About file location

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.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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Ig repertoire analysis from Immunoverse sequencing of ccRCC tumors and blood samples.

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.

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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
EGAF50001035684 fastq.gz 531.0 MB
EGAF50001035685 fastq.gz 388.1 MB
EGAF50001035686 fastq.gz 606.2 MB
EGAF50001035687 fastq.gz 361.7 MB
EGAF50001035688 fastq.gz 434.8 MB
EGAF50001035689 fastq.gz 463.9 MB
EGAF50001035690 fastq.gz 435.9 MB
EGAF50001035691 fastq.gz 388.3 MB
EGAF50001035692 fastq.gz 449.5 MB
EGAF50001035693 fastq.gz 447.5 MB
EGAF50001035694 fastq.gz 525.4 MB
EGAF50001035695 fastq.gz 434.9 MB
EGAF50001035696 fastq.gz 515.0 MB
EGAF50001035697 fastq.gz 499.5 MB
EGAF50001035698 fastq.gz 563.0 MB
EGAF50001035699 fastq.gz 398.0 MB
EGAF50001035700 fastq.gz 333.9 MB
EGAF50001035701 fastq.gz 408.9 MB
EGAF50001035702 fastq.gz 292.9 MB
EGAF50001035703 fastq.gz 358.7 MB
EGAF50001035704 fastq.gz 309.3 MB
EGAF50001035705 fastq.gz 373.4 MB
EGAF50001035706 fastq.gz 457.0 MB
EGAF50001035707 fastq.gz 547.6 MB
EGAF50001035708 fastq.gz 318.5 MB
EGAF50001035709 fastq.gz 220.4 MB
EGAF50001035710 fastq.gz 272.9 MB
EGAF50001035711 fastq.gz 576.5 MB
EGAF50001035712 fastq.gz 697.9 MB
EGAF50001035713 fastq.gz 285.5 MB
EGAF50001035714 fastq.gz 350.2 MB
EGAF50001035715 fastq.gz 613.5 MB
EGAF50001035716 fastq.gz 734.9 MB
EGAF50001035717 fastq.gz 236.9 MB
EGAF50001035718 fastq.gz 263.4 MB
EGAF50001035719 fastq.gz 257.4 MB
EGAF50001035720 fastq.gz 295.7 MB
EGAF50001035721 fastq.gz 390.1 MB
EGAF50001035722 fastq.gz 456.3 MB
EGAF50001035723 fastq.gz 382.5 MB
EGAF50001035724 fastq.gz 465.5 MB
EGAF50001035725 fastq.gz 483.9 MB
EGAF50001035726 fastq.gz 572.5 MB
EGAF50001035727 fastq.gz 282.7 MB
EGAF50001035728 fastq.gz 338.6 MB
EGAF50001035729 fastq.gz 376.5 MB
EGAF50001035730 fastq.gz 458.9 MB
EGAF50001035731 fastq.gz 386.4 MB
EGAF50001035732 fastq.gz 362.9 MB
EGAF50001035733 fastq.gz 427.8 MB
EGAF50001035734 fastq.gz 423.5 MB
EGAF50001035735 fastq.gz 498.6 MB
EGAF50001035736 fastq.gz 339.0 MB
EGAF50001035737 fastq.gz 401.5 MB
EGAF50001035738 fastq.gz 406.1 MB
EGAF50001035739 fastq.gz 492.1 MB
EGAF50001035740 fastq.gz 602.0 MB
EGAF50001035741 fastq.gz 366.5 MB
EGAF50001035742 fastq.gz 427.5 MB
EGAF50001035743 fastq.gz 337.3 MB
EGAF50001035744 fastq.gz 418.0 MB
EGAF50001035745 fastq.gz 286.1 MB
EGAF50001035746 fastq.gz 351.4 MB
EGAF50001035747 fastq.gz 320.2 MB
EGAF50001035748 fastq.gz 396.0 MB
EGAF50001035749 fastq.gz 547.2 MB
EGAF50001035750 fastq.gz 676.5 MB
EGAF50001035751 fastq.gz 420.3 MB
EGAF50001035752 fastq.gz 505.0 MB
EGAF50001035753 fastq.gz 327.2 MB
EGAF50001035754 fastq.gz 385.9 MB
EGAF50001035755 fastq.gz 920.6 MB
EGAF50001035756 fastq.gz 1.0 GB
EGAF50001035757 fastq.gz 449.7 MB
EGAF50001035758 fastq.gz 378.5 MB
EGAF50001035759 fastq.gz 392.2 MB
EGAF50001035760 fastq.gz 325.3 MB
EGAF50001035761 fastq.gz 386.7 MB
EGAF50001035762 fastq.gz 354.1 MB
EGAF50001035763 fastq.gz 419.4 MB
EGAF50001035764 fastq.gz 443.2 MB
EGAF50001035765 fastq.gz 537.8 MB
EGAF50001035766 fastq.gz 288.0 MB
EGAF50001035767 fastq.gz 358.1 MB
EGAF50001035768 fastq.gz 269.4 MB
EGAF50001035769 fastq.gz 283.9 MB
EGAF50001035770 fastq.gz 347.1 MB
EGAF50001035771 fastq.gz 372.6 MB
EGAF50001035772 fastq.gz 464.7 MB
EGAF50001035773 fastq.gz 616.6 MB
EGAF50001035774 fastq.gz 403.2 MB
EGAF50001035775 fastq.gz 431.8 MB
EGAF50001035776 fastq.gz 509.7 MB
EGAF50001035777 fastq.gz 357.5 MB
EGAF50001035778 fastq.gz 460.8 MB
EGAF50001035779 fastq.gz 558.9 MB
EGAF50001035780 fastq.gz 515.6 MB
EGAF50001035781 fastq.gz 609.0 MB
EGAF50001035782 fastq.gz 504.8 MB
EGAF50001035783 fastq.gz 725.6 MB
EGAF50001035784 fastq.gz 818.6 MB
EGAF50001035785 fastq.gz 468.3 MB
EGAF50001035786 fastq.gz 567.0 MB
EGAF50001035787 fastq.gz 287.2 MB
EGAF50001035788 fastq.gz 351.4 MB
EGAF50001035789 fastq.gz 373.2 MB
EGAF50001035790 fastq.gz 453.8 MB
EGAF50001035791 fastq.gz 531.9 MB
EGAF50001035792 fastq.gz 638.1 MB
EGAF50001035793 fastq.gz 331.5 MB
EGAF50001035794 fastq.gz 403.0 MB
EGAF50001035795 fastq.gz 63.1 MB
EGAF50001035796 fastq.gz 73.9 MB
EGAF50001035797 fastq.gz 502.7 MB
EGAF50001035798 fastq.gz 598.9 MB
EGAF50001035799 fastq.gz 215.5 MB
EGAF50001035800 fastq.gz 253.0 MB
EGAF50001035805 fastq.gz 356.4 MB
EGAF50001035806 fastq.gz 443.4 MB
EGAF50001035807 fastq.gz 233.5 MB
EGAF50001035808 fastq.gz 287.8 MB
EGAF50001035809 fastq.gz 366.1 MB
EGAF50001035810 fastq.gz 295.2 MB
EGAF50001035811 fastq.gz 345.5 MB
EGAF50001035812 fastq.gz 336.1 MB
EGAF50001035813 fastq.gz 317.1 MB
EGAF50001035814 fastq.gz 327.6 MB
EGAF50001035815 fastq.gz 383.1 MB
EGAF50001035816 fastq.gz 461.3 MB
EGAF50001035817 fastq.gz 347.6 MB
EGAF50001035818 fastq.gz 383.8 MB
EGAF50001035819 fastq.gz 203.6 MB
EGAF50001035820 fastq.gz 235.4 MB
EGAF50001035821 fastq.gz 451.6 MB
EGAF50001035822 fastq.gz 427.5 MB
EGAF50001035823 fastq.gz 435.7 MB
EGAF50001035824 fastq.gz 546.2 MB
EGAF50001035825 fastq.gz 331.5 MB
EGAF50001035826 fastq.gz 404.3 MB
EGAF50001035827 fastq.gz 367.5 MB
EGAF50001035828 fastq.gz 323.0 MB
EGAF50001035829 fastq.gz 457.7 MB
EGAF50001035830 fastq.gz 394.8 MB
EGAF50001035831 fastq.gz 306.5 MB
EGAF50001035832 fastq.gz 379.8 MB
EGAF50001035833 fastq.gz 245.1 MB
EGAF50001035834 fastq.gz 307.9 MB
EGAF50001035835 fastq.gz 295.6 MB
EGAF50001035836 fastq.gz 355.5 MB
EGAF50001035837 fastq.gz 353.7 MB
EGAF50001035838 fastq.gz 289.4 MB
EGAF50001035839 fastq.gz 373.1 MB
EGAF50001035840 fastq.gz 451.5 MB
EGAF50001035841 fastq.gz 326.1 MB
EGAF50001035842 fastq.gz 398.4 MB
EGAF50001035843 fastq.gz 386.8 MB
EGAF50001035844 fastq.gz 443.4 MB
EGAF50001035845 fastq.gz 427.9 MB
EGAF50001035846 fastq.gz 297.8 MB
EGAF50001035847 fastq.gz 352.0 MB
EGAF50001035848 fastq.gz 336.8 MB
EGAF50001035849 fastq.gz 408.2 MB
EGAF50001035850 fastq.gz 334.2 MB
EGAF50001035851 fastq.gz 401.7 MB
EGAF50001035852 fastq.gz 349.4 MB
EGAF50001035853 fastq.gz 437.1 MB
EGAF50001035854 fastq.gz 303.9 MB
EGAF50001035855 fastq.gz 364.7 MB
EGAF50001035856 fastq.gz 183.7 MB
EGAF50001035857 fastq.gz 226.4 MB
EGAF50001035858 fastq.gz 429.6 MB
EGAF50001035859 fastq.gz 329.2 MB
EGAF50001035860 fastq.gz 265.0 MB
EGAF50001035861 fastq.gz 229.1 MB
EGAF50001035862 fastq.gz 316.9 MB
EGAF50001035863 fastq.gz 376.1 MB
EGAF50001035864 fastq.gz 464.6 MB
EGAF50001035865 fastq.gz 698.3 MB
EGAF50001035866 fastq.gz 829.4 MB
EGAF50001035867 fastq.gz 505.2 MB
EGAF50001035868 fastq.gz 589.3 MB
EGAF50001035869 fastq.gz 266.5 MB
EGAF50001035870 fastq.gz 256.4 MB
EGAF50001035871 fastq.gz 365.5 MB
EGAF50001035878 fastq.gz 726.1 MB
EGAF50001035879 fastq.gz 427.6 MB
EGAF50001035881 fastq.gz 330.7 MB
EGAF50001035882 fastq.gz 331.1 MB
EGAF50001035883 fastq.gz 574.4 MB
EGAF50001035884 fastq.gz 657.4 MB
EGAF50001035886 fastq.gz 480.6 MB
EGAF50001035887 fastq.gz 331.3 MB
EGAF50001035893 csv 18.0 kB
EGAF50001035894 csv 8.5 MB
EGAF50001035895 csv 46.2 kB
EGAF50001035896 csv 128.9 kB
EGAF50001035897 csv 138.5 kB
EGAF50001035898 csv 138.7 kB
EGAF50001035899 csv 22.1 MB
EGAF50001035900 csv 146.7 kB
EGAF50001035901 csv 130.9 kB
EGAF50001035902 csv 133.7 kB
EGAF50001035903 tsv 2.2 GB
EGAF50001035904 csv 24.9 MB
EGAF50001035905 csv 247.9 MB
EGAF50001035906 tsv 2.2 GB
EGAF50001035907 csv 13.9 kB
EGAF50001035908 tsv 6.1 GB
208 Files (89.9 GB)