{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T00:40:02Z","timestamp":1788482402163,"version":"build-2803163510"},"reference-count":71,"publisher":"Elsevier BV","issue":"3","license":[{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T00:00:00Z","timestamp":1770249600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["R21 AG072738"],"award-info":[{"award-number":["R21 AG072738"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["T32AG071444"],"award-info":[{"award-number":["T32AG071444"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["R01 AG071281"],"award-info":[{"award-number":["R01 AG071281"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["U01AG076804"],"award-info":[{"award-number":["U01AG076804"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["R01 AG077829"],"award-info":[{"award-number":["R01 AG077829"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["RF1 AG074543"],"award-info":[{"award-number":["RF1 AG074543"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004312","name":"Eli Lilly and Company","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004312","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006976","name":"Lilly Endowment","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006976","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004316","name":"International Business Machines Corporation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004316","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010249","name":"Indiana University School of Medicine","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010249","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006733","name":"Indiana University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006733","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports Methods"],"published-print":{"date-parts":[[2026,3]]},"DOI":"10.1016\/j.crmeth.2026.101337","type":"journal-article","created":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T14:56:17Z","timestamp":1774277777000},"page":"101337","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":6,"title":["Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing"],"prefix":"10.1016","volume":"6","author":[{"given":"Holly N.","family":"Kersey","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominic J.","family":"Acri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luke C.","family":"Dabin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly A.","family":"Hartigan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Mustaklem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jung Hyun","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6931-8581","authenticated-orcid":false,"given":"Jungsu","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.crmeth.2026.101337_bib1","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1016\/j.neuron.2024.11.016","article-title":"snRNA-seq stratifies multiple sclerosis patients into distinct white matter glial responses","volume":"113","author":"Macnair","year":"2025","journal-title":"Neuron"},{"key":"10.1016\/j.crmeth.2026.101337_bib2","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1038\/s41597-023-02552-x","article-title":"Single-nucleus transcriptomic mapping of blast-induced traumatic brain injury in mice hippocampus","volume":"10","author":"Zhang","year":"2023","journal-title":"Sci. Data"},{"key":"10.1016\/j.crmeth.2026.101337_bib3","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1186\/s12964-024-01686-8","article-title":"Altered Glia-Neuron Communication in Alzheimer\u2019s Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq","volume":"22","author":"Soelter","year":"2024","journal-title":"Cell Commun Signal"},{"key":"10.1016\/j.crmeth.2026.101337_bib4","doi-asserted-by":"crossref","DOI":"10.1016\/j.isci.2024.111065","article-title":"Single-nucleus RNA sequencing-based construction of a hippocampal neuron atlas in mice with epileptic cognitive impairment","volume":"27","author":"Ma","year":"2024","journal-title":"iScience"},{"key":"10.1016\/j.crmeth.2026.101337_bib5","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0209648","article-title":"Single-nucleus and single-cell transcriptomes compared in matched cortical cell types","volume":"13","author":"Bakken","year":"2018","journal-title":"PLoS One"},{"key":"10.1016\/j.crmeth.2026.101337_bib6","doi-asserted-by":"crossref","DOI":"10.1002\/cpz1.919","article-title":"Single-Nucleus RNA-Sequencing in Brain Tissue","volume":"3","author":"Waag","year":"2023","journal-title":"Curr. Protoc."},{"key":"10.1016\/j.crmeth.2026.101337_bib7","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/s41587-020-0465-8","article-title":"Systematic comparison of single-cell and single-nucleus RNA-sequencing methods","volume":"38","author":"Ding","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.crmeth.2026.101337_bib8","article-title":"Nuclear RNA-seq of single neurons reveals molecular signatures of activation","volume":"7","author":"Lacar","year":"2016","journal-title":"Nat. Commun."},{"key":"10.1016\/j.crmeth.2026.101337_bib9","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nmeth.4437","article-title":"Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations","volume":"14","author":"van den Brink","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.crmeth.2026.101337_bib10","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1038\/s41593-022-01022-8","article-title":"Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain","volume":"25","author":"Marsh","year":"2022","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.crmeth.2026.101337_bib11","doi-asserted-by":"crossref","first-page":"6031","DOI":"10.1038\/s41598-017-04426-w","article-title":"A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA","volume":"7","author":"Lake","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.crmeth.2026.101337_bib12","doi-asserted-by":"crossref","first-page":"52","DOI":"10.4132\/jptm.2022.12.19","article-title":"Perspectives on single-nucleus RNA sequencing in different cell types and tissues","volume":"57","author":"Kim","year":"2023","journal-title":"J. Pathol. Transl. Med."},{"key":"10.1016\/j.crmeth.2026.101337_bib13","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1186\/s13059-020-02048-6","article-title":"Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows","volume":"21","author":"Denisenko","year":"2020","journal-title":"Genome Biol."},{"key":"10.1016\/j.crmeth.2026.101337_bib14","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1126\/science.aaf1204","article-title":"Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain","volume":"352","author":"Lake","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.crmeth.2026.101337_bib15","doi-asserted-by":"crossref","first-page":"3088","DOI":"10.1016\/j.neuron.2021.09.001","article-title":"Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain","volume":"109","author":"Tran","year":"2021","journal-title":"Neuron"},{"key":"10.1016\/j.crmeth.2026.101337_bib16","doi-asserted-by":"crossref","first-page":"2788","DOI":"10.1038\/s41596-021-00514-4","article-title":"Extraction of nuclei from archived postmortem tissues for single-nucleus sequencing applications","volume":"16","author":"Maitra","year":"2021","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.crmeth.2026.101337_bib17","doi-asserted-by":"crossref","first-page":"2314","DOI":"10.1038\/s41467-023-37437-5","article-title":"Single-nucleus RNA-sequencing of autosomal dominant Alzheimer disease and risk variant carriers","volume":"14","author":"Brase","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.crmeth.2026.101337_bib18","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.27041","article-title":"The Human Cell Atlas","volume":"6","author":"Regev","year":"2017","journal-title":"eLife"},{"key":"10.1016\/j.crmeth.2026.101337_bib19","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1016\/j.neuron.2017.10.007","article-title":"The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas","volume":"96","author":"Ecker","year":"2017","journal-title":"Neuron"},{"key":"10.1016\/j.crmeth.2026.101337_bib20","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1038\/s41586-023-06812-z","article-title":"A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain","volume":"624","author":"Yao","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2026.101337_bib21","doi-asserted-by":"crossref","first-page":"D996","DOI":"10.1093\/nar\/gks1042","article-title":"Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system","volume":"41","author":"Sunkin","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.crmeth.2026.101337_bib22","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/s41573-023-00688-4","article-title":"Applications of single-cell RNA sequencing in drug discovery and development","volume":"22","author":"Van de Sande","year":"2023","journal-title":"Nat. Rev. Drug Discov."},{"key":"10.1016\/j.crmeth.2026.101337_bib23","doi-asserted-by":"crossref","first-page":"2021","DOI":"10.1158\/0008-5472.CAN-23-3005","article-title":"Integration of Pan-Cancer Cell Line and Single-Cell Transcriptomic Profiles Enables Inference of Therapeutic Vulnerabilities in Heterogeneous Tumors","volume":"84","author":"Zhang","year":"2024","journal-title":"Cancer Res."},{"key":"10.1016\/j.crmeth.2026.101337_bib24","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/s10038-020-00844-3","article-title":"Single-cell genomics to understand disease pathogenesis","volume":"66","author":"Nomura","year":"2021","journal-title":"J. Hum. Genet."},{"key":"10.1016\/j.crmeth.2026.101337_bib25","doi-asserted-by":"crossref","first-page":"2595","DOI":"10.1038\/s41467-024-46912-6","article-title":"Single cell deciphering of progression trajectories of the tumor ecosystem in head and neck cancer","volume":"15","author":"Liu","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.crmeth.2026.101337_bib26","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1186\/s12943-021-01419-2","article-title":"Single-cell RNA sequencing reveals markers of disease progression in primary cutaneous T-cell lymphoma","volume":"20","author":"Rindler","year":"2021","journal-title":"Mol. Cancer"},{"key":"10.1016\/j.crmeth.2026.101337_bib27","article-title":"A multi-omics atlas of the human retina at single-cell resolution","volume":"3","author":"Liang","year":"2023","journal-title":"Cell Genom."},{"key":"10.1016\/j.crmeth.2026.101337_bib28","article-title":"The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans","volume":"376","author":"Jones","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.crmeth.2026.101337_bib29","doi-asserted-by":"crossref","first-page":"1330","DOI":"10.1053\/j.gastro.2020.11.010","article-title":"Single-Nucleus and In Situ RNA-Sequencing Reveal Cell Topographies in the Human Pancreas","volume":"160","author":"Tosti","year":"2021","journal-title":"Gastroenterology"},{"key":"10.1016\/j.crmeth.2026.101337_bib30","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.aat8573","article-title":"Accelerating a paradigm shift: The Common Fund Single Cell Analysis Program","volume":"4","author":"Roy","year":"2018","journal-title":"Sci. Adv."},{"key":"10.1016\/j.crmeth.2026.101337_bib31","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1016\/j.celrep.2016.12.066","article-title":"Primary Cell Culture of Live Neurosurgically Resected Aged Adult Human Brain Cells and Single Cell Transcriptomics","volume":"18","author":"Spaethling","year":"2017","journal-title":"Cell Rep."},{"key":"10.1016\/j.crmeth.2026.101337_bib32","doi-asserted-by":"crossref","first-page":"1688","DOI":"10.1038\/s41467-022-29212-9","article-title":"Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data","volume":"13","author":"Hong","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.crmeth.2026.101337_bib33","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1016\/j.tcb.2021.05.004","article-title":"Stress relief: emerging methods to mitigate dissociation-induced artefacts","volume":"31","author":"Machado","year":"2021","journal-title":"Trends Cell Biol."},{"key":"10.1016\/j.crmeth.2026.101337_bib34","doi-asserted-by":"crossref","first-page":"4043","DOI":"10.1016\/j.neuron.2022.09.010","article-title":"Neuronal ambient RNA contamination causes misinterpreted and masked cell types in brain single-nuclei datasets","volume":"110","author":"Caglayan","year":"2022","journal-title":"Neuron"},{"key":"10.1016\/j.crmeth.2026.101337_bib35","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1186\/s12974-023-02831-9","article-title":"Ambient RNAs removal of cortex-specific snRNA-seq reveals Apoe(+) microglia\/macrophage after deeper cerebral hypoperfusion in mice","volume":"20","author":"Zhang","year":"2023","journal-title":"J. Neuroinflammation"},{"key":"10.1016\/j.crmeth.2026.101337_bib36","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-020-67513-5","article-title":"Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM","volume":"10","author":"Alvarez","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.crmeth.2026.101337_bib37","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giaa151","article-title":"SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data","volume":"9","author":"Young","year":"2020","journal-title":"GigaScience"},{"key":"10.1016\/j.crmeth.2026.101337_bib38","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","article-title":"DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors","volume":"8","author":"McGinnis","year":"2019","journal-title":"Cell Syst."},{"key":"10.1016\/j.crmeth.2026.101337_bib39","doi-asserted-by":"crossref","first-page":"1323","DOI":"10.1038\/s41592-023-01943-7","article-title":"Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender","volume":"20","author":"Fleming","year":"2023","journal-title":"Nat. Methods"},{"key":"10.1016\/j.crmeth.2026.101337_bib40","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1186\/s13059-019-1874-1","article-title":"Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression","volume":"20","author":"Hafemeister","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.crmeth.2026.101337_bib41","series-title":"Frankenstein\u2019 protocol for nuclei isolation from fresh and frozen tissue for snRNAseq","author":"Martelotto","year":"2020"},{"key":"10.1016\/j.crmeth.2026.101337_bib42","series-title":"Document Number CG000505 Rev A","year":"2022"},{"key":"10.1016\/j.crmeth.2026.101337_bib43","unstructured":"S2Genomics Nuclei Isolation from Frozen Mouse Brain Tissue for Single Nuclei Sequencing Applications P\/N 100-272-080. https:\/\/info.s2genomics.com\/hubfs\/2024%20Website%20Update%20Resources\/s2-genomics-demonstrated-protocol-nuclei-isolation-and-cleanup-frozen-mouse-brain-v241018.pdf."},{"key":"10.1016\/j.crmeth.2026.101337_bib44","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1016\/j.cell.2018.02.001","article-title":"Mapping the Mouse Cell Atlas by Microwell-Seq","volume":"172","author":"Han","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.crmeth.2026.101337_bib45","doi-asserted-by":"crossref","first-page":"baz046","DOI":"10.1093\/database\/baz046","article-title":"PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data","volume":"2019","author":"Franzen","year":"2019","journal-title":"Database"},{"key":"10.1016\/j.crmeth.2026.101337_bib46","doi-asserted-by":"crossref","first-page":"3155","DOI":"10.1038\/s41467-020-16904-3","article-title":"An entropy-based metric for assessing the purity of single cell populations","volume":"11","author":"Liu","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.crmeth.2026.101337_bib47","article-title":"MALAT1 expression indicates cell quality in single-cell RNA sequencing data","author":"Clarke","year":"2024","journal-title":"bioRxiv"},{"key":"10.1016\/j.crmeth.2026.101337_bib48","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1186\/s12864-024-11015-5","article-title":"High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction","volume":"25","author":"Montserrat-Ayuso","year":"2024","journal-title":"BMC Genom."},{"key":"10.1016\/j.crmeth.2026.101337_bib49","doi-asserted-by":"crossref","DOI":"10.1126\/science.abj2685","article-title":"Complement factor C1q mediates sleep spindle loss and epileptic spikes after mild brain injury","volume":"373","author":"Holden","year":"2021","journal-title":"Science"},{"key":"10.1016\/j.crmeth.2026.101337_bib50","doi-asserted-by":"crossref","first-page":"47","DOI":"10.2147\/NDT.S348682","article-title":"Elevated Serum Complement C1q Levels After Traumatic Brain Injury and Its Association with Poor Prognosis","volume":"18","author":"Yan","year":"2022","journal-title":"Neuropsychiatr. Dis. Treat."},{"key":"10.1016\/j.crmeth.2026.101337_bib51","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s12868-024-00846-3","article-title":"Tmem119 expression is downregulated in a subset of brain metastasis-associated microglia","volume":"25","author":"Ma","year":"2024","journal-title":"BMC Neurosci."},{"key":"10.1016\/j.crmeth.2026.101337_bib52","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1002\/jnr.24267","article-title":"Astrocytes and Glutamine Synthetase in Epileptogenesis","volume":"97","author":"Eid","year":"2019","journal-title":"J. Neurosci. Res."},{"key":"10.1016\/j.crmeth.2026.101337_bib53","doi-asserted-by":"crossref","DOI":"10.3389\/fneur.2021.665334","article-title":"Astroglial Glutamine Synthetase and the Pathogenesis of Mesial Temporal Lobe Epilepsy","volume":"12","author":"Sandhu","year":"2021","journal-title":"Front. Neurol."},{"key":"10.1016\/j.crmeth.2026.101337_bib54","doi-asserted-by":"crossref","first-page":"3796","DOI":"10.1016\/j.csbj.2021.06.043","article-title":"UCell: Robust and scalable single-cell gene signature scoring","volume":"19","author":"Andreatta","year":"2021","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"10.1016\/j.crmeth.2026.101337_bib55","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1111\/1755-0998.12779","article-title":"Batch effects in a multiyear sequencing study: False biological trends due to changes in read lengths","volume":"18","author":"Leigh","year":"2018","journal-title":"Mol. Ecol. Resour."},{"key":"10.1016\/j.crmeth.2026.101337_bib56","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.90214","article-title":"Avoiding false discoveries in single-cell RNA-seq by revisiting the first Alzheimer's disease dataset","volume":"12","author":"Murphy","year":"2023","journal-title":"eLife"},{"key":"10.1016\/j.crmeth.2026.101337_bib57","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1038\/nrg2825","article-title":"Tackling the widespread and critical impact of batch effects in high-throughput data","volume":"11","author":"Leek","year":"2010","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.crmeth.2026.101337_bib58","first-page":"1537","article-title":"Microglia and Astrocytes in Alzheimer's Disease: Significance and Summary of Recent Advances","volume":"15","author":"Deng","year":"2024","journal-title":"Aging Dis."},{"key":"10.1016\/j.crmeth.2026.101337_bib59","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1038\/s41590-018-0110-6","article-title":"Re-evaluating microglia expression profiles using RiboTag and cell isolation strategies","volume":"19","author":"Haimon","year":"2018","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.crmeth.2026.101337_bib60","doi-asserted-by":"crossref","first-page":"2235","DOI":"10.1084\/jem.20180653","article-title":"Microglial translational profiling reveals a convergent APOE pathway from aging, amyloid, and tau","volume":"215","author":"Kang","year":"2018","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.crmeth.2026.101337_bib61","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1038\/s41392-023-01588-0","article-title":"Microglia in neurodegenerative diseases: mechanism and potential therapeutic targets","volume":"8","author":"Gao","year":"2023","journal-title":"Signal Transduct. Target. Ther."},{"key":"10.1016\/j.crmeth.2026.101337_bib62","doi-asserted-by":"crossref","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"10.1016\/j.crmeth.2026.101337_bib63","unstructured":"OpenAI (2024). ChatGPT [Large language model]."},{"key":"10.1016\/j.crmeth.2026.101337_bib64","unstructured":"Google (2024). Gemini [Large language model]."},{"key":"10.1016\/j.crmeth.2026.101337_bib65","unstructured":"AI, P. (2024). Perplexity [AI search engine]."},{"key":"10.1016\/j.crmeth.2026.101337_bib66","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms14049","article-title":"Massively parallel digital transcriptional profiling of single cells","volume":"8","author":"Zheng","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.crmeth.2026.101337_bib67","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Hao","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.crmeth.2026.101337_bib68","article-title":"neurogenetics\/SAHA: ALL VERSIONS.","author":"Acri","year":"2024","journal-title":"Zenodo"},{"key":"10.1016\/j.crmeth.2026.101337_bib69","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1038\/nature05453","article-title":"Genome-wide atlas of gene expression in the adult mouse brain","volume":"445","author":"Lein","year":"2007","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2026.101337_bib70","doi-asserted-by":"crossref","first-page":"4720","DOI":"10.1093\/bioinformatics\/btac582","article-title":"propeller: testing for differences in cell type proportions in single cell data","volume":"38","author":"Phipson","year":"2022","journal-title":"Bioinformatics"},{"key":"10.1016\/j.crmeth.2026.101337_bib71","article-title":"Fast gene set enrichment analysis","author":"Korotkevich","year":"2021","journal-title":"bioRxiv"}],"container-title":["Cell Reports Methods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667237526000378?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667237526000378?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T23:18:04Z","timestamp":1783552684000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2667237526000378"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3]]},"references-count":71,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,3]]}},"alternative-id":["S2667237526000378"],"URL":"https:\/\/doi.org\/10.1016\/j.crmeth.2026.101337","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.03.25.645306","asserted-by":"object"}]},"ISSN":["2667-2375"],"issn-type":[{"value":"2667-2375","type":"print"}],"subject":[],"published":{"date-parts":[[2026,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing","name":"articletitle","label":"Article Title"},{"value":"Cell Reports Methods","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.crmeth.2026.101337","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"101337"}}