{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T22:41:10Z","timestamp":1789425670101,"version":"build-2803163510"},"reference-count":30,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2024,11,6]],"date-time":"2024-11-06T00:00:00Z","timestamp":1730851200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UK Dementia Research Institute"},{"name":"Medical Research Council"},{"name":"MS Society UK"},{"name":"University of Edinburgh, Institute for Regeneration and Repair and School of Biological Sciences"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: High-throughput single-cell RNA sequencing (scRNA-seq) workflows produce libraries that demand extensive sequencing. However, standard next-generation sequencing (NGS) methods remain expensive, contributing to the high running costs of single-cell experiments and often negatively affecting the sample numbers and statistical strength of such projects. In recent years, a plethora of new sequencing technologies have become available to researchers through several manufacturers, often providing lower-cost alternatives to standard NGS. Methods: In this study, we compared data generated from mouse scRNA-seq libraries sequenced with both standard Illumina sequencing by synthesis (Illumina SBS) and MGI\u2019s DNA nanoball sequencing (DNBSEQ). Results: Our findings reveal similar overall performance using both technologies. DNBSEQ exhibited mildly superior sequence quality compared to Illumina SBS, as evidenced by higher Phred scores, lower read duplication rates and a greater number of genes mapping to the reference genome. Yet these improvements did not translate into meaningful differences in single-cell analysis parameters in our experiments, including detection of additional genes within cells, gene expression saturation levels and numbers of identified cells, with both technologies demonstrating equally robust performance in these aspects. The data produced by both sequencing platforms also produced comparable analytical outcomes for single-cell analysis. No significant difference in the annotation of cells into different cell types was observed and the same top genes were differentially expressed between populations and experimental conditions. Conclusions: Overall, our data demonstrate that alternative technologies can be applied to sequence scRNA-seq libraries, generating virtually indistinguishable results compared to standard methods, and providing cost-effective alternatives.<\/jats:p>","DOI":"10.3390\/genes15111436","type":"journal-article","created":{"date-parts":[[2024,11,6]],"date-time":"2024-11-06T06:27:39Z","timestamp":1730874459000},"page":"1436","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Illumina SBS Sequencing and DNBSEQ Perform Similarly for Single-Cell Transcriptomics"],"prefix":"10.3390","volume":"15","author":[{"given":"Nadine","family":"Bestard-Cuche","sequence":"first","affiliation":[{"name":"Centre for Regenerative Medicine, Institute for Regeneration and Repair, MS Society Edinburgh Centre for MS Research, University of Edinburgh, Edinburgh EH16 4UU, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Munro","sequence":"additional","affiliation":[{"name":"UK Dementia Research Institute, University of Edinburgh, Edinburgh EH8 9AL, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meryam","family":"Beniazza","sequence":"additional","affiliation":[{"name":"Centre for Regenerative Medicine, Institute for Regeneration and Repair, MS Society Edinburgh Centre for MS Research, University of Edinburgh, Edinburgh EH16 4UU, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Josef","family":"Priller","sequence":"additional","affiliation":[{"name":"UK Dementia Research Institute, University of Edinburgh, Edinburgh EH8 9AL, UK"},{"name":"Department of Psychiatry and Psychotherapy, School of Medicine and Health, Klinikum Rechts der Isar, Technical University Munich, and German Center for Mental Health (DZPG), 80333 Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6329-382X","authenticated-orcid":false,"given":"Anna","family":"Williams","sequence":"additional","affiliation":[{"name":"Centre for Regenerative Medicine, Institute for Regeneration and Repair, MS Society Edinburgh Centre for MS Research, University of Edinburgh, Edinburgh EH16 4UU, UK"},{"name":"UK Dementia Research Institute, University of Edinburgh, Edinburgh EH8 9AL, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4481-0999","authenticated-orcid":false,"given":"Andrea","family":"Corsinotti","sequence":"additional","affiliation":[{"name":"Centre for Regenerative Medicine, Institute for Regeneration and Repair, MS Society Edinburgh Centre for MS Research, University of Edinburgh, Edinburgh EH16 4UU, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1038\/s41592-024-02263-0","article-title":"ScRNA-Seq: Oh, the Joys","volume":"21","author":"Marx","year":"2024","journal-title":"Nat. Methods"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"e694","DOI":"10.1002\/ctm2.694","article-title":"Single-Cell RNA Sequencing Technologies and Applications: A Brief Overview","volume":"12","author":"Jovic","year":"2022","journal-title":"Clin. Transl. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1038\/d41586-023-00512-4","article-title":"Innovative Technologies Crowd the Short-Read Sequencing Market","volume":"614","author":"Eisenstein","year":"2023","journal-title":"Nature"},{"key":"ref_4","unstructured":"(2024, June 04). Illumina and Gene Sequencing Technology\u2014SBIR Success Story\u2014NCI, Available online: https:\/\/sbir.cancer.gov\/portfolio\/success-stories\/illumina."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1126\/science.1181498","article-title":"Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays","volume":"327","author":"Drmanac","year":"2010","journal-title":"Science"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"e32","DOI":"10.5808\/GI.2019.17.3.e32","article-title":"Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 Sequencing Platforms for RNA Sequencing","volume":"17","author":"Jeon","year":"2019","journal-title":"Genom. Inform."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s13007-018-0337-0","article-title":"Comparative Performance of the BGISEQ-500 and Illumina HiSeq4000 Sequencing Platforms for Transcriptome Analysis in Plants","volume":"14","author":"Zhu","year":"2018","journal-title":"Plant Methods"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Senabouth, A., Andersen, S., Shi, Q., Shi, L., Jiang, F., Zhang, W., Wing, K., Daniszewski, M., Lukowski, S.W., and Hung, S.S.C. (2020). Comparative Performance of the BGI and Illumina Sequencing Technology for Single-Cell RNA-Sequencing. NAR Genom. Bioinform., 2.","DOI":"10.1093\/nargab\/lqaa034"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Natarajan, K.N., Miao, Z., Jiang, M., Huang, X., Zhou, H., Xie, J., Wang, C., Qin, S., Zhao, Z., and Wu, L. (2019). Comparative Analysis of Sequencing Technologies for Single-Cell Transcriptomics. Genome Biol., 20.","DOI":"10.1186\/s13059-019-1676-5"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1038\/s41467-019-11053-8","article-title":"Deletion of a Csf1r Enhancer Selectively Impacts CSF1R Expression and Development of Tissue Macrophage Populations","volume":"10","author":"Rojo","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1038\/s41593-022-01104-7","article-title":"A Shared Disease-Associated Oligodendrocyte Signature among Multiple CNS Pathologies","volume":"25","author":"Kenigsbuch","year":"2022","journal-title":"Nat. Neurosci."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2732","DOI":"10.1016\/j.neuron.2024.05.018","article-title":"Microglia Protect against Age-Associated Brain Pathologies","volume":"112","author":"Munro","year":"2024","journal-title":"Neuron"},{"key":"ref_13","unstructured":"(2024, July 13). Sequencing Requirements for Single Cell 3\u2032\u2014Official 10X Genomics Support. Available online: https:\/\/www.10xgenomics.com\/support\/single-cell-gene-expression\/documentation\/steps\/sequencing\/sequencing-requirements-for-single-cell-3."},{"key":"ref_14","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":"ref_15","unstructured":"Bushnell, B. (2014, January 17\u201320). BBMap: A Fast, Accurate, Splice-Aware Aligner. Proceedings of the 9th Annual Genomics of Energy & Environment Meeting, Walnut Creek, CA, USA."},{"key":"ref_16","unstructured":"(2024, September 14). Babraham Bioinformatics\u2014FastQC A Quality Control Tool for High Throughput Sequence Data. Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1093\/bioinformatics\/btw777","article-title":"Scater: Pre-Processing, Quality Control, Normalization and Visualization of Single-Cell RNA-Seq Data in R","volume":"33","author":"McCarthy","year":"2017","journal-title":"Bioinformatics"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Lun, A.T.L., Bach, K., and Marioni, J.C. (2016). Pooling across Cells to Normalize Single-Cell RNA Sequencing Data with Many Zero Counts. Genome Biol., 17.","DOI":"10.1186\/s13059-016-0947-7"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s41590-018-0276-y","article-title":"Reference-Based Analysis of Lung Single-Cell Sequencing Reveals a Transitional Profibrotic Macrophage","volume":"20","author":"Aran","year":"2019","journal-title":"Nat. Immunol."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Finak, G., McDavid, A., Yajima, M., Deng, J., Gersuk, V., Shalek, A.K., Slichter, C.K., Miller, H.W., McElrath, M.J., and Prlic, M. (2015). MAST: A Flexible Statistical Framework for Assessing Transcriptional Changes and Characterizing Heterogeneity in Single-Cell RNA Sequencing Data. Genome Biol., 16.","DOI":"10.1186\/s13059-015-0844-5"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1093\/nar\/gkp1137","article-title":"The Sanger FASTQ File Format for Sequences with Quality Scores, and the Solexa\/Illumina FASTQ Variants","volume":"38","author":"Cock","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref_23","unstructured":"(2024, May 03). Illumina Quality Scores for Next-Generation Sequencing. Available online: https:\/\/www.illumina.com\/documents\/products\/technotes\/technote_Q-Scores.pdf."},{"key":"ref_24","unstructured":"(2024, June 04). Cell Ranger\u2014Official 10X Genomics Support. Available online: https:\/\/www.10xgenomics.com\/support\/software\/cell-ranger\/latest."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1002\/0471250953.bi1114s51","article-title":"Mapping RNA-Seq Reads with STAR","volume":"51","author":"Dobin","year":"2015","journal-title":"Curr. Protoc. Bioinform."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/s41586-022-05534-y","article-title":"Microglia Regulate Central Nervous System Myelin Growth and Integrity","volume":"613","author":"McNamara","year":"2023","journal-title":"Nature"},{"key":"ref_27","unstructured":"(2024, July 30). Common Considerations for Quality Control Filters for Single Cell RNA-Seq Data\u201410X Genomics. Available online: https:\/\/www.10xgenomics.com\/analysis-guides\/common-considerations-for-quality-control-filters-for-single-cell-rna-seq-data."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"P\u00f3liska, S., Fareh, C., Lengyel, A., G\u00f6czi, L., T\u0151zs\u00e9r, J., and Szatmari, I. (2023). Comparative Transcriptomic Analysis of Illumina and MGI Next-Generation Sequencing Platforms Using RUNX3- and ZBTB46-Instructed Embryonic Stem Cells. Front. Genet., 14.","DOI":"10.3389\/fgene.2023.1275383"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1007\/s13258-021-01096-x","article-title":"Comparison between MGI and Illumina Sequencing Platforms for Whole Genome Sequencing","volume":"43","author":"Jeon","year":"2021","journal-title":"Genes Genom."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1038\/s41587-022-01632-4","article-title":"Illumina Faces Short-Read Rivals","volume":"41","author":"Eisenstein","year":"2023","journal-title":"Nat. Biotechnol."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/15\/11\/1436\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T16:27:12Z","timestamp":1760113632000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/15\/11\/1436"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,6]]},"references-count":30,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2024,11]]}},"alternative-id":["genes15111436"],"URL":"https:\/\/doi.org\/10.3390\/genes15111436","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,6]]}}}