{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:38:36Z","timestamp":1772138316534,"version":"3.50.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,4,2]],"date-time":"2024-04-02T00:00:00Z","timestamp":1712016000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Erythropoiesis is a finely regulated and complex process that involves multiple transformations from hematopoietic stem cells to mature red blood cells at hematopoietic sites from the embryonic to adult stages. Investigations into its molecular mechanisms have generated a wealth of expression data, including bulk and single-cell RNA sequencing data. A comprehensively integrated and well-curated erythropoiesis-specific database will greatly facilitate the mining of gene expression data and enable large-scale research of erythropoiesis and erythroid-related diseases. Here, we present EryDB, an open-access and comprehensive database dedicated to the collection, integration, analysis, and visualization of transcriptomic data for erythropoiesis and erythroid-related diseases. Currently, the database includes expertly curated quality-assured data of 3803 samples and 1,187,119 single cells derived from 107 public studies of three species (Homo sapiens, Mus musculus, and Danio rerio), nine tissue types, and five diseases. EryDB provides users with the ability to not only browse the molecular features of erythropoiesis between tissues and species, but also perform computational analyses of single-cell and bulk RNA sequencing data, thus serving as a convenient platform for customized queries and analyses. EryDB v1.0 is freely accessible at https:\/\/ngdc.cncb.ac.cn\/EryDB\/home.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzae029","type":"journal-article","created":{"date-parts":[[2024,4,2]],"date-time":"2024-04-02T19:56:05Z","timestamp":1712087765000},"source":"Crossref","is-referenced-by-count":2,"title":["EryDB: A Transcriptomic Profile Database for Erythropoiesis and Erythroid-related Diseases"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3781-170X","authenticated-orcid":false,"given":"Guangmin","family":"Zheng","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0923-639X","authenticated-orcid":false,"given":"Song","family":"Wu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0490-6507","authenticated-orcid":false,"given":"Zhaojun","family":"Zhang","sequence":"additional","affiliation":[{"name":"China National Center for Bioinformation , Beijing 100101,","place":["China"]},{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing 100049,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9418-4848","authenticated-orcid":false,"given":"Zijuan","family":"Xin","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0009-0009-4246-929X","authenticated-orcid":false,"given":"Lijuan","family":"Zhang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2341-4989","authenticated-orcid":false,"given":"Siqi","family":"Zhao","sequence":"additional","affiliation":[{"name":"China National Center for Bioinformation , Beijing 100101,","place":["China"]},{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing 100049,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6032-0979","authenticated-orcid":false,"given":"Jing","family":"Wu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0608-2217","authenticated-orcid":false,"given":"Yanxia","family":"Liu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0369-5867","authenticated-orcid":false,"given":"Meng","family":"Li","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2181-1529","authenticated-orcid":false,"given":"Xiuyan","family":"Ruan","sequence":"additional","affiliation":[{"name":"China National Center for Bioinformation , Beijing 100101,","place":["China"]},{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2740-262X","authenticated-orcid":false,"given":"Nan","family":"Qiao","sequence":"additional","affiliation":[{"name":"Huawei Cloud Computing Technologies Co., Ltd. , Guiyang 550029,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9922-9723","authenticated-orcid":false,"given":"Yiming","family":"Bao","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7013-8409","authenticated-orcid":false,"given":"Hongzhu","family":"Qu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6628-8620","authenticated-orcid":false,"given":"Xiangdong","family":"Fang","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2024,4,2]]},"reference":[{"key":"2025121705424918700_qzae029-B1","doi-asserted-by":"crossref","first-page":"3","DOI":"10.3389\/fphys.2014.00003","article-title":"Primitive and definitive erythropoiesis in mammals","volume":"5","author":"Palis","year":"2014","journal-title":"Front Physiol"},{"key":"2025121705424918700_qzae029-B2","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1111\/bjh.13978","article-title":"Advances in understanding the pathogenesis of congenital erythropoietic porphyria","volume":"173","author":"Di Pierro","year":"2016","journal-title":"Br J Haematol"},{"key":"2025121705424918700_qzae029-B3","doi-asserted-by":"crossref","first-page":"2450","DOI":"10.1182\/blood.2021011044","article-title":"Molecular and cellular mechanisms that regulate human erythropoiesis","volume":"139","author":"Caulier","year":"2022","journal-title":"Blood"},{"key":"2025121705424918700_qzae029-B4","doi-asserted-by":"crossref","first-page":"1330","DOI":"10.5966\/sctm.2016-0039","article-title":"Concise review: recent advances in the in vitro derivation of blood cell populations","volume":"5","author":"Batta","year":"2016","journal-title":"Stem Cells Transl Med"},{"key":"2025121705424918700_qzae029-B5","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.transci.2018.12.015","article-title":"Ex vivo generation of transfusable red blood cells from various stem cell sources: a concise revisit of where we are now","volume":"58","author":"Christaki","year":"2019","journal-title":"Transfus Apher Sci"},{"key":"2025121705424918700_qzae029-B6","doi-asserted-by":"crossref","first-page":"2136","DOI":"10.1182\/blood-2008-09-115238","article-title":"Chaperoning erythropoiesis","volume":"113","author":"Weiss","year":"2009","journal-title":"Blood"},{"key":"2025121705424918700_qzae029-B7","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1038\/s41422-020-0378-6","article-title":"Comparative analysis of cell lineage differentiation during hepatogenesis in humans and mice at the single-cell transcriptome level","volume":"30","author":"Wang","year":"2020","journal-title":"Cell Res"},{"key":"2025121705424918700_qzae029-B8","doi-asserted-by":"crossref","first-page":"D52","DOI":"10.1093\/nar\/gkx1017","article-title":"3DIV: a 3D-genome Interaction Viewer and database","volume":"46","author":"Yang","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2025121705424918700_qzae029-B9","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1038\/nature25741","article-title":"Population snapshots predict early haematopoietic and erythroid hierarchies","volume":"555","author":"Tusi","year":"2018","journal-title":"Nature"},{"key":"2025121705424918700_qzae029-B10","doi-asserted-by":"crossref","first-page":"E2467","DOI":"10.1073\/pnas.1714723115","article-title":"Fundamental limits on dynamic inference from single-cell snapshots","volume":"115","author":"Weinreb","year":"2018","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025121705424918700_qzae029-B11","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1038\/s41586-019-1652-y","article-title":"Decoding human fetal liver haematopoiesis","volume":"574","author":"Popescu","year":"2019","journal-title":"Nature"},{"key":"2025121705424918700_qzae029-B12","doi-asserted-by":"crossref","first-page":"eaba7721","DOI":"10.1126\/science.aba7721","article-title":"A human cell atlas of fetal gene expression","volume":"370","author":"Cao","year":"2020","journal-title":"Science"},{"key":"2025121705424918700_qzae029-B13","doi-asserted-by":"crossref","first-page":"1998","DOI":"10.1182\/bloodadvances.2018020560","article-title":"Induced pluripotent stem cell-based mapping of beta-globin expression throughout human erythropoietic development","volume":"2","author":"Vanuytsel","year":"2018","journal-title":"Blood Adv"},{"key":"2025121705424918700_qzae029-B14","doi-asserted-by":"crossref","first-page":"D27","DOI":"10.1093\/nar\/gkab951","article-title":"Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2022","volume":"50","author":"CNCB-NGDC Members and Partners","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025121705424918700_qzae029-B15","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1016\/j.gpb.2021.08.001","article-title":"The Genome Sequence Archive Family: toward explosive data growth and diverse data types","volume":"19","author":"Chen","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2025121705424918700_qzae029-B16","doi-asserted-by":"crossref","first-page":"D19","DOI":"10.1093\/nar\/gkq1019","article-title":"The Sequence Read Archive","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2025121705424918700_qzae029-B17","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/nrg3394","article-title":"Reuse of public genome-wide gene expression data","volume":"14","author":"Rung","year":"2013","journal-title":"Nat Rev Genet"},{"key":"2025121705424918700_qzae029-B18","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/s41591-020-0752-4","article-title":"An immune-cell signature of bacterial sepsis","volume":"26","author":"Reyes","year":"2020","journal-title":"Nat Med"},{"key":"2025121705424918700_qzae029-B19","doi-asserted-by":"crossref","first-page":"D760","DOI":"10.1093\/nar\/gkl887","article-title":"NCBI GEO: mining tens of millions of expression profiles\u2013database and tools update","volume":"35","author":"Barrett","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2025121705424918700_qzae029-B20","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1016\/j.gpb.2021.03.009","article-title":"Mapping human pluripotent stem cell-derived erythroid differentiation by single-cell transcriptome analysis","volume":"19","author":"Xin","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2025121705424918700_qzae029-B21","doi-asserted-by":"crossref","first-page":"5396","DOI":"10.1182\/bloodadvances.2021005167","article-title":"Regulatory association of long noncoding RNAs and chromatin accessibility facilitates erythroid differentiation","volume":"5","author":"Ren","year":"2021","journal-title":"Blood Adv"},{"key":"2025121705424918700_qzae029-B22","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1007\/s11684-016-0452-0","article-title":"Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation","volume":"10","author":"Ding","year":"2016","journal-title":"Front Med"},{"key":"2025121705424918700_qzae029-B23","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/j.ygeno.2013.09.005","article-title":"Transcriptome dynamics during human erythroid differentiation and development","volume":"102","author":"Yang","year":"2013","journal-title":"Genomics"},{"key":"2025121705424918700_qzae029-B24","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2025121705424918700_qzae029-B25","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat Methods"},{"key":"2025121705424918700_qzae029-B26","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2025121705424918700_qzae029-B27","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025121705424918700_qzae029-B28","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"2025121705424918700_qzae029-B29","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat Methods"},{"key":"2025121705424918700_qzae029-B30","doi-asserted-by":"crossref","first-page":"2996","DOI":"10.1016\/j.celrep.2019.08.020","article-title":"A unique epigenomic landscape defines human erythropoiesis","volume":"28","author":"Schulz","year":"2019","journal-title":"Cell Rep"},{"key":"2025121705424918700_qzae029-B31","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1093\/nar\/27.1.200","article-title":"EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis","volume":"27","author":"Stoeckert","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2025121705424918700_qzae029-B32","doi-asserted-by":"crossref","first-page":"D572","DOI":"10.1093\/nar\/gkh129","article-title":"Hembase: browser and genome portal for hematology and erythroid biology","volume":"32","author":"Goh","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2025121705424918700_qzae029-B33","doi-asserted-by":"crossref","first-page":"e5\u201313","DOI":"10.1182\/blood-2012-04-422394","article-title":"Ontogeny of erythroid gene expression","volume":"121","author":"Kingsley","year":"2013","journal-title":"Blood"},{"key":"2025121705424918700_qzae029-B34","doi-asserted-by":"crossref","first-page":"D1023","DOI":"10.1093\/nar\/gkr958","article-title":"BGMUT: NCBI dbRBC database of allelic variations of genes encoding antigens of blood group systems","volume":"40","author":"Patnaik","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2025121705424918700_qzae029-B35","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1111\/j.1365-2141.2008.07091.x","article-title":"Disorders of red cell membrane","volume":"141","author":"An","year":"2008","journal-title":"Br J Haematol"},{"key":"2025121705424918700_qzae029-B36","doi-asserted-by":"crossref","first-page":"D917","DOI":"10.1093\/nar\/gkv1101","article-title":"BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis","volume":"44","author":"Bagger","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2025121705424918700_qzae029-B37","doi-asserted-by":"crossref","first-page":"D881","DOI":"10.1093\/nar\/gky1076","article-title":"BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles","volume":"47","author":"Bagger","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025121705424918700_qzae029-B38","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1126\/science.aad3312","article-title":"Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin","volume":"351","author":"Masuda","year":"2016","journal-title":"Science"},{"key":"2025121705424918700_qzae029-B39","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1038\/nature14326","article-title":"PPAR-\u03b1 and glucocorticoid receptor synergize to promote erythroid progenitor self-renewal","volume":"522","author":"Lee","year":"2015","journal-title":"Nature"},{"key":"2025121705424918700_qzae029-B40","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s12920-016-0174-9","article-title":"Transcriptome analysis reveals a ribosome constituents disorder involved in the RPL5 downregulated zebrafish model of Diamond-Blackfan anemia","volume":"9","author":"Wan","year":"2016","journal-title":"BMC Med Genomics"},{"key":"2025121705424918700_qzae029-B41","doi-asserted-by":"crossref","first-page":"eabf0113","DOI":"10.1126\/scitranslmed.abf0113","article-title":"Single-cell profiling of human bone marrow progenitors reveals mechanisms of failing erythropoiesis in Diamond-Blackfan anemia","volume":"13","author":"Iskander","year":"2021","journal-title":"Sci Transl Med"},{"key":"2025121705424918700_qzae029-B42","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1016\/j.gpb.2022.12.004","article-title":"Database Commons: a catalog of worldwide biological databases","volume":"21","author":"Ma","year":"2023","journal-title":"Genomics Proteomics Bioinformatics"}],"container-title":["Genomics, Proteomics &amp; Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gpb\/advance-article-pdf\/doi\/10.1093\/gpbjnl\/qzae029\/57141540\/qzae029.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/23\/2\/qzae029\/57141540\/qzae029.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/23\/2\/qzae029\/57141540\/qzae029.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T10:42:56Z","timestamp":1765968176000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gpb\/article\/doi\/10.1093\/gpbjnl\/qzae029\/7639389"}},"subtitle":[],"editor":[{"given":"An-Yuan","family":"Guo","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,4,2]]},"references-count":42,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2025,5,30]]}},"URL":"https:\/\/doi.org\/10.1093\/gpbjnl\/qzae029","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.12.22.572961","asserted-by":"object"}]},"ISSN":["1672-0229","2210-3244"],"issn-type":[{"value":"1672-0229","type":"print"},{"value":"2210-3244","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,4]]},"published":{"date-parts":[[2024,4,2]]},"article-number":"qzae029"}}