{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T19:51:49Z","timestamp":1790020309721,"version":"4.0.1"},"reference-count":30,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,10,4]],"date-time":"2023-10-04T00:00:00Z","timestamp":1696377600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Mol. Neurosci."],"abstract":"<jats:p>Single-cell RNA sequencing (scRNA-seq) provides a powerful tool to evaluate the transcriptomic landscape and heterogeneity of thousands of cells in parallel. However, complex study designs or the unavailability of in-house instruments require the temporal disconnection between sample preparation and library construction, raising the need for efficient sample preservation methods which are compatible with scRNA-seq downstream analysis. Several studies evaluated the effect of methanol fixation as preservation method, yet none of them deeply assessed its effect on adult primary dissociated brain tissue. Here, we evaluated its effect on murine dentate gyrus (DG) single cell suspensions and on subsequent scRNA-seq downstream analysis by performing SOrting and Robot-assisted Transcriptome SEQuencing (SORT-seq), a partially robotized version of the CEL-seq2 protocol. Our results show that MeOH fixation preserves RNA integrity and has no apparent effects on cDNA library construction. They also suggest that fixation protects from sorting-induced cell stress and increases the proportion of high-quality cells. Despite evidence of mRNA leakage in fixed cells, their relative gene expression levels correlate well with those of fresh cells and fixation does not significantly affect the variance of the dataset. Moreover, it allows the identification of all major DG cell populations, including neural precursors, granule neurons and different glial cell types, with a tendency to preserve more neurons that are underrepresented in fresh samples. Overall, our data show that MeOH fixation is suitable for preserving primary neural cells for subsequent single-cell RNA profiling, helping to overcome challenges arising from complex workflows, improve experimental flexibility and facilitate scientific collaboration.<\/jats:p>","DOI":"10.3389\/fnmol.2023.1223798","type":"journal-article","created":{"date-parts":[[2023,10,4]],"date-time":"2023-10-04T08:37:41Z","timestamp":1696408661000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":10,"title":["Effect of methanol fixation on single-cell RNA sequencing of the murine dentate gyrus"],"prefix":"10.3389","volume":"16","author":[{"given":"Marta","family":"S\u00e1nchez-Carbonell","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patricia","family":"Jim\u00e9nez Peinado","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cathrin","family":"Bayer-Kaufmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Christopher","family":"Hennings","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yvonne","family":"Hofmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvio","family":"Schmidt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Otto W.","family":"Witte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anja","family":"Urbach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,10,4]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1186\/s12915-017-0383-5","article-title":"Cell fixation and preservation for droplet-based single-cell transcriptomics","volume":"15","author":"Alles","year":"2017","journal-title":"BMC Biol."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1186\/s12967-018-1578-4","article-title":"PBMC fixation and processing for chromium single-cell RNA sequencing","volume":"16","author":"Chen","year":"2018","journal-title":"J. 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Pathol."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cells"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"e113380","DOI":"10.1371\/journal.pone.0113380","article-title":"On the normalization of the minimum free energy of RNAs by sequence length","volume":"9","author":"Trotta","year":"2014","journal-title":"PLoS One"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1111\/j.1460-9568.2006.04862.x","article-title":"Microarray-based long-term detection of genes differentially expressed after cortical spreading depression","volume":"24","author":"Urbach","year":"2006","journal-title":"Eur. J. 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