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BIONIKK_Translational Research_Data Access Committee

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Dr Eve M LEPICARD
eve.lepicard@association-artic.org

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This DAC controls 3 datasets

Dataset ID	Description	Technology	Samples
EGAD50000003105	This dataset contains immunoglobulin (Ig) repertoire data inferred from bulk RNA-seq of 95 frozen clear cell renal cell carcinoma (ccRCC) tumor samples from the BIONIKK cohort. Ig repertoires were reconstructed from raw RNA-seq FASTQ files using MiXCR. The same bulk RNA-seq data were aligned to the human GRCh38 reference genome using STAR to generate a gene expression count matrix and to calculate transcriptomic signatures related to tertiary lymphoid structures (TLS).The dataset contains processed data including: (i) MiXCR-reconstructed Ig clonotype repertoires and associated sample metadata; (ii) TLS-related transcriptomic signatures and their scores; and (iii) the bulk RNA-seq normalized gene expression count matrix.The raw bulk RNA-seq FASTQ files are not included in this dataset because they were generated previously by collaborators within the BIONIKK cohort for the study by Davidson et al., 2023, Cancer Research. These raw data are available upon reasonable request to the study sponsor (ARTIC; contact@association-artic.org).	Illumina HiSeq 4000	95
EGAD50000003106	This dataset contains immunoglobulin (Ig) repertoire data and spatial transcriptomics data generated from frozen clear cell renal cell carcinoma (ccRCC) tumor samples. It combines Ig repertoire analyses from previously generated Visium spatial transcriptomics datasets and a newly generated SpatialVDJ dataset. First, Ig repertoires were inferred using MiXCR from raw FASTQ files generated by Visium V1 spatial transcriptomics experiments on 12 frozen ccRCC tumor samples included in the study by Meylan et al., 2022, Immunity. The corresponding raw FASTQ files are not included in this dataset because they were generated previously and were not deposited at the time of the original study. They are available upon reasonable request to the study sponsor (ARTIC; contact@association-artic.org). Processed Ig repertoire data inferred from these samples are included in this dataset. Second, the dataset contains raw and processed data generated from a SpatialVDJ experiment performed on four frozen ccRCC tumor sections. For each section, spatial gene expression (SpatialGEX) was generated using Visium V1 technology and Illumina short-read sequencing, while Ig-targeted sequencing was performed using a SpatialVDJ protocol followed by PacBio HiFi long-read sequencing. The raw data generated for the four SpatialVDJ samples include: (i) Illumina paired-end FASTQ files from SpatialGEX; (ii) raw histology images of the corresponding tumor sections (not deposited in EGA, available in complementary Zenodo repository, see article); (iii) manual alignment files linking spatial spots to the histology images, generated using Loupe Browser (10x Genomics) (not deposited in EGA, available in complementary Zenodo repository, see article); and (iv) PacBio HiFi FASTQ files from SpatialVDJ. Processed data include: (i) Space Ranger outputs for SpatialGEX, including raw and filtered feature-barcode matrices (in EGA), spot coordinates, tissue images and scale factors (not deposited in EGA, available in complementary Zenodo repository, see article); (ii) an aggregated Seurat object containing spatial gene expression data from the four SpatialGEX samples (not deposited in EGA, available in complementary Zenodo repository, see article); (iii) Ig repertoire data processed using the Immcantation framework, including clonotype tables, clone statistics and IGH clonotypes with clonal group identifiers; and (iv) selected input and output files from TRIBAL for reconstruction of clone lineage trees. Processed Ig repertoire data inferred with MiXCR from the 12 previously generated Visium datasets are also included.	Illumina NovaSeq 6000 Illumina NovaSeq X Sequel IIe	20
EGAD50000003107	This dataset contains immunoglobulin (Ig) repertoire data generated using the Immunoverse targeted Ig sequencing assay (IDT, Invitae, Archer) from 96 bulk RNA samples. The samples include frozen ccRCC tumor and blood samples from patients enrolled in the BIONIKK cohort, as well as blood samples from healthy donors. Raw data consist of paired-end Illumina FASTQ files (R1 and R2) for all 96 samples. Processed data were generated using the Immcantation framework and include sample metadata and Ig repertoire analyses. Sample metadata include clinical and experimental information, including immune checkpoint inhibitor (ICI) response groups and IgG/IgA antibody coverage measurements on tumor cells. Processed Ig repertoire data include clonotype tables for all Ig chains, IGH clonotype tables with clonal group identifiers defined either within individual samples or across samples to assess clonotype sharing, clone statistics tables, and clonotype-sharing analyses performed using CompAIRR.	Illumina MiSeq	96