{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T05:24:52Z","timestamp":1784093092776,"version":"3.55.0"},"reference-count":83,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2023,5,25]],"date-time":"2023-05-25T00:00:00Z","timestamp":1684972800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Science and Technology Major Program of Hubei Province","award":["2021ABA011"],"award-info":[{"award-number":["2021ABA011"]}]},{"name":"Foundation of Hubei Hongshan Laboratory","award":["2021hszd012"],"award-info":[{"award-number":["2021hszd012"]}]},{"name":"Foundation of Hubei Hongshan Laboratory","award":["2022hszd024"],"award-info":[{"award-number":["2022hszd024"]}]},{"name":"HZAU-AGIS Cooperation Fund","award":["SZYJY2021010"],"award-info":[{"award-number":["SZYJY2021010"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The volume of ribonucleic acid (RNA)-seq data has increased exponentially, providing numerous new insights into various biological processes. However, due to significant practical challenges, such as data heterogeneity, it is still difficult to ensure the quality of these data when integrated. Although some quality control methods have been developed, sample consistency is rarely considered and these methods are susceptible to artificial factors. Here, we developed MassiveQC, an unsupervised machine learning-based approach, to automatically download and filter large-scale high-throughput data. In addition to the read quality used in other tools, MassiveQC also uses the alignment and expression quality as model features. Meanwhile, it is user-friendly since the cutoff is generated from self-reporting and is applicable to multimodal data. To explore its value, we applied MassiveQC to Drosophila RNA-seq data and generated a comprehensive transcriptome atlas across 28 tissues from embryogenesis to adulthood. We systematically characterized fly gene expression dynamics and found that genes with high expression dynamics were likely to be evolutionarily young and expressed at late developmental stages, exhibiting high nonsynonymous substitution rates and low phenotypic severity, and they were involved in simple regulatory programs. We also discovered that human and Drosophila had strong positive correlations in gene expression in orthologous organs, revealing the great potential of the Drosophila system for studying human development and disease.<\/jats:p>","DOI":"10.1093\/bib\/bbad177","type":"journal-article","created":{"date-parts":[[2023,5,26]],"date-time":"2023-05-26T10:25:14Z","timestamp":1685096714000},"source":"Crossref","is-referenced-by-count":5,"title":["Integrating massive RNA-seq data to elucidate transcriptome dynamics in <i>Drosophila melanogaster<\/i>"],"prefix":"10.1093","volume":"24","author":[{"given":"Sheng","family":"Hu Qian","sequence":"first","affiliation":[{"name":"Hubei Hongshan Laboratory , College of Biomedicine and Health, , Wuhan 430070 , China"},{"name":"Huazhong Agricultural University , College of Biomedicine and Health, , Wuhan 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meng-Wei","family":"Shi","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory , College of Biomedicine and Health, , Wuhan 430070 , China"},{"name":"Huazhong Agricultural University , College of Biomedicine and Health, , Wuhan 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan-Yang","family":"Wang","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory , College of Biomedicine and Health, , Wuhan 430070 , China"},{"name":"Huazhong Agricultural University , College of Biomedicine and Health, , Wuhan 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justin M","family":"Fear","sequence":"additional","affiliation":[{"name":"Section of Developmental Genomics, National Institute of Diabetes and Kidney and Digestive Diseases , National Institutes of Health, Bethesda, MD 20892 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu","family":"Chen","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory , College of Biomedicine and Health, , Wuhan 430070 , China"},{"name":"Huazhong Agricultural University , College of Biomedicine and Health, , Wuhan 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Xuan","family":"Tu","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory , College of Biomedicine and Health, , Wuhan 430070 , China"},{"name":"Huazhong Agricultural University , College of Biomedicine and Health, , Wuhan 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong-Shan","family":"Liu","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory , College of Biomedicine and Health, , Wuhan 430070 , China"},{"name":"Huazhong Agricultural University , College of Biomedicine and Health, , Wuhan 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory , College of Biomedicine and Health, , Wuhan 430070 , China"},{"name":"Huazhong Agricultural University , College of Biomedicine and Health, , Wuhan 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuai-Jie","family":"Zhang","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory , College of Biomedicine and Health, , Wuhan 430070 , China"},{"name":"Huazhong Agricultural University , College of Biomedicine and Health, , Wuhan 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shan-Shan","family":"Yu","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory , College of Biomedicine and Health, , Wuhan 430070 , China"},{"name":"Huazhong Agricultural University , College of Biomedicine and Health, , Wuhan 430070 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Oliver","sequence":"additional","affiliation":[{"name":"Section of Developmental Genomics, National Institute of Diabetes and Kidney and Digestive Diseases , National Institutes of Health, Bethesda, MD 20892 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen-Xia","family":"Chen","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory , College of Biomedicine and Health, , Wuhan 430070 , China"},{"name":"Huazhong Agricultural University , College of Biomedicine and Health, , Wuhan 430070 , China"},{"name":"Section of Developmental Genomics, National Institute of Diabetes and Kidney and Digestive Diseases , National Institutes of Health, Bethesda, MD 20892 , USA"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics , College of Life Science and Technology, , Wuhan 430070 , China"},{"name":"Huazhong Agricultural University , College of Life Science and Technology, , Wuhan 430070 , China"},{"name":"Interdisciplinary Sciences Institute, Huazhong Agricultural University , Wuhan 430070 , China"},{"name":"Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University , Shenzhen 518000 , China"},{"name":"Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen 518000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,25]]},"reference":[{"key":"2023091714552798100_ref1","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1093\/bioinformatics\/btx575","article-title":"SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles","volume":"34","author":"Papili 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