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Single cell RNA-seq, TCR-seq and bulk TCR-seq on HNSCC patients treated with ICB

We performed single cell RNA- and TCR-sequencing (10x Genomics) on immune infiltrates (CD45+ cells) from 18 HNSCC patients enrolled in the IMCISION trial (Vos et al. 2021). Viable immune cells were isolated from pre-treatment and post-treatment primary tumor biopsies of 10 patients responding (1 partial pathological response and 9 major pathological responses) and 7 patients non-responding to anti-PD-1 and anti-CTLA4 combination immunotherapy. One patient treated with anti-PD-1 monotherapy (1 major pathological response) was included in the dataset. Bulk TCR-seq was performed on the PBMCs of responding patients, pre- and post-treatment.

Request Access

DAC for requesting access to the single cell datasets (scRNAseq and scTCRseq) and bulk TCR on HNSCC patients treated with neoadj NIVO/IPI.

To request access to the single cell datasets on HNSCC patients treated with neoadj NIVO/IPI, please provide the following information in your Data Access Request: - Recipient and Recipient Institution - Details of dataset requested, i.e. EGA Study and Dataset Accession Number(s) - Brief abstract of the Project in which the Data will be used (500 words max.) - All Individuals who will be allowed access to the requested datasets by the Recipient Institution. After receipt and review of your Data Access Request by the Data Access Committee, you will receive a Data Transfer Agreement to be completed, signed and returned to KT&C and the Data Access Committee, prior to being granted access to the requested dataset(s). For the avoidance of doubt, the Data Access Committee reserves the right to withhold granting access.

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
EGAS00001007368 Other

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 Located in
EGAF00008202428 fastq.gz 77.1 MB
EGAF00008202429 fastq.gz 192.4 MB
EGAF00008202430 fastq.gz 105.2 MB
EGAF00008202431 fastq.gz 262.4 MB
EGAF00008202432 fastq.gz 76.5 MB
EGAF00008202433 fastq.gz 190.4 MB
EGAF00008202434 fastq.gz 1.0 GB
EGAF00008202435 fastq.gz 3.5 GB
EGAF00008202436 fastq.gz 840.6 MB
EGAF00008202437 fastq.gz 2.9 GB
EGAF00008202438 fastq.gz 564.7 MB
EGAF00008202439 fastq.gz 1.9 GB
EGAF00008202440 fastq.gz 746.0 MB
EGAF00008202441 fastq.gz 2.6 GB
EGAF00008202442 fastq.gz 784.3 MB
EGAF00008202443 fastq.gz 2.7 GB
EGAF00008202444 fastq.gz 373.8 MB
EGAF00008202445 fastq.gz 642.0 MB
EGAF00008202446 fastq.gz 500.3 MB
EGAF00008202447 fastq.gz 861.9 MB
EGAF00008202448 fastq.gz 165.4 MB
EGAF00008202449 fastq.gz 511.9 MB
EGAF00008202450 fastq.gz 125.9 MB
EGAF00008202451 fastq.gz 384.4 MB
EGAF00008202452 fastq.gz 241.4 MB
EGAF00008202453 fastq.gz 740.8 MB
EGAF00008202454 fastq.gz 57.4 MB
EGAF00008202455 fastq.gz 142.3 MB
EGAF00008202456 fastq.gz 71.8 MB
EGAF00008202457 fastq.gz 178.9 MB
EGAF00008202458 fastq.gz 128.1 MB
EGAF00008202459 fastq.gz 255.1 MB
EGAF00008202460 fastq.gz 121.3 MB
EGAF00008202461 fastq.gz 241.2 MB
EGAF00008202462 fastq.gz 119.3 MB
EGAF00008202463 fastq.gz 238.6 MB
EGAF00008202464 fastq.gz 95.7 MB
EGAF00008202465 fastq.gz 190.4 MB
EGAF00008202466 fastq.gz 40.9 MB
EGAF00008202467 fastq.gz 60.0 MB
EGAF00008202468 fastq.gz 38.9 MB
EGAF00008202469 fastq.gz 57.0 MB
EGAF00008202470 fastq.gz 38.0 MB
EGAF00008202471 fastq.gz 55.9 MB
EGAF00008202472 fastq.gz 30.5 MB
EGAF00008202473 fastq.gz 44.7 MB
EGAF00008202474 fastq.gz 30.2 MB
EGAF00008202475 fastq.gz 44.4 MB
EGAF00008202476 fastq.gz 23.3 MB
EGAF00008202477 fastq.gz 34.2 MB
EGAF00008202478 fastq.gz 21.1 MB
EGAF00008202479 fastq.gz 31.0 MB
EGAF00008202480 fastq.gz 26.2 MB
EGAF00008202481 fastq.gz 38.5 MB
EGAF00008202482 fastq.gz 17.4 MB
EGAF00008202483 fastq.gz 25.5 MB
EGAF00008202484 fastq.gz 25.8 MB
EGAF00008202485 fastq.gz 38.1 MB
EGAF00008202486 fastq.gz 13.1 MB
EGAF00008202487 fastq.gz 19.2 MB
EGAF00008202488 fastq.gz 25.5 MB
EGAF00008202489 fastq.gz 37.7 MB
EGAF00008202490 fastq.gz 13.8 MB
EGAF00008202491 fastq.gz 20.2 MB
EGAF00008202492 fastq.gz 15.3 MB
EGAF00008202493 fastq.gz 22.4 MB
EGAF00008202494 fastq.gz 13.8 MB
EGAF00008202495 fastq.gz 20.3 MB
EGAF00008202496 fastq.gz 16.0 MB
EGAF00008202497 fastq.gz 23.3 MB
EGAF00008202498 fastq.gz 35.7 MB
EGAF00008202499 fastq.gz 52.5 MB
EGAF00008202500 fastq.gz 39.4 MB
EGAF00008202501 fastq.gz 58.0 MB
EGAF00008202502 fastq.gz 34.8 MB
EGAF00008202503 fastq.gz 51.0 MB
EGAF00008202504 fastq.gz 30.3 MB
EGAF00008202505 fastq.gz 44.4 MB
EGAF00008202506 fastq.gz 76.4 MB
EGAF00008202507 fastq.gz 113.2 MB
EGAF00008202508 fastq.gz 93.5 MB
EGAF00008202509 fastq.gz 138.3 MB
EGAF00008202510 fastq.gz 92.2 MB
EGAF00008202511 fastq.gz 136.4 MB
EGAF00008202512 fastq.gz 92.6 MB
EGAF00008202513 fastq.gz 137.3 MB
EGAF00008202514 fastq.gz 74.4 MB
EGAF00008202515 fastq.gz 110.0 MB
EGAF00008202516 fastq.gz 35.0 MB
EGAF00008202517 fastq.gz 51.8 MB
EGAF00008202518 fastq.gz 63.5 MB
EGAF00008202519 fastq.gz 93.9 MB
EGAF00008202520 fastq.gz 43.0 MB
EGAF00008202521 fastq.gz 63.6 MB
EGAF00008202522 fastq.gz 915.5 MB
EGAF00008202523 fastq.gz 3.1 GB
EGAF00008202524 fastq.gz 674.8 MB
EGAF00008202525 fastq.gz 2.3 GB
EGAF00008202526 fastq.gz 1.2 GB
EGAF00008202527 fastq.gz 4.1 GB
EGAF00008202528 fastq.gz 357.5 MB
EGAF00008202529 fastq.gz 615.3 MB
EGAF00008202530 fastq.gz 406.0 MB
EGAF00008202531 fastq.gz 704.0 MB
EGAF00008202532 fastq.gz 339.5 MB
EGAF00008202533 fastq.gz 586.3 MB
EGAF00008202534 fastq.gz 456.1 MB
EGAF00008202535 fastq.gz 789.2 MB
EGAF00008202536 fastq.gz 326.9 MB
EGAF00008202537 fastq.gz 565.5 MB
EGAF00008202538 fastq.gz 370.6 MB
EGAF00008202539 fastq.gz 646.4 MB
EGAF00008202540 fastq.gz 243.5 MB
EGAF00008202541 fastq.gz 415.3 MB
EGAF00008202542 fastq.gz 242.4 MB
EGAF00008202543 fastq.gz 412.6 MB
EGAF00008202544 fastq.gz 221.6 MB
EGAF00008202545 fastq.gz 378.3 MB
EGAF00008202546 fastq.gz 264.3 MB
EGAF00008202547 fastq.gz 452.6 MB
EGAF00008202548 fastq.gz 141.0 MB
EGAF00008202549 fastq.gz 236.5 MB
EGAF00008202550 fastq.gz 120.7 MB
EGAF00008202551 fastq.gz 201.9 MB
EGAF00008202552 fastq.gz 195.8 MB
EGAF00008202553 fastq.gz 328.8 MB
EGAF00008202554 fastq.gz 195.5 MB
EGAF00008202555 fastq.gz 329.6 MB
EGAF00008202556 fastq.gz 596.9 MB
EGAF00008202557 fastq.gz 941.9 MB
EGAF00008202558 fastq.gz 595.3 MB
EGAF00008202559 fastq.gz 938.2 MB
EGAF00008202560 fastq.gz 545.8 MB
EGAF00008202561 fastq.gz 860.0 MB
EGAF00008202562 fastq.gz 648.7 MB
EGAF00008202563 fastq.gz 1.0 GB
EGAF00008202564 fastq.gz 204.9 MB
EGAF00008202565 fastq.gz 315.9 MB
EGAF00008202566 fastq.gz 176.3 MB
EGAF00008202567 fastq.gz 271.5 MB
EGAF00008202568 fastq.gz 279.6 MB
EGAF00008202569 fastq.gz 431.3 MB
EGAF00008202570 fastq.gz 284.2 MB
EGAF00008202571 fastq.gz 440.9 MB
EGAF00008202572 fastq.gz 180.3 MB
EGAF00008202573 fastq.gz 305.0 MB
EGAF00008202574 fastq.gz 118.4 MB
EGAF00008202575 fastq.gz 200.1 MB
EGAF00008202576 fastq.gz 85.2 MB
EGAF00008202577 fastq.gz 144.0 MB
EGAF00008202578 fastq.gz 87.6 MB
EGAF00008202579 fastq.gz 148.6 MB
EGAF00008202580 fastq.gz 43.6 MB
EGAF00008202581 fastq.gz 67.3 MB
EGAF00008202582 fastq.gz 28.7 MB
EGAF00008202583 fastq.gz 44.3 MB
EGAF00008202584 fastq.gz 20.7 MB
EGAF00008202585 fastq.gz 31.9 MB
EGAF00008202586 fastq.gz 21.2 MB
EGAF00008202587 fastq.gz 33.0 MB
EGAF00008202588 fastq.gz 260.6 MB
EGAF00008202589 fastq.gz 441.3 MB
EGAF00008202590 fastq.gz 298.6 MB
EGAF00008202591 fastq.gz 515.8 MB
EGAF00008202592 fastq.gz 365.9 MB
EGAF00008202593 fastq.gz 623.8 MB
EGAF00008202594 fastq.gz 272.0 MB
EGAF00008202595 fastq.gz 463.9 MB
EGAF00008202596 fastq.gz 650.2 MB
EGAF00008202597 fastq.gz 1.0 GB
EGAF00008202598 fastq.gz 742.2 MB
EGAF00008202599 fastq.gz 1.2 GB
EGAF00008202600 fastq.gz 908.6 MB
EGAF00008202601 fastq.gz 1.4 GB
EGAF00008202602 fastq.gz 679.5 MB
EGAF00008202603 fastq.gz 1.1 GB
EGAF00008202604 fastq.gz 834.4 MB
EGAF00008202605 fastq.gz 1.5 GB
EGAF00008202606 fastq.gz 770.3 MB
EGAF00008202607 fastq.gz 1.4 GB
EGAF00008202608 fastq.gz 900.2 MB
EGAF00008202609 fastq.gz 1.6 GB
EGAF00008202610 fastq.gz 23.8 MB
EGAF00008202611 fastq.gz 40.6 MB
EGAF00008202612 fastq.gz 439.0 MB
EGAF00008202613 fastq.gz 762.6 MB
EGAF00008202614 fastq.gz 570.2 MB
EGAF00008202615 fastq.gz 998.1 MB
EGAF00008202616 fastq.gz 220.8 MB
EGAF00008202617 fastq.gz 381.1 MB
EGAF00008202618 fastq.gz 572.0 MB
EGAF00008202619 fastq.gz 995.9 MB
EGAF00008202620 fastq.gz 1.1 GB
EGAF00008202621 fastq.gz 1.7 GB
EGAF00008202622 fastq.gz 986.2 MB
EGAF00008202623 fastq.gz 1.6 GB
EGAF00008202624 fastq.gz 1.2 GB
EGAF00008202625 fastq.gz 1.9 GB
EGAF00008202626 fastq.gz 31.6 MB
EGAF00008202627 fastq.gz 49.6 MB
EGAF00008202628 fastq.gz 401.8 MB
EGAF00008202629 fastq.gz 637.4 MB
EGAF00008202630 fastq.gz 518.1 MB
EGAF00008202631 fastq.gz 833.0 MB
EGAF00008202632 fastq.gz 201.4 MB
EGAF00008202633 fastq.gz 317.8 MB
EGAF00008202634 fastq.gz 519.8 MB
EGAF00008202635 fastq.gz 827.2 MB
EGAF00008202636 fastq.gz 160.4 MB
EGAF00008202637 fastq.gz 491.2 MB
EGAF00008202638 fastq.gz 185.8 MB
EGAF00008202639 fastq.gz 569.6 MB
EGAF00008202640 fastq.gz 345.2 MB
EGAF00008202641 fastq.gz 1.1 GB
EGAF00008202642 fastq.gz 200.6 MB
EGAF00008202643 fastq.gz 615.4 MB
EGAF00008202644 fastq.gz 221.4 MB
EGAF00008202645 fastq.gz 692.8 MB
EGAF00008202646 fastq.gz 295.7 MB
EGAF00008202647 fastq.gz 698.0 MB
EGAF00008202648 fastq.gz 418.8 MB
EGAF00008202649 fastq.gz 990.4 MB
EGAF00008202650 fastq.gz 309.1 MB
EGAF00008202651 fastq.gz 733.5 MB
EGAF00008202652 fastq.gz 277.1 MB
EGAF00008202653 fastq.gz 655.7 MB
EGAF00008202654 fastq.gz 64.9 MB
EGAF00008202655 fastq.gz 227.0 MB
EGAF00008202656 fastq.gz 80.3 MB
EGAF00008202657 fastq.gz 267.9 MB
EGAF00008202658 fastq.gz 103.1 MB
EGAF00008202659 fastq.gz 350.9 MB
EGAF00008202660 fastq.gz 73.0 MB
EGAF00008202661 fastq.gz 242.3 MB
EGAF00008202662 fastq.gz 51.1 MB
EGAF00008202663 fastq.gz 170.0 MB
EGAF00008202664 fastq.gz 39.9 MB
EGAF00008202665 fastq.gz 133.9 MB
EGAF00008202666 fastq.gz 77.1 MB
EGAF00008202667 fastq.gz 258.4 MB
EGAF00008202668 fastq.gz 68.1 MB
EGAF00008202669 fastq.gz 225.8 MB
EGAF00008202670 fastq.gz 40.6 MB
EGAF00008202671 fastq.gz 133.8 MB
EGAF00008202672 fastq.gz 49.6 MB
EGAF00008202673 fastq.gz 174.0 MB
EGAF00008202674 fastq.gz 38.0 MB
EGAF00008202675 fastq.gz 125.2 MB
EGAF00008202676 fastq.gz 37.6 MB
EGAF00008202677 fastq.gz 123.7 MB
EGAF00008202678 fastq.gz 93.3 MB
EGAF00008202679 fastq.gz 310.2 MB
EGAF00008202680 fastq.gz 116.7 MB
EGAF00008202681 fastq.gz 401.7 MB
EGAF00008202682 fastq.gz 89.3 MB
EGAF00008202683 fastq.gz 297.2 MB
EGAF00008202684 fastq.gz 75.6 MB
EGAF00008202685 fastq.gz 252.5 MB
EGAF00008202686 fastq.gz 145.7 MB
EGAF00008202687 fastq.gz 489.1 MB
EGAF00008202688 fastq.gz 227.1 MB
EGAF00008202689 fastq.gz 768.1 MB
EGAF00008202690 fastq.gz 235.0 MB
EGAF00008202691 fastq.gz 812.6 MB
EGAF00008202692 fastq.gz 218.0 MB
EGAF00008202693 fastq.gz 738.3 MB
EGAF00008202694 fastq.gz 112.1 MB
EGAF00008202695 fastq.gz 395.4 MB
EGAF00008202696 fastq.gz 147.3 MB
EGAF00008202697 fastq.gz 493.4 MB
EGAF00008202698 fastq.gz 154.5 MB
EGAF00008202699 fastq.gz 521.3 MB
EGAF00008202700 fastq.gz 111.0 MB
EGAF00008202701 fastq.gz 371.1 MB
274 Files (115.7 GB)