{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T02:10:49Z","timestamp":1773108649771,"version":"3.50.1"},"reference-count":47,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T00:00:00Z","timestamp":1698796800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T00:00:00Z","timestamp":1698796800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T00:00:00Z","timestamp":1698796800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T00:00:00Z","timestamp":1698796800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T00:00:00Z","timestamp":1698796800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T00:00:00Z","timestamp":1698796800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T00:00:00Z","timestamp":1698796800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81827901"],"award-info":[{"award-number":["81827901"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Analytica Chimica Acta"],"published-print":{"date-parts":[[2023,11]]},"DOI":"10.1016\/j.aca.2023.341861","type":"journal-article","created":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T17:28:25Z","timestamp":1697131705000},"page":"341861","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":6,"special_numbering":"C","title":["Transcriptomic profiling of nuclei from paraformaldehyde-fixed and formalin-fixed paraffin-embedded brain tissues"],"prefix":"10.1016","volume":"1281","author":[{"given":"Yunxia","family":"Guo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junjie","family":"Ma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhengyue","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kaitong","family":"Dang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qinyu","family":"Ge","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guang-zhong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0678-5219","authenticated-orcid":false,"given":"Xiangwei","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.aca.2023.341861_bib1","doi-asserted-by":"crossref","first-page":"5636","DOI":"10.1038\/s41467-021-25871-2","article-title":"High-throughput RNA sequencing of paraformaldehyde-fixed single cells","volume":"12","author":"Phan","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.aca.2023.341861_bib2","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1371\/journal.pone.0001261","article-title":"Determinants of RNA quality from FFPE samples","volume":"2","author":"Fraser","year":"2007","journal-title":"PLoS One"},{"key":"10.1016\/j.aca.2023.341861_bib3","series-title":"High Resolution Mapping of the Breast Cancer Tumor Microenvironment Using Integrated Single Cell, Spatial and in Situ Analysis of FFPE Tissue","author":"Janesick","year":"2022"},{"key":"10.1016\/j.aca.2023.341861_bib4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1177\/0300060520931259","article-title":"Effect of preservation time of formalin-fixed paraffin-embedded tissues on extractable DNA and RNA quantity","volume":"48","author":"Yi","year":"2020","journal-title":"J. Int. Med. Res."},{"key":"10.1016\/j.aca.2023.341861_bib5","doi-asserted-by":"crossref","first-page":"1816","DOI":"10.1101\/gr.234807.118","article-title":"Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ","volume":"29","author":"Foley","year":"2019","journal-title":"Genome Res."},{"key":"10.1016\/j.aca.2023.341861_bib6","series-title":"Micro-region Transcriptomics of Fixed Human Tissue Using Pick-Seq","author":"Maliga","year":"2021"},{"key":"10.1016\/j.aca.2023.341861_bib7","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/s12867-018-0103-x","article-title":"Recommendations for mRNA analysis of micro-dissected glomerular tufts from paraffin-embedded human kidney biopsy samples","volume":"19","author":"Bockmeyer","year":"2018","journal-title":"BMC Mol. Biol."},{"key":"10.1016\/j.aca.2023.341861_bib8","series-title":"Genome-wide Spatial Expression Profiling in FFPE Tissues","author":"Villacampa","year":"2020"},{"key":"10.1016\/j.aca.2023.341861_bib9","doi-asserted-by":"crossref","first-page":"10774","DOI":"10.3390\/ijms231810774","article-title":"Defining specific cell states of MPTP-induced Parkinson's disease by single-nucleus RNA sequencing","volume":"23","author":"Guo","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.aca.2023.341861_bib10","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/S1050-3862(98)00037-0","article-title":"Nucleus extraction from single mounted tissue sections","volume":"15","author":"Liehr","year":"1999","journal-title":"Genet. Anal. Biomol. Eng."},{"key":"10.1016\/j.aca.2023.341861_bib11","doi-asserted-by":"crossref","DOI":"10.1177\/31.11.6619538","article-title":"Method for analysis of cellular DNA content of paraffin-embedded pathological material using flow cytometry","volume":"31","author":"Hedley","year":"1983","journal-title":"J. Histochem. Cytochem."},{"key":"10.1016\/j.aca.2023.341861_bib12","doi-asserted-by":"crossref","first-page":"1967","DOI":"10.1016\/S0002-9440(10)61146-7","article-title":"A new method to extract nuclei from paraffin-embedded tissue to study lymphomas using interphase fluorescence in situ hybridization","volume":"160","author":"Paternoster","year":"2002","journal-title":"Am. J. Pathol."},{"key":"10.1016\/j.aca.2023.341861_bib13","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nm.4279","article-title":"Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples","volume":"23","author":"Martelotto","year":"2017","journal-title":"Nat. Med."},{"key":"10.1016\/j.aca.2023.341861_bib14","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1002\/cyto.990060106","article-title":"Flow cytometric determination of DNA ploidy level in nuclei isolated from paraffin-embedded tissue","volume":"6","author":"Schutte","year":"1985","journal-title":"Cytometry"},{"key":"10.1016\/j.aca.2023.341861_bib15","author":"Chin"},{"key":"10.1016\/j.aca.2023.341861_bib16","first-page":"4436","article-title":"Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples","author":"Norikazu","year":"1999","journal-title":"Nucleic Acids Reasearch"},{"key":"10.1016\/j.aca.2023.341861_bib17","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1097\/01.MP.0000026054.62220.FC","article-title":"Effect of duration of fixation on quantitative reverse transcription polymerase chain reaction analyses","volume":"15","author":"Macabeo-Ong","year":"2002","journal-title":"Mod. Pathol."},{"key":"10.1016\/j.aca.2023.341861_bib18","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/S0002-9440(10)63093-3","article-title":"Measurement of gene expression in archival paraffin-embedded tissues","volume":"164","author":"Cronin","year":"2004","journal-title":"Am. J. Pathol."},{"key":"10.1016\/j.aca.2023.341861_bib19","doi-asserted-by":"crossref","first-page":"1016","DOI":"10.1097\/00000478-200007000-00014","article-title":"Effect of formalin tissue fixation and processing on immunohistochemistry","volume":"24","author":"Werner","year":"2000","journal-title":"Am. J. Surg. Pathol."},{"key":"10.1016\/j.aca.2023.341861_bib20","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1126\/science.1226339","article-title":"Transcriptional architecture and chromatin landscape of the core circadian clock in mammals","volume":"338","author":"Koike","year":"2012","journal-title":"Science"},{"key":"10.1016\/j.aca.2023.341861_bib21","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1038\/s41467-018-08023-x","article-title":"Bulk tissue cell type deconvolution with multi-subject single-cell expression reference","volume":"10","author":"Wang","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.aca.2023.341861_bib22","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.aca.2020.10.046","article-title":"Effects of brain tissue section processing and storage time on gene expression","volume":"1142","author":"Jia","year":"2021","journal-title":"Anal. Chim. Acta"},{"key":"10.1016\/j.aca.2023.341861_bib23","doi-asserted-by":"crossref","first-page":"19802","DOI":"10.1073\/pnas.1319700110","article-title":"RNA-sequencing from single nuclei","volume":"110","author":"Grindberg","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.aca.2023.341861_bib24","doi-asserted-by":"crossref","DOI":"10.1186\/1755-8794-3-36","article-title":"Impact of RNA degradation on gene expression profiling","volume":"3","author":"Opitz","year":"2010","journal-title":"BMC Med. Genom."},{"key":"10.1016\/j.aca.2023.341861_bib25","doi-asserted-by":"crossref","first-page":"376","DOI":"10.2741\/grant","article-title":"Roles of ERBB family receptor tyrosine kinases, and downstream signaling pathways, in the control of cell growth and survival","volume":"7","author":"Grant","year":"2002","journal-title":"Front. Biosci."},{"key":"10.1016\/j.aca.2023.341861_bib26","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.jbior.2018.11.008","article-title":"Effective angiogenesis requires regulation of phosphoinositide signaling","volume":"71","author":"Davies","year":"2018","journal-title":"Adv. Biolog. Regul."},{"key":"10.1016\/j.aca.2023.341861_bib27","doi-asserted-by":"crossref","DOI":"10.1016\/j.bbi.2019.05.008","article-title":"Altered microbiomes distinguish Alzheimer's disease from amnestic mild cognitive impairment and health in a Chinese cohort","volume":"80","author":"Liu","year":"2019","journal-title":"Brain Behav. Immun."},{"key":"10.1016\/j.aca.2023.341861_bib28","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1186\/1471-2164-8-127","article-title":"House-keeping and tissue-specific genes in mouse tissues","volume":"8","author":"Kouadjo","year":"2007","journal-title":"BMC Genom."},{"key":"10.1016\/j.aca.2023.341861_bib29","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1016\/j.vetimm.2007.08.006","article-title":"A validation of 10 feline reference genes for gene expression measurements in snap-frozen tissues","volume":"120","author":"Penning","year":"2007","journal-title":"Vet. Immunol. Immunopathol."},{"key":"10.1016\/j.aca.2023.341861_bib30","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/S0014-5793(00)01816-0","article-title":"Inhibition of glucocorticoid-induced apoptosis by the expression of antisense gene of mitochondrial ATPase subunit 6(1)","volume":"478","author":"Sato","year":"2000","journal-title":"FEBS Lett."},{"key":"10.1016\/j.aca.2023.341861_bib31","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1186\/1471-2377-14-116","article-title":"Association of the mtDNA m.4171C>A\/MT-ND1 mutation with both optic neuropathy and bilateral brainstem lesions","volume":"14","author":"Morgia","year":"2014","journal-title":"BMC Neurol."},{"key":"10.1016\/j.aca.2023.341861_bib32","doi-asserted-by":"crossref","first-page":"1374","DOI":"10.1007\/s12035-019-01819-y","article-title":"Alterations of transcription of genes coding anti-oxidative and mitochondria-related proteins in amyloid \u03b2 toxicity: relevance to alzheimer's disease","volume":"57","author":"Cie\u015blik","year":"2019","journal-title":"Mol. Neurobiol."},{"key":"10.1016\/j.aca.2023.341861_bib33","doi-asserted-by":"crossref","DOI":"10.1016\/j.neulet.2021.135903","article-title":"The association between multiple risk factors, clinical correlations and molecular insights in Parkinson's disease patients from Tamil Nadu population, India","volume":"755","author":"Venkatesan","year":"2021","journal-title":"Neurosci. Lett."},{"key":"10.1016\/j.aca.2023.341861_bib34","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1093\/hmg\/ddg122","article-title":"Congenital hydrocephalus in hy3 mice is caused by a frameshift mutation in Hydin, a large novel gene","volume":"12","author":"Davy","year":"2003","journal-title":"Hum. Mol. Genet."},{"key":"10.1016\/j.aca.2023.341861_bib35","first-page":"1","article-title":"Knock-in mice with Myo3a Y137C mutation displayed progressive hearing loss and hair cell degeneration in the inner ear","volume":"2018","author":"Peipei","year":"2018","journal-title":"Neural Plast."},{"key":"10.1016\/j.aca.2023.341861_bib36","doi-asserted-by":"crossref","first-page":"43","DOI":"10.4161\/epi.3.1.5469","article-title":"Real-time PCR analysis of candidate imprinted genes on mouse chromosome 11 shows balanced expression from the maternal and paternal chromosomes and strain-specific variation in expression levels","volume":"3","author":"Tuskan","year":"2014","journal-title":"Epigenetics"},{"key":"10.1016\/j.aca.2023.341861_bib37","doi-asserted-by":"crossref","first-page":"2985","DOI":"10.1038\/s41380-022-01539-1","article-title":"A recurrent SHANK1 mutation implicated in autism spectrum disorder causes autistic-like core behaviors in mice via downregulation of mGluR1-IP3R1-calcium signaling","volume":"27","author":"Qin","year":"2022","journal-title":"Mol. Psychiatr."},{"key":"10.1016\/j.aca.2023.341861_bib38","first-page":"1","article-title":"Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state","author":"Smaji\u0107","year":"2022","journal-title":"Brain"},{"key":"10.1016\/j.aca.2023.341861_bib39","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1038\/s41591-019-0695-9","article-title":"Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer's disease","volume":"26","author":"Zhou","year":"2020","journal-title":"Nat. Med."},{"key":"10.1016\/j.aca.2023.341861_bib40","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1038\/s41593-020-0624-8","article-title":"Disease-associated astrocytes in Alzheimer's disease and aging","volume":"23","author":"Habib","year":"2020","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.aca.2023.341861_bib41","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-020-71521-w","article-title":"Direct formalin fixation induces widespread transcriptomic effects in archival tissue samples","volume":"10","author":"Wehmas","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.aca.2023.341861_bib42","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1080\/15476286.2022.2065116","article-title":"A comprehensive coverage insurance for cells: revealing links between ribosome collisions, stress responses and mRNA surveillance","volume":"19","author":"De","year":"2022","journal-title":"RNA Biol."},{"key":"10.1016\/j.aca.2023.341861_bib43","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/s00294-020-01111-w","article-title":"A cellular handbook for collided ribosomes: surveillance pathways and collision types","volume":"67","author":"Meydan","year":"2021","journal-title":"Curr. Genet."},{"key":"10.1016\/j.aca.2023.341861_bib44","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1089\/omi.2022.0053","article-title":"Age-associated molecular changes in human Hippocampus subfields as determined by quantitative proteomics","volume":"26","author":"Mol","year":"2022","journal-title":"OMICS"},{"key":"10.1016\/j.aca.2023.341861_bib45","doi-asserted-by":"crossref","first-page":"978","DOI":"10.1016\/j.tibs.2020.06.004","article-title":"Molecular mechanisms of lysosome and nucleus communication","volume":"45","author":"Zhao","year":"2020","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/j.aca.2023.341861_bib46","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1038\/s41593-018-0106-4","article-title":"B-1a lymphocytes promote oligodendrogenesis during brain development","volume":"21","author":"Tanabe","year":"2018","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.aca.2023.341861_bib47","doi-asserted-by":"crossref","first-page":"3928","DOI":"10.1093\/nar\/gkm347","article-title":"Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors","volume":"35","author":"Chen","year":"2007","journal-title":"Nucleic Acids Res."}],"container-title":["Analytica Chimica Acta"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0003267023010826?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0003267023010826?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,9,12]],"date-time":"2025-09-12T20:04:43Z","timestamp":1757707483000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0003267023010826"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11]]},"references-count":47,"alternative-id":["S0003267023010826"],"URL":"https:\/\/doi.org\/10.1016\/j.aca.2023.341861","relation":{},"ISSN":["0003-2670"],"issn-type":[{"value":"0003-2670","type":"print"}],"subject":[],"published":{"date-parts":[[2023,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Transcriptomic profiling of nuclei from paraformaldehyde-fixed and formalin-fixed paraffin-embedded brain tissues","name":"articletitle","label":"Article Title"},{"value":"Analytica Chimica Acta","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.aca.2023.341861","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 Elsevier B.V. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"341861"}}