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As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

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Ig repertoire analysis from spatial transcriptomics data of frozen ccRCC tumors

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.

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TLS and ICI response

Before any access can be granted through EGA, each request shall be jointly reviewed by representatives of the BIONIKK study Sponsor, the Coordinating Investigator of the BIONIKK clinical trial, and designated scientific representatives of the UMR-S 1138 research team at the Centre de Recherche des Cordeliers. For the datasets covered by this Policy, the following persons are designated to review each access request and provide their documented approval: • Eve Lepicard, Scientific Director of ARTIC, representing ARTIC, Sponsor of the BIONIKK study and Data Controller; • Professor Stéphane Oudard, Coordinating Investigator of the BIONIKK clinical trial; • Professor Hervé Fridman, designated scientific representative of UMR-S 1138, Centre de Recherche des Cordeliers; • Professor Catherine Sautès-Fridman, designated scientific representative of UMR-S 1138, Centre de Recherche des Cordeliers; • Each investigator responsible for the scientific analyses underlying one or several datasets covered by this policy. Each access request shall be assessed with regard to: • compatibility of the proposed research with the information and consent provided to BIONIKK participants and with applicable data-protection requirements; • scientific relevance and feasibility of the proposed research; • adequacy and proportionality of the data requested in relation to the stated research objectives; • potential overlap with ongoing or planned research using the same datasets; • appropriate acknowledgement, citation and publication arrangements; • compliance with the applicable Data Access Agreement and with the security, confidentiality, non-reidentification and non-redistribution requirements governing the datasets. Access shall only be granted once the documented approval of all the persons designated above has been obtained. If one or more of the designated reviewers do not approve the request, access shall not be granted unless the disagreement has been resolved in accordance with the governance arrangements applicable to the BIONIKK TLS translational research project. The documented outcome of this review procedure shall then be transmitted to the BIONIKK Translational Research Data Access Committee, which shall record and implement the resulting access decision through EGA. applicable Data Access Agreement.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS50000002165 Transcriptome Analysis

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Quality Report
Located in
i
EGAF50001035801 fastq.gz 449.4 MB
EGAF50001035802 fastq.gz 337.6 MB
EGAF50001035803 fastq.gz 361.6 MB
EGAF50001035804 fastq.gz 464.4 MB
EGAF50001035872 fastq.gz 21.8 GB
EGAF50001035873 fastq.gz 25.1 GB
EGAF50001035874 fastq.gz 23.8 GB
EGAF50001035875 fastq.gz 27.5 GB
EGAF50001035876 fastq.gz 22.3 GB
EGAF50001035877 fastq.gz 28.0 GB
EGAF50001035880 fastq.gz 25.6 GB
EGAF50001035885 fastq.gz 24.0 GB
EGAF50001035891 h5 11.4 MB
EGAF50001035892 h5 9.2 MB
EGAF50001035909 csv 379.7 kB
EGAF50001035910 tsv 348.9 MB
EGAF50001035911 csv 332.3 kB
EGAF50001035912 tsv 55.0 MB
EGAF50001035913 csv 6.6 MB
EGAF50001035914 txt 3.4 kB
EGAF50001035915 csv 207.9 kB
EGAF50001035916 csv 3.5 kB
EGAF50001035917 txt 2.0 kB
EGAF50001035918 csv 2.1 kB
EGAF50001035919 csv 1.7 MB
EGAF50001035920 csv 2.7 MB
EGAF50001035922 h5 8.3 MB
EGAF50001035923 h5 9.9 MB
EGAF50001035924 h5 11.9 MB
EGAF50001035925 h5 10.4 MB
EGAF50001035926 h5 6.6 MB
EGAF50001035927 h5 9.4 MB
32 Files (200.2 GB)