biostudies-arrayexpressMaria PuschhofMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16835Murine adenocarcinoma models VAKPS (Villin1-CreER Apc-fl/+ Kras-G12D/+ Trp5-3fl/fl Smad4-fl/fl) and VKPN (Villin1-CreER Kras-G12D/+ Trp53-fl/fl Rosa26-N1icd/+) were injected into mice to grow into subcutaneous tumors. Tumors were profiled through multiplexed single-cell RNA-sequencing.biostudies-arrayexpressSequencing - Next generation sequencing was performed at the German Cancer Research Center using an Illumina NovaSeq 6000 SP instrument (paired-end, one lane per library).Library Construction - After cell lysis inside of GEMs, mRNA is reverse transcribed to cDNA with droplet-specific barcodes. After GEM breakdown, the library is being prepared according to the protocol including cDNA amplification by PCR.Nucleic Acid Extraction - Hashtag oligo-labelled samples were pooled and processed for single-cell RNA-sequencing using the 10X Chromium Next GEM Single Cell Reagent Kit 3.1 according to the manufacturer’s instructions (Dual Index protocol). First, cells are resuspended in a master mix and loaded onto a chip. After encapsulation, cells were lysed inside their GEMs.Sample Collection - Organoids were enzymatically dissociated and strained to obtain single cells and frozen until processed for single-cell sequencing. For sample multiplexing, single cells were incubated with hashing antibodies (Total-Seq-B, BioLegend, 1 µg antibody) and additional cell sorting antibodies (EpCAM, Miltenyi) according to the manufacturer’s protocol. In short, single cells were thawed and washed in FACS buffer. Cells were resuspended in 50-100 µl with Fc Blocking Reagent Mouse (Miltenyi) in FACS buffer (ratio 1:50) and incubated with the antibody cocktail at 4°C for 30 min in the dark. Then, samples were washed three times in FACS buffer before resuspending in 600 µl FACS buffer with ZombieNIR (BioLegend) for live tumor cell isolation.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Quality control and filtering was performed at library level. After demultiplexing, cells were filtered for having at least 290 genes. Count matrices were normalized and log1p transformed for downstream analysis.Sequence Alignment - Reads were mapped to the mouse reference genome assembly refdata-gex-mm10-2020-A using the cellranger count pipeline of the 10X Genomics Cell Ranger (v6.1.0) with default settings, while providing the hashtag oligo (HTO) sequences as feature library. Demultiplexing was subsequently performed in R using the filtered_feature_bc_matrix as input. HTO counts were normalized using CLR normalization. Using Seurat’s HTODemux function with default settings, cells were assigned to samples using the \"HTO_maxID\" assignment. Only singlet cells were kept for downstream analysis. The full dataset comprises cancer and TME cells, while the \"epi\" dataset has been subsetted to cancer cells only.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNA from single cellsMus musculusTROP2 targeting reveals therapy-driven cell state dynamics and vulnerabilities in colorectal cancerNuria Vaquero-Siguero, Nikolaos Georgakopoulos, Maria C Puschhof, Ioannis Chiotakakos, Jasmin Meier, Sigrid K Fey, Gabriele Diamante, Manuel Mastel, Aitana Guiseris Martinez, Guillaume Belthier, Nikolai Schleußner, Julia Volk, Carolin Artmann, Bryce Lim, Ronald Koschny, Cyrill Wehling, Kyanna S Ouyang, Michael Günther, Solveig Kuss, Paula Hoffmeister, Moritz Mall, Jens Neumann, Steffen Ormanns, Martin Schneider, Thomas Schmidt, Jens Puschhof, Andreas Trumpp, Jacco van Rheenen, Julio Saez-Rodriguez, Bruno C Köhler, Rene JackstadtMaria PuschhoffalseSingle-cell RNA-sequencing of murine colorectal cancer tumorsMurine adenocarcinoma models VAKPS (Villin1-CreER Apc-fl/+ Kras-G12D/+ Trp5-3fl/fl Smad4-fl/fl) and VKPN (Villin1-CreER Kras-G12D/+ Trp53-fl/fl Rosa26-N1icd/+) were injected into mice to grow into subcutaneous tumors. Tumors were profiled through multiplexed single-cell RNA-sequencing.2026-04-01T00:00:00Z2026-05-01T12:47:02.806Z2026-03-31T11:07:01.402ZE-MTAB-16835ERP191619EFO_0002944EFO_0004170EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184