biostudies-arrayexpressManuel MastelMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17106Genetically engineered organoids with the genetic background VBPNA were injected subcutaneously into immunocompetent mice. The mice were treated with CD4 T cells depletion antibody, CD8 T cell depletion antibody or IgG control. The tumors sizes were measured weekly. The intent of the experiment was to determine if the distinct T cell population have an effect on tumor growth, cancer cell state and immune cells.biostudies-arrayexpressSequencing - Next generation sequencing was performed at the German Cancer Research Center using an Illumina NovaSeq 6000 SP instrument (paired-end, two lanes per library).Sample Collection - Tumors were surgically removed from the mice and 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 in recovery media until processed for single-cell sequencing. For sample multiplexing, single cells were incubated with hashing antibodies (Total-Seq-B, BioLegend, 1 µg antibody) 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 200 µl FACS buffer with ZombieNIR (BioLegend) or DAPI (BioLegend) for live cell isolation.Nucleic Acid Extraction - Hashtag oligo-labelled samples were pooled (up to 9,000 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.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.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Reads were mapped to the human reference genome assembly refdata-gex-GA and demultiplexed into their original samples using the cellranger multi pipeline with default settings of the 10X Genomics Cell Ranger (v7.1.0). Cell barcodes with barcode assignment confidence >= 0.7 were used for downstream analysis.Data Transformation - Sequencing data from conventional 10x Genomics 3' single-cell RNA-seq libraries combined with hashing antibodies for sample barcoding were processed using the 10x Genomics Cell Ranger pipeline. Raw base call files were demultiplexed into FASTQ files, and gene expression reads were aligned to the appropriate reference transcriptome to generate feature-barcode count matrices. Hashtag oligo reads derived from hashing antibodies were processed in parallel to produce HTO count matrices. The resulting gene expression and HTO matrices were imported into Seurat for downstream quality control, normalization, and hashtag-based demultiplexing, allowing assignment of individual cells to their sample of origin and identification of singlets, doublets, and negative cells.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNA from single cellsMus musculusManuel MastelfalsescRNA-seq of organoids injected subcutaneously into C57BL/6 mice. Mice were treated with CD4 depletion antibody, CD8 depletion antibody or IgG controlGenetically engineered organoids with the genetic background VBPNA were injected subcutaneously into immunocompetent mice. The mice were treated with CD4 T cells depletion antibody, CD8 T cell depletion antibody or IgG control. The tumors sizes were measured weekly. The intent of the experiment was to determine if the distinct T cell population have an effect on tumor growth, cancer cell state and immune cells.2026-06-11T00:00:00Z2026-06-11T01:00:46.9Z2026-06-01T15:55:40.467ZE-MTAB-17106ERP194192EFO_0002944EFO_0004170EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184