biostudies-arrayexpressManuel MastelMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17099BRAF mutant colorectal cancer displays a unmet clinical need with poor overall survival. Here we modeled this cancer in the murine system and created organoids with Braf activation mutation, Trp53 deletion and Nicd1 expression. Additionally, we created cell lines that have a Apc deletion (VBPNA) or Ctnnb1 activation mutation (VBPNC). These mutations activate the WNT pathway which plays a critical role in the tumor progression but is under-explored in BRAF mutated colorectal cancer. To investigate the effect of the WNT pathway genes mutations on the cancer cell state and the tumor microenvironment, we performed CITE-seq.biostudies-arrayexpressSample Collection - Tumor-derived single-cell suspensions were prepared as previously described. After preparation, living single cells were sorted, and a minimum of 500,000 viable cells per sample were subjected to further CITE-seq processing.Sequencing - Single-cell libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end, dual-index sequencing. The sequencing cycle configuration was 28 cycles for Read 1, 10 cycles for each i7 and i5 index read, and 90 cycles for Read 2. The target sequencing depth was approximately 30,000 read pairs per cell for gene expression libraries and approximately 500 read pairs per cell for each CITE-seq antibody.Library Construction - After live single-cell sorting, at least 500,000 cells were incubated with the TotalSeq™-B Mouse Universal Cocktail V1.0 according to the manufacturer’s protocol for 30 minutes on ice. Cells were then washed three times with FACS buffer and resuspended in 100 µl PBS containing 2% FBS. CITE-seq libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1 with Dual Indexing. For each sample, one gene expression library and one cell surface protein plus hashtag oligo library were generated.Nucleic Acid Extraction - No separate nucleic acid extraction protocol is described in the provided text. Cells were processed directly as viable single-cell suspensions for 10x Genomics single-cell library preparation following live cell sorting.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw sequencing data were processed with Cell Ranger to generate gene expression, antibody-derived tag (ADT/CITE-seq), and hashtag oligonucleotide (HTO) count matrices. Gene expression counts were imported into Seurat. RNA counts were normalized using Seurat LogNormalize normalization. Variable features were identified and scaled prior to downstream analysis. HTO and ADT count matrices were added as separate Seurat assays and normalized using centered log-ratio (CLR) transformation. Hashtag-based sample assignment was performed using Seurat HTODemux. Cell-level metadata, including barcode, hashtag assignment, singlet/doublet/negative classification, RNA QC metrics, ADT metrics, and HTO metrics, were exported as tab-delimited processed data files.Sequence Alignment - No explicit sequence alignment protocol is described in the provided text. The paper states that CITE-seq gene expression, hashtag oligo, and antibody-derived tag data were processed using the Seurat framework. Antibody-derived tag counts generated from TotalSeq™-B antibodies were loaded with Seurat’s Read10X function and stored as a separate assay. ADT data were normalized using centered log-ratio transformation with Seurat’s NormalizeData function. After quality control and HTO-based sample demultiplexing, RNA, ADT, and HTO modalities were integrated using Seurat’s Weighted Nearest Neighbor algorithm.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNA from single cellsMus musculusManuel MastelfalseCITE-seq from tumors generated via subcutaneous injection of VBPN, VBPNA, VBPNC organoids into C57BL/6 miceBRAF mutant colorectal cancer displays a unmet clinical need with poor overall survival. Here we modeled this cancer in the murine system and created organoids with Braf activation mutation, Trp53 deletion and Nicd1 expression. Additionally, we created cell lines that have a Apc deletion (VBPNA) or Ctnnb1 activation mutation (VBPNC). These mutations activate the WNT pathway which plays a critical role in the tumor progression but is under-explored in BRAF mutated colorectal cancer. To investigate the effect of the WNT pathway genes mutations on the cancer cell state and the tumor microenvironment, we performed CITE-seq.2026-06-11T00:00:00Z2026-06-11T01:00:46.389Z2026-06-01T14:47:39.739ZE-MTAB-17099ERP194190EFO_0002944EFO_0004170EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184