{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Maria Puschhof"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16849"],"description":["Human colorectal cancer organoids were injected intrasplenically to form liver metastasis in mice were treated with the TROP2-targeting antibody-drug conjugate Sacituzumab Govitecan (SG) or non-targeting control IgG1-SN-38 (ADC). Tumors were harvested at different time points: 0 h, 6 h,  24 h, 48 h, 72 h and 120 h} and subjected to single-cell RNA-seq using sample hashtag multiplexing."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Tumors were enzymatically dissociated with a tumor dissociation kit (Miltenyi) following the manufacturer’s instructions. In short, tumor fragments were incubated together with an enzyme cocktail in a gentleMACS Octo Dissociator with heaters (Miltenyi) using the default programs 37C_h_TDK_1 (for human tissue). Afterwards, the sample was 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 (anti-human EpCAM, Miltenyi; anti-mouse CD45, BioLegend) 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 (EpCAM-positive, CD45-negative, CD31-negative).","Sample Treatment - Patient-derived tumor organoids were injected into the flank of mice. Treatment with either the TROP2-directed ADC Sacituzumab Govitecan (SG) or untargeted ADC (containing the payload SN-38) was started when the tumor size had reached 100 mm3.  Tumors were harvested at indicated time points.","Nucleic Acid Extraction - Hashtag oligo-labelled samples were pooled (up to 12,000 cells each) 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.","Sequencing - Next generation sequencing was performed at the German Cancer Research Center using an Illumina NovaSeq X Plus 10B instrument (paired-end, three lanes 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 in 11 cycles."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Quality control and filtering was performed at sample level. First, the fraction of mitochondrial reads (scanpy.pp.calculate_qc_metrics) and the doublet probability per cell barcode (scanpy.external.pp.scrublet) was computed. Cells were filtered for having at least 1,200 genes, while genes were filtered for being expressed in at least 3 cells. Finally, cells with a gene count exceeding the 99.5 % percentile or with a mitochondrial fraction larger than 20 % or with a doublet score larger than 0.15 were excluded. Count matrices of high quality cells were concatenated (across samples), normalized and log1p transformed for downstream analysis.   For trajectory inference, the SG treatment data was extracted and split by time points into time points reflecting build-up and decay of the treatment effect (0h-48h and 48h-120h, resp.). This data is available as anndata objects ending with \\\"palantir.h5ad\\\". For each subset, cell cycle regression was performed prior to dimension reduction. This counts layer is available as “counts_log1p_woCC”. Counts tables based on missing value inference using MAGIC are available as files ending with \\\"magic\\\"."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_title":["TROP2 targeting reveals therapy-driven cell state dynamics and vulnerabilities in colorectal cancer"],"pubmed_authors":["Nuria 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 Jackstadt","Maria Puschhof"],"additional_accession":[]},"is_claimable":false,"name":"Time course analysis of human colorectal cancer liver metastasis models under Sacituzumab Govitecan (SG) treatment or untargeted control","description":"Human colorectal cancer organoids were injected intrasplenically to form liver metastasis in mice were treated with the TROP2-targeting antibody-drug conjugate Sacituzumab Govitecan (SG) or non-targeting control IgG1-SN-38 (ADC). Tumors were harvested at different time points: 0 h, 6 h,  24 h, 48 h, 72 h and 120 h} and subjected to single-cell RNA-seq using sample hashtag multiplexing.","dates":{"release":"2026-04-01T00:00:00Z","modification":"2026-04-29T16:52:19.808Z","creation":"2026-04-02T11:20:19.301Z"},"accession":"E-MTAB-16849","cross_references":{"ENA":["ERP191723"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}