{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:59:52Z","timestamp":1785427192698,"version":"3.56.0"},"posted":{"date-parts":[[2025,9,26]]},"group-title":"Genomics","reference-count":70,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T00:00:00Z","timestamp":1758844800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006312","name":"BrightFocus Foundation","doi-asserted-by":"crossref","award":["929965"],"award-info":[{"award-number":["929965"]}],"id":[{"id":"10.13039\/100006312","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"crossref","award":["2958\/21"],"award-info":[{"award-number":["2958\/21"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"crossref","award":["2141\/20"],"award-info":[{"award-number":["2141\/20"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"crossref"}]},{"name":"European Research Council","award":["101117324"],"award-info":[{"award-number":["101117324"]}]},{"award":["0005965"],"award-info":[{"award-number":["0005965"]}],"id":[{"id":"https:\/\/ror.org\/02heb2n75","id-type":"ROR","asserted-by":"publisher"}]},{"award":["3-17970"],"award-info":[{"award-number":["3-17970"]}],"id":[{"id":"https:\/\/ror.org\/02heb2n75","id-type":"ROR","asserted-by":"publisher"}]},{"award":["1001576154"],"award-info":[{"award-number":["1001576154"]}],"id":[{"id":"https:\/\/ror.org\/02heb2n75","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015326","name":"NIH Common Fund","doi-asserted-by":"crossref","award":["1R21AG074846-01A1"],"award-info":[{"award-number":["1R21AG074846-01A1"]}],"id":[{"id":"10.13039\/100015326","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000864","name":"Michael J. 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We uncovered early alterations in RNA spatial organization and gene expression, including 23 genes showing altered localization without changes in abundance in the 5xFAD hippocampus. Using spatial expression analysis and single-cell neighborhood analysis, we identified cell-type- and region-specific molecular programs associated with synaptic function, neuroinflammation, and metabolic stress that differed between 5xFAD and WT mice. Spatial RNA velocity further revealed state differences influenced by local cell to cell interactions. Together, these results suggest that RNA positioning and transcriptional programs are perturbed at early disease stages. Finally, we provide the full super-resolution ExSeq dataset as an open resource for spatial and cell-type-specific analyses in early Alzheimer\u2019s disease research.<\/jats:p>\n                <jats:sec>\n                  <jats:title>Highlights<\/jats:title>\n                  <jats:list list-type=\"bullet\">\n                    <jats:list-item>\n                      <jats:p>Super-resolved transcriptomic profiling of the hippocampus at early disease stages<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>Identification of 23 genes with altered spatial localization without changes in abundance<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>Early alterations in single-cell neighborhood organization in the 5xFAD hippocampus<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>Spatial RNA velocity reveals cell-type-specific cell state differences shaped by cell-cell proximity<\/jats:p>\n                    <\/jats:list-item>\n                  <\/jats:list>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Graphical abstract<\/jats:title>\n                  <jats:fig id=\"ufig1\" position=\"float\" orientation=\"portrait\" fig-type=\"figure\">\n                    <jats:graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"678295v2_ufig1\" position=\"float\" orientation=\"portrait\"\/>\n                  <\/jats:fig>\n                <\/jats:sec>","DOI":"10.1101\/2025.09.24.678295","type":"posted-content","created":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T23:20:13Z","timestamp":1758928813000},"source":"Crossref","is-referenced-by-count":0,"title":["Super-resolved spatial transcriptomics reveals early hippocampal RNA localization changes in a mouse model of Alzheimer\u2019s disease"],"prefix":"10.64898","author":[{"given":"Yaara","family":"Karasik","sequence":"first","affiliation":[{"name":"Faculty of Engineering, Bar-Ilan University, Israel"},{"name":"Institute for Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Israel"},{"name":"The Multidisciplinary Brain Research Center, Bar-Ilan University, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hadar","family":"Eger Ronsky","sequence":"additional","affiliation":[{"name":"Faculty of Engineering, Bar-Ilan University, Israel"},{"name":"Institute for Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Israel"},{"name":"The Multidisciplinary Brain Research Center, Bar-Ilan University, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tal","family":"Goldberg","sequence":"additional","affiliation":[{"name":"Faculty of Engineering, Bar-Ilan University, Israel"},{"name":"Institute for Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Israel"},{"name":"The Multidisciplinary Brain Research Center, Bar-Ilan University, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yeela","family":"Seri Huri","sequence":"additional","affiliation":[{"name":"School of Neurobiology, Biochemistry and Biophysics, The George S. 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