fatcat:5japm56eorcplkmqm5tcyc4ojm
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