000300359 001__ 300359
000300359 005__ 20251002115234.0
000300359 0247_ $$2doi$$a10.1038/s41598-025-97053-9
000300359 0247_ $$2pmid$$apmid:40229354
000300359 037__ $$aDKFZ-2025-00793
000300359 041__ $$aEnglish
000300359 082__ $$a600
000300359 1001_ $$0P:(DE-He78)bac03ea8237bbc7b1290321d845ddef7$$aErnst, Kati$$b0$$eFirst author$$udkfz
000300359 245__ $$aA simplified preparation method for single-nucleus RNA-sequencing using long-term frozen brain tumor tissues.
000300359 260__ $$a[London]$$bSpringer Nature$$c2025
000300359 3367_ $$2DRIVER$$aarticle
000300359 3367_ $$2DataCite$$aOutput Types/Journal article
000300359 3367_ $$0PUB:(DE-HGF)16$$2PUB:(DE-HGF)$$aJournal Article$$bjournal$$mjournal$$s1744724024_5437
000300359 3367_ $$2BibTeX$$aARTICLE
000300359 3367_ $$2ORCID$$aJOURNAL_ARTICLE
000300359 3367_ $$00$$2EndNote$$aJournal Article
000300359 500__ $$a#EA:B360#EA:B062#LA:B360#LA:B062#
000300359 520__ $$aSingle-cell RNA-sequencing has provided intriguing new insights into research areas such as developmental processes and tumor heterogeneity. Most approaches, however, rely on the availability of fresh surgical specimens, thereby dramatically reducing the ability to profile particularly rare tissue types. Here, we optimized a method to isolate intact nuclei from long-term frozen pediatric glioma tissues. We performed a technical comparison between different single-nucleus RNA-sequencing (snRNA-seq) systems and applied the established nucleus isolation method to analyze frozen primary glioma tissues. The results show that our fast, simple and low-cost nuclear isolation protocol provides intact nuclei, which can be used in both droplet- and plate-based single-cell sequencing platforms - allowing the identification of distinct tumor cell populations and infiltrating microglia. Additional optimization to include shorter RNA fragments in the 3' sequencing library improved gene detection and cell type annotation. Taken together, the method dramatically increases the potential of studying rare tumor entities and is specifically tailored for using frozen brain tumor tissue.
000300359 536__ $$0G:(DE-HGF)POF4-312$$a312 - Funktionelle und strukturelle Genomforschung (POF4-312)$$cPOF4-312$$fPOF IV$$x0
000300359 588__ $$aDataset connected to CrossRef, PubMed, , Journals: inrepo02.dkfz.de
000300359 650_2 $$2MeSH$$aHumans
000300359 650_2 $$2MeSH$$aBrain Neoplasms: genetics
000300359 650_2 $$2MeSH$$aBrain Neoplasms: pathology
000300359 650_2 $$2MeSH$$aSingle-Cell Analysis: methods
000300359 650_2 $$2MeSH$$aSequence Analysis, RNA: methods
000300359 650_2 $$2MeSH$$aGlioma: genetics
000300359 650_2 $$2MeSH$$aGlioma: pathology
000300359 650_2 $$2MeSH$$aCell Nucleus: genetics
000300359 650_2 $$2MeSH$$aChild
000300359 650_2 $$2MeSH$$aFreezing
000300359 7001_ $$0P:(DE-He78)34b3639de467b2c700920d7cbc3d2110$$aOkonechnikov, Konstantin$$b1$$eFirst author$$udkfz
000300359 7001_ $$0P:(DE-He78)159272f458e2803e25f14656e80cdd17$$aBageritz, Josephine$$b2$$udkfz
000300359 7001_ $$0P:(DE-He78)a42658b653667a6ef624186eb844fe10$$aPerera, Ashwyn A$$b3$$udkfz
000300359 7001_ $$0P:(DE-He78)697cb039ca08f3b7e5a2a52dbf020b46$$aMallm, Jan-Philipp$$b4$$udkfz
000300359 7001_ $$0P:(DE-He78)adf0bc22f6c87d09ddb939645a7870ed$$aWittmann, Andrea$$b5$$udkfz
000300359 7001_ $$0P:(DE-He78)5100059e746b377e2e0a37c0e24f6bf7$$aMaaß, Kendra K$$b6$$udkfz
000300359 7001_ $$0P:(DE-He78)c66792177fe889fde8058c5b76f86ba6$$aLeible, Svenja$$b7$$udkfz
000300359 7001_ $$0P:(DE-He78)3c0da8e3caa2aa50cad85152aa0465ad$$aBoutros, Michael$$b8$$udkfz
000300359 7001_ $$0P:(DE-He78)f746aa965c4e1af518b016de3aaff5d9$$aPfister, Stefan M$$b9$$udkfz
000300359 7001_ $$0P:(DE-He78)2a8fbc2efe7e5e468472d57f724fe39b$$aZuckermann, Marc$$b10$$eLast author$$udkfz
000300359 7001_ $$0P:(DE-He78)551bb92841f634070997aa168d818492$$aJones, David$$b11$$eLast author$$udkfz
000300359 773__ $$0PERI:(DE-600)2615211-3$$a10.1038/s41598-025-97053-9$$gVol. 15, no. 1, p. 12849$$n1$$p12849$$tScientific reports$$v15$$x2045-2322$$y2025
000300359 8767_ $$8SN-2025-00915-b$$92025-08-27$$d2025-10-01$$eAPC$$jZahlung erfolgt$$v1864.65
000300359 909CO $$ooai:inrepo02.dkfz.de:300359$$pVDB$$pOpenAPC$$popenCost
000300359 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)bac03ea8237bbc7b1290321d845ddef7$$aDeutsches Krebsforschungszentrum$$b0$$kDKFZ
000300359 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)34b3639de467b2c700920d7cbc3d2110$$aDeutsches Krebsforschungszentrum$$b1$$kDKFZ
000300359 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)159272f458e2803e25f14656e80cdd17$$aDeutsches Krebsforschungszentrum$$b2$$kDKFZ
000300359 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)a42658b653667a6ef624186eb844fe10$$aDeutsches Krebsforschungszentrum$$b3$$kDKFZ
000300359 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)697cb039ca08f3b7e5a2a52dbf020b46$$aDeutsches Krebsforschungszentrum$$b4$$kDKFZ
000300359 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)adf0bc22f6c87d09ddb939645a7870ed$$aDeutsches Krebsforschungszentrum$$b5$$kDKFZ
000300359 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)5100059e746b377e2e0a37c0e24f6bf7$$aDeutsches Krebsforschungszentrum$$b6$$kDKFZ
000300359 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)c66792177fe889fde8058c5b76f86ba6$$aDeutsches Krebsforschungszentrum$$b7$$kDKFZ
000300359 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)3c0da8e3caa2aa50cad85152aa0465ad$$aDeutsches Krebsforschungszentrum$$b8$$kDKFZ
000300359 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)f746aa965c4e1af518b016de3aaff5d9$$aDeutsches Krebsforschungszentrum$$b9$$kDKFZ
000300359 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)2a8fbc2efe7e5e468472d57f724fe39b$$aDeutsches Krebsforschungszentrum$$b10$$kDKFZ
000300359 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)551bb92841f634070997aa168d818492$$aDeutsches Krebsforschungszentrum$$b11$$kDKFZ
000300359 9131_ $$0G:(DE-HGF)POF4-312$$1G:(DE-HGF)POF4-310$$2G:(DE-HGF)POF4-300$$3G:(DE-HGF)POF4$$4G:(DE-HGF)POF$$aDE-HGF$$bGesundheit$$lKrebsforschung$$vFunktionelle und strukturelle Genomforschung$$x0
000300359 9141_ $$y2025
000300359 915__ $$0StatID:(DE-HGF)0100$$2StatID$$aJCR$$bSCI REP-UK : 2022$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)0200$$2StatID$$aDBCoverage$$bSCOPUS$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)0300$$2StatID$$aDBCoverage$$bMedline$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)0501$$2StatID$$aDBCoverage$$bDOAJ Seal$$d2024-07-29T15:28:26Z
000300359 915__ $$0StatID:(DE-HGF)0500$$2StatID$$aDBCoverage$$bDOAJ$$d2024-07-29T15:28:26Z
000300359 915__ $$0StatID:(DE-HGF)0030$$2StatID$$aPeer Review$$bDOAJ : Anonymous peer review$$d2024-07-29T15:28:26Z
000300359 915__ $$0StatID:(DE-HGF)0600$$2StatID$$aDBCoverage$$bEbsco Academic Search$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)0030$$2StatID$$aPeer Review$$bASC$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)0199$$2StatID$$aDBCoverage$$bClarivate Analytics Master Journal List$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)1040$$2StatID$$aDBCoverage$$bZoological Record$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)1150$$2StatID$$aDBCoverage$$bCurrent Contents - Physical, Chemical and Earth Sciences$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)1050$$2StatID$$aDBCoverage$$bBIOSIS Previews$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)0160$$2StatID$$aDBCoverage$$bEssential Science Indicators$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)1190$$2StatID$$aDBCoverage$$bBiological Abstracts$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)0113$$2StatID$$aWoS$$bScience Citation Index Expanded$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)0150$$2StatID$$aDBCoverage$$bWeb of Science Core Collection$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)9900$$2StatID$$aIF < 5$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)0561$$2StatID$$aArticle Processing Charges$$d2024-12-18
000300359 915__ $$0StatID:(DE-HGF)0700$$2StatID$$aFees$$d2024-12-18
000300359 915pc $$0PC:(DE-HGF)0000$$2APC$$aAPC keys set
000300359 915pc $$0PC:(DE-HGF)0001$$2APC$$aLocal Funding
000300359 915pc $$0PC:(DE-HGF)0002$$2APC$$aDFG OA Publikationskosten
000300359 915pc $$0PC:(DE-HGF)0003$$2APC$$aDOAJ Journal
000300359 9202_ $$0I:(DE-He78)B360-20160331$$kB360$$lPädiatrische Gliomforschung$$x0
000300359 9202_ $$0I:(DE-He78)B062-20160331$$kB062$$lB062 Pädiatrische Neuroonkologie$$x1
000300359 9201_ $$0I:(DE-He78)B360-20160331$$kB360$$lPädiatrische Gliomforschung$$x0
000300359 9201_ $$0I:(DE-He78)B062-20160331$$kB062$$lB062 Pädiatrische Neuroonkologie$$x1
000300359 9201_ $$0I:(DE-He78)B110-20160331$$kB110$$lB110 Signalwege funktionelle Genomik$$x2
000300359 9201_ $$0I:(DE-He78)W192-20160331$$kW192$$lSingle-cell Open Lab$$x3
000300359 9200_ $$0I:(DE-He78)B360-20160331$$kB360$$lPädiatrische Gliomforschung$$x0
000300359 9200_ $$0I:(DE-He78)B062-20160331$$kB062$$lB062 Pädiatrische Neuroonkologie$$x1
000300359 980__ $$ajournal
000300359 980__ $$aVDB
000300359 980__ $$aI:(DE-He78)B360-20160331
000300359 980__ $$aI:(DE-He78)B062-20160331
000300359 980__ $$aI:(DE-He78)B110-20160331
000300359 980__ $$aI:(DE-He78)W192-20160331
000300359 980__ $$aUNRESTRICTED
000300359 980__ $$aAPC