{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T10:47:10Z","timestamp":1782730030343,"version":"3.54.5"},"reference-count":9,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T00:00:00Z","timestamp":1777939200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T00:00:00Z","timestamp":1782691200000},"content-version":"vor","delay-in-days":55,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Swiss Federal Institute of Technology Zurich"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The Gene Expression Omnibus (GEO) (Clough and Barrett in: methods in molecular biology, Clifton, 2016) repository requires complex multistep submissions involving metadata preparation, FTP uploads, and MD5 validation. Current manual processes are error-prone, time-consuming, and require significant bioinformatics expertise, creating barriers for many researchers.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present GEO Uploader, a web-based tool that automates the entire GEO submission workflow through an intuitive interface. The application reduces the submission initiation time from 2\u20133\u00a0h to under 20\u00a0s by automating file uploads, MD5 calculations, and metadata template population. Key features include parallel processing of uploads and checksum calculations, automated error prevention through template-based metadata completion, real-time progress tracking, and support for complex submission structures. Deployment across 30\u2009+\u2009users with 50\u2009+\u2009upload sessions, including datasets exceeding hundreds of gigabytes, demonstrates practical utility and reliability in research environments.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>GEO Uploader significantly reduces the technical barrier for GEO submissions while minimizing errors through comprehensive automation. The tool supports data sharing by enabling researchers without specialized bioinformatics expertise to complete submissions independently. Available as open-source software with multiuser deployment capabilities, GEO Uploader represents a substantial improvement in research data sharing accessibility and supports broader adoption of open science practices in the genomics community.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-026-06466-4","type":"journal-article","created":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T13:14:58Z","timestamp":1777986898000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["GEO uploader: simplifying the data deposition in the GEO repository"],"prefix":"10.1186","volume":"27","author":[{"given":"Ronald","family":"Domi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Falko","family":"No\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Leary","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hubert","family":"Rehrauer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,5,5]]},"reference":[{"key":"6466_CR1","doi-asserted-by":"crossref","unstructured":"Clough E, Barrett T. The gene expression omnibus database. In: methods in molecular biology (Clifton, N.J.) 2016, 1418.","DOI":"10.1007\/978-1-4939-3578-9_5"},{"key":"6466_CR2","unstructured":"Reporting standards and availability of data, materials, code and protocols [https:\/\/www.nature.com\/nature-portfolio\/editorial-policies\/reporting-standards#mandates-for-specific-datasets]."},{"key":"6466_CR3","unstructured":"Home - GEO - NCBI [https:\/\/www.ncbi.nlm.nih.gov\/geo\/]."},{"key":"6466_CR4","unstructured":"GitHub - uc-bd2k\/GREIN: GREIN : GEO RNA-seq experiments interactive navigator [https:\/\/github.com\/uc-bd2k\/GREIN]."},{"key":"6466_CR5","unstructured":"GitHub - NICHD-BSPC\/geo_prepper: tool to help prepare data for GEO submission [https:\/\/github.com\/NICHD-BSPC\/geo_prepper]."},{"key":"6466_CR6","unstructured":"GitHub - CBMR-single-cell-omics-platform\/GEO-submission-guide: guidelines and helper scripts for preparing sequencing data for submission to NCBI GEO [https:\/\/github.com\/CBMR-Single-Cell-Omics-Platform\/GEO-submission-guide]."},{"key":"6466_CR7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-016-1104-8","volume":"17","author":"M Hatakeyama","year":"2016","unstructured":"Hatakeyama M, Opitz L, Russo G, Qi W, Schlapbach R, Rehrauer H. SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis. BMC Bioinformatics. 2016;17:1\u20139.","journal-title":"BMC Bioinformatics"},{"key":"6466_CR8","doi-asserted-by":"publisher","unstructured":"B-Fabric [https:\/\/dl.acm.org\/doi\/https:\/\/doi.org\/10.1145\/1739041.1739135].","DOI":"10.1145\/1739041.1739135"},{"key":"6466_CR9","unstructured":"geo-uploader\/documentation\/GEO_instructions.md at main \u00b7 fgcz\/geo-uploader [https:\/\/github.com\/fgcz\/geo-uploader\/blob\/main\/documentation\/GEO_instructions.md]."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-026-06466-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-026-06466-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-026-06466-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T10:15:32Z","timestamp":1782728132000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12859-026-06466-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,5]]},"references-count":9,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["6466"],"URL":"https:\/\/doi.org\/10.1186\/s12859-026-06466-4","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,5]]},"assertion":[{"value":"12 November 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 April 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 May 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"140"}}