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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 | Größe | Format | |
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gkaa1127.pdf | 4,72 MB | Adobe PDF | Öffnen/Anzeigen |
Diese Ressource wurde unter folgender Copyright-Bestimmung veröffentlicht: Lizenz von Creative Commons