biostudies-arrayexpressManuel MastelMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15044This dataset contains single-cell RNA sequencing data from murine colorectal tumors engineered using the SOCRATES platform, a CRISPR-based multiplex genome engineering system. Tumors were initiated in genetically engineered mouse models via lentiviral delivery of pooled sgRNAs targeting key driver genes in colorectal cancer, including Apc, Kras, Trp53, Smad4, and Pten. Following tumor formation, tissues were dissociated and processed using the 10x Genomics Chromium platform. Cells were multiplexed using TotalSeq-B hashing antibodies, and both gene expression and hashtag libraries were generated using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1. Sequencing was performed on a NovaSeq6000 platform. Fastq files, raw counts (gene-by-cell matrix), and associated cell metadata (including sample identifiers, genotypes, classification categories, and run information) are provided. The individual reads of the respective tumours need to be demultiplexed and assigned to the individual samples. In the raw counts file and the cell metadata file, the individual samples are already demultiplexed and the cells can be assigned with the metadata file. This dataset enables the exploration of genotype-dependent transcriptional states, and microenvironmental composition at single-cell resolution.biostudies-arrayexpressSample Collection - Tumor tissues were collected from genetically engineered mouse models (LCas, VAKP, VAKPS) following colonoscopy-guided submucosal injection of lentivirus encoding SOCRATES constructs. Tumors were dissected at defined timepoints, processed into fragments, and enzymatically dissociated using the Miltenyi Tumor Dissociation Kit (#130-095-929) on the gentleMACS Octo Dissociator. Single-cell suspensions were filtered through 100 μm cell strainers and processed for downstream single-cell RNA sequencing.Nucleic Acid Extraction - Total RNA was captured directly during single-cell encapsulation using the 10x Genomics Chromium Single Cell 3' v3.1 platform. No separate nucleic acid extraction was performed. Cell hashing antibodies (TotalSeq-B, BioLegend) were used for sample multiplexing and demultiplexing.Library Construction - Single-cell libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (Dual Index) according to the manufacturer’s instructions. This protocol generated one gene expression (GEX) library and one hashtag oligo (HTO) library per reaction. Cells were stained and sorted for viability prior to encapsulation.Sequencing - Libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end sequencing with dual indexing: 28 cycles for Read 1, 10 cycles for i7 Index, 10 cycles for i5 Index, and 90 cycles for Read 2. The target sequencing depth was approximately 30,000 read pairs per cell for GEX libraries and 500 read pairs per cell for HTO libraries.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Single-cell RNA-seq data were processed and normalized using the Seurat (v5.0.2) R package. After quality control and filtering, normalization was performed using the SCTransform or LogNormalize method depending on the analysis context. For LogNormalize, gene expression counts for each cell were normalized by the total expression, multiplied by a scale factor of 10,000, and log-transformed using natural logarithm. Highly variable genes were identified, and data were scaled to unit variance and zero mean prior to dimensionality reduction and clustering. Batch effects were corrected using the Harmony algorithm when applicable.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNA from single cellsMus musculusRene JackstadtManuel MastelfalseTranscriptomic profiling of genetically engineered mouse tumors using SOCRATESThis dataset contains single-cell RNA sequencing data from murine colorectal tumors engineered using the SOCRATES platform, a CRISPR-based multiplex genome engineering system. Tumors were initiated in genetically engineered mouse models via lentiviral delivery of pooled sgRNAs targeting key driver genes in colorectal cancer, including Apc, Kras, Trp53, Smad4, and Pten. Following tumor formation, tissues were dissociated and processed using the 10x Genomics Chromium platform. Cells were multiplexed using TotalSeq-B hashing antibodies, and both gene expression and hashtag libraries were generated using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1. Sequencing was performed on a NovaSeq6000 platform. Fastq files, raw counts (gene-by-cell matrix), and associated cell metadata (including sample identifiers, genotypes, classification categories, and run information) are provided. The individual reads of the respective tumours need to be demultiplexed and assigned to the individual samples. In the raw counts file and the cell metadata file, the individual samples are already demultiplexed and the cells can be assigned with the metadata file. This dataset enables the exploration of genotype-dependent transcriptional states, and microenvironmental composition at single-cell resolution.2026-05-01T00:00:00Z2026-05-01T01:03:27.165Z2025-04-17T09:19:23.683ZE-MTAB-15044ERP171753EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_0004184