{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T03:44:19Z","timestamp":1764906259499,"version":"3.41.2"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,10,10]],"date-time":"2024-10-10T00:00:00Z","timestamp":1728518400000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81921003","32170605"],"award-info":[{"award-number":["81921003","32170605"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of cellular diversity with unprecedented resolution. However, many current methods are limited in capturing full-length transcripts and discerning strand orientation. Here, we present RAG-seq, an innovative strand-specific total RNA sequencing technique that combines not-so-random (NSR) primers with Tn5 transposase-mediated tagmentation. RAG-seq overcomes previous limitations by delivering comprehensive transcript coverage and maintaining strand orientation, which are essential for accurate quantification of overlapping genes and detection of antisense transcripts. Through optimized reverse transcription with oligo-dT primers, rRNA depletion via Depletion of Abundant Sequences by Hybridization (DASH), and linear amplification, RAG-seq enhances sensitivity and reproducibility, especially for low-input samples and single cells. Application to mouse oocytes and early embryos highlights RAG-seq\u2019s superior performance in identifying stage-specific antisense transcripts, shedding light on their regulatory roles during early development. This advancement represents a significant leap in transcriptome analysis within complex biological contexts.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzae072","type":"journal-article","created":{"date-parts":[[2024,10,10]],"date-time":"2024-10-10T15:40:07Z","timestamp":1728574807000},"source":"Crossref","is-referenced-by-count":1,"title":["RAG-seq: NSR-primed and Transposase Tagmentation-mediated Strand-specific Total RNA Sequencing in Single Cells"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2829-2116","authenticated-orcid":false,"given":"Ping","family":"Xu","sequence":"first","affiliation":[{"name":"China-Japan Union Hospital of Jilin University, Jilin University , Changchun 130033,","place":["China"]},{"name":"School of Life Sciences, Jilin University , Changchun 130012,","place":["China"]},{"name":"Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University , Guangzhou 510623,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-9901-2236","authenticated-orcid":false,"given":"Zhiheng","family":"Yuan","sequence":"additional","affiliation":[{"name":"Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University , Guangzhou 510623,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-2150-5635","authenticated-orcid":false,"given":"Xiaohua","family":"Lu","sequence":"additional","affiliation":[{"name":"Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-1625-3586","authenticated-orcid":false,"given":"Peng","family":"Zhou","sequence":"additional","affiliation":[{"name":"Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University , Guangzhou 510623,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0807-1749","authenticated-orcid":false,"given":"Ding","family":"Qiu","sequence":"additional","affiliation":[{"name":"Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University , Guangzhou 510623,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-2229-5758","authenticated-orcid":false,"given":"Zhenghao","family":"Qiao","sequence":"additional","affiliation":[{"name":"Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University , Guangzhou 510623,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7067-4006","authenticated-orcid":false,"given":"Zhongcheng","family":"Zhou","sequence":"additional","affiliation":[{"name":"Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University , Guangzhou 510623,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-4880-4300","authenticated-orcid":false,"given":"Li","family":"Guan","sequence":"additional","affiliation":[{"name":"Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University , Guangzhou 510623,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-3433-6619","authenticated-orcid":false,"given":"Yongkang","family":"Jia","sequence":"additional","affiliation":[{"name":"Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University , Guangzhou 510623,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-1081-9267","authenticated-orcid":false,"given":"Xuan","family":"He","sequence":"additional","affiliation":[{"name":"Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University , Guangzhou 510623,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4267-8210","authenticated-orcid":false,"given":"Ling","family":"Sun","sequence":"additional","affiliation":[{"name":"Center for Reproductive Medicine, Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University , Guangzhou 510623,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9818-9555","authenticated-orcid":false,"given":"Youzhong","family":"Wan","sequence":"additional","affiliation":[{"name":"China-Japan Union Hospital of Jilin University, Jilin University , Changchun 130033,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1959-4879","authenticated-orcid":false,"given":"Ming","family":"Wang","sequence":"additional","affiliation":[{"name":"Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University , Guangzhou 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