Bitte benutzen Sie diese Referenz, um auf diese Ressource zu verweisen: doi:10.22028/D291-33738
Titel: CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method
VerfasserIn: Hahn, Oliver
Fehlmann, Tobias
Zhang, Hui
Munson, Christy N.
Vest, Ryan T.
Borcherding, Adam
Liu, Sophie
Villarosa, Christian
Drmanac, Snezana
Drmanac, Rade
Keller, Andreas
Wyss-Coray, Tony
Sprache: Englisch
Titel: Nucleic Acids Research
Bandnummer: 49 (2021)
Heft: 2
Verlag/Plattform: Oxford University Press
Erscheinungsjahr: 2020
DDC-Sachgruppe: 610 Medizin, Gesundheit
Dokumenttyp: Journalartikel / Zeitschriftenartikel
Abstract: Massively-parallel single-cell and single-nucleus RNA sequencing (scRNA-seq, snRNA-seq) requires extensive sequencing to achieve proper per-cell coverage, making sequencing resources and availability of sequencers critical factors for conducting deep transcriptional profiling. CoolMPS is a novel sequencing-by-synthesis approach that relies on nucleotide labeling by re-usable antibodies, but whether it is applicable to snRNA-seq has not been tested. Here, we use a low-cost and off-the-shelf protocol to chemically convert libraries generated with the widely-used Chromium 10X technology to be sequenceable with CoolMPS technology. To assess the quality and performance of converted libraries sequenced with CoolMPS, we generated a snRNA-seq dataset from the hippocampus of young and old mice. Native libraries were sequenced on an Illumina Novaseq and libraries that were converted to be compatible with CoolMPS were sequenced on a DNBSEQ-400RS. CoolMPS-derived data faithfully replicated key characteristics of the native library dataset, including correct estimation of ambient RNA-contamination, detection of captured cells, cell clustering results, spatial marker gene expression, inter- and intra-replicate differences and gene expression changes during aging. In conclusion, our results show that CoolMPS provides a viable alternative to standard sequencing of RNA from droplet-based libraries.
DOI der Erstveröffentlichung: 10.1093/nar/gkaa1127
Link zu diesem Datensatz: urn:nbn:de:bsz:291--ds-337381
hdl:20.500.11880/31076
http://dx.doi.org/10.22028/D291-33738
ISSN: 1362-4962
0305-1048
Datum des Eintrags: 7-Apr-2021
Bezeichnung des in Beziehung stehenden Objekts: Supplementary data
In Beziehung stehendes Objekt: https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/nar/49/2/10.1093_nar_gkaa1127/1/gkaa1127_supplemental_files.zip?Expires=1620807326&Signature=Q7jQpLKRscMVhM3y2GHatvKujdsqVOgWtwrrmHWHEtuI9comD9jPMqRpYq820WtVLIn4GM60vBbZIJdmzzsyrRcXQ2rtjjz~I6SR549fjZypsXKZI4fS3CkLVrNlYSDHIo4RLTve89kkk3yeYh3w5JxhNPpUQVHokMzDJAfwL5EuDVqOa-~3IEbwlH17DmT3e8NofJCCZrhaF~p3ON8eWjUylWZRD-0myLNtLgx4OFI528-1OHK~FYhhuitfaHBs3jAg2de3FaM1caPJPVC8IBw5T5gku6M6TgC8pXwLZMiPJlaPeD9DzpzWhVzUkbthu6cNzq6Rk1NXGLxB0mffwA__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA
Fakultät: M - Medizinische Fakultät
ZE - Zentrale Einrichtungen
Fachrichtung: M - Medizinische Biometrie, Epidemiologie und medizinische Informatik
ZE - Zentrum für Bioinformatik(ZBI)
Professur: M - Keiner Professur zugeordnet
ZE - Sonstige
Sammlung:SciDok - Der Wissenschaftsserver der Universität des Saarlandes

Dateien zu diesem Datensatz:
Datei Beschreibung GrößeFormat 
gkaa1127.pdf4,72 MBAdobe PDFÖffnen/Anzeigen


Diese Ressource wurde unter folgender Copyright-Bestimmung veröffentlicht: Lizenz von Creative Commons Creative Commons