A constitutive interferon-high immunophenotype defines response to immunotherapy in colorectal cancer. (Q10369)

Laser capture microdissection (LCM) RNA-seq, NanoString CosMx spatial transcriptomics and in-vitro cell line (HCT116) CD8 co-culture RNA-seq data supporting the paper: "A constitutive interferon-high immunophenotype defines response to immunotherapy in colorectal cancer". This dataset is accessible under request because it includes sensitive data. Users wishing to access the dataset will need to sign a Data Sharing Agreement document that will be provided at the time of the request submission. Please write your request at human-biology@crick.ac.uk. For unrestriced access to in-vitro cell line RNA-seq data only, see https://doi.org/10.5281/zenodo.14246643 The provided data includes: LCM RNA-seq: CRC_LCM-salmon-counts.tsv (tab-delimited text file includes raw salmon counts for each sample) CRC_LCM-normalised-counts.txt (tab-delimited text file includes DESeq2 vst-normalised values for each sample) CRC_LCM-metadata.txt (tab-delimited text file of associated metadata) NanoString CosMx data: SeuratObject_Base.RDS (Seurat R object containing the aggregated single cell raw count matrix for all four samples. Cells below the minimum transcripts, genes and negative probes/transcripts ratio are included in the Seurat object as well. The recommended Seurat version to work with this object is =5.0.0.) CosMx_S0_processed_metadata_plus_cell_anno.rds (data frame containing metadata for all cells from samples CR48 and UH20 (Slide1) remained after initial filtering steps and clustering. Results from the unsupervised cell clustering can be found in column 'final_anno'. The 'geometry' column contains single cell polygon shapes defined using the R package sf. Use st_as_sf() function on the data frame to convert it into a sf data frame.) CosMx_S1_processed_metadata_plus_cell_anno.rds (data frame containing metadata for all cells from samples CR21 and CR36 (Slide2) remained after initial filtering steps and clustering. Results from the unsupervised cell clustering can be found in column 'final_anno'. The 'geometry' column contains single cell polygon shapes defined using the R package sf. Use st_as_sf() function on the data frame to convert it into a sf data frame) CosMx raw csv flat files for each sample:- raw count expression matrix ('_exprMat_file_')- single cell centroid coordinates + metadata table ('_metadata_file_')- cell polygon coordinates file ('-polygons_')- transcript coordinates + metadata file ('_tx_file_')- fov coordinates file ('_fov_position_file_') In-vitro cell line co-culture RNA-seq: salmon.merged.gene_counts.tsv(tab-delimited text file, includes raw gene counts for each sample) HCT116_EpiT_EpiOnly_dds_object_NCG7.rds (DESeq2 R object containing raw counts for NCG7 genes with =10 counts in =1 sample).