TY  - JOUR
AU  - Otonicar, Jan
AU  - Lazareva, Olga
AU  - Mallm, Jan-Philipp
AU  - Simovic-Lorenz, Milena
AU  - Philippos, George
AU  - Sant, Pooja
AU  - Parekh, Urja
AU  - Hammann, Linda
AU  - Li, Albert
AU  - Yildiz, Umut
AU  - Marttinen, Mikael
AU  - Zaugg, Judith
AU  - Noh, Kyung Min
AU  - Stegle, Oliver
AU  - Ernst, Aurélie
TI  - HIPSD</td><td width="150">
TI  - amp;R-seq enables scalable genomic copy number and transcriptome profiling.
JO  - Genome biology
VL  - 25
IS  - 1
SN  - 1465-6906
CY  - London
PB  - BioMed Central
M1  - DKFZ-2024-02739
SP  - 316
PY  - 2024
N1  - #EA:B420#EA:B260#EA:W192#EA:E250#LA:B420#LA:B260#
AB  - Single-cell DNA sequencing (scDNA-seq) enables decoding somatic cancer variation. Existing methods are hampered by low throughput or cannot be combined with transcriptome sequencing in the same cell. We propose HIPSD</td><td width="150">
AB  - R-seq (HIgh-throughPut Single-cell Dna and Rna-seq), a scalable yet simple and accessible assay to profile low-coverage DNA and RNA in thousands of cells in parallel. Our approach builds on a modification of the 10X Genomics platform for scATAC and multiome profiling. In applications to human cell models and primary tissue, we demonstrate the feasibility to detect rare clones and we combine the assay with combinatorial indexing to profile over 17,000 cells.
KW  - Humans
KW  - Single-Cell Analysis: methods
KW  - Gene Expression Profiling: methods
KW  - High-Throughput Nucleotide Sequencing: methods
KW  - Genomics: methods
KW  - Transcriptome
KW  - Sequence Analysis, DNA: methods
KW  - Sequence Analysis, RNA: methods
KW  - DNA Copy Number Variations
KW  - Single Cell DNA sequencing (Other)
KW  - Single Cell copy Number profiling (Other)
KW  - Single Cell multiome (Other)
LB  - PUB:(DE-HGF)16
C6  - pmid:39696535
C2  - pmc:PMC11657747
DO  - DOI:10.1186/s13059-024-03450-0
UR  - https://inrepo02.dkfz.de/record/295958
ER  -