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Ig repertoire analysis from bulk RNAseq data of frozen ccRCC tumors

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).

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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
EGAF50001035888 csv 206.0 MB
EGAF50001035889 csv 26.7 kB
EGAF50001035890 csv 3.7 kB
EGAF50001035921 csv 81.0 MB
4 Files (287.0 MB)