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Comparison of the antiviral immune response between individuals of Indian and European origin

We purified peripheral blood mononuclear cells from individuals living in India (N=10) and the Netherlands (N=10) at baseline and 10-12 weeks after BCG vaccination. We compared chromatin accessibility between the two populations at baseline, as well as gene transcription profiles and cytokine production capacities upon viral stimulation with influenza and SARS-CoV-2

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Data access policy for the Helmholtz Centre for Infection Research, Centre for Individualised Medicine.

Data access policy Data management refers to processes that guard and maintain the consistency and accuracy of collected data and facilitate the re-use of data. This document provides information about procedures of data management. Responsibilities Researchers have the obligation to provide accompanying metadata. Supervisors (group leaders), together with the data steward, have the responsibility to check and enforce the archiving of appropriate metadata. Included data Two categories of research data are to be distinguished:  Published data. Data belonging to research published in peer-reviewed journals  Unpublished data. Data belonging to unpublished research. This includes work-in-progress data but also, data that was not selected for publication. Two types of data types are to be distinguished, regardless of data category:  Raw data  Depending on the platform used for generation of the data this includes data formats according to standards in the field:  FASTQ for raw DNA sequencing data  BAM for mapped DNA sequencing data  RAW for mass-spectrometry data (Thermo RAW)  Processed data  This includes data resulting from any additional analysis of the raw data.  The format of processed data is inherently loosely specified, as it is specific to the analysis conducted. Formats are mostly non-binary (flat-text) files, such as tab-delimited or Microsoft Excel files. Metadata Metadata should include experimental variables that are crucial to repeat the experiment, and to correctly interpret the results of the experiment. Metadata should include at least:  Source of biological material (cell line, tissue, organism)  Treatment (chemical, biological, compound)  Protocol by which the sample was prepared  Instrument settings  Date  Researcher Metadata for published data • Depending on the database used (see below) metadata is included in different ways: • GEO, dbGAP, ENA, and EGA explicitly specify which metadata must be included with data submission to their databases. This includes both experimental and technical (‘machine’) variables. Upon submission, this metadata is linked to the accompanying data files. • PRIDE accepts RAW files, which contain both the raw data as well as the metadata of the corresponding experiment, as such providing an ‘in-file’ metadata-data link. Data storage • For published data, several public databases are used, according standards in our field: o GEO (https://www.ncbi.nlm.nih.gov/gds) for DNA sequencing and array data (USA), open access o dbGAP (https://www.ncbi.nlm.nih.gov/gap) for DNA sequencing and array data (USA), controlled access o ENA (https://www.ebi.ac.uk/ena) for DNA sequencing and array data (EU), open access o EGA (https://www.ebi.ac.uk/ega) for DNA sequencing and array data (EU), controlled access o PRIDE (https://www.ebi.ac.uk/pride) for mass-spectrometry data (EU), open access o Database choice is dependent on data-type (mass-spectrometry vs. DNA sequencing data), and per-project restrictions (e.g. EU/USA) o In publications, the respective data is referenced using unique persistent identifiers provided by the database. These identifiers link to the databases. o At the publishers’ request, processed data is primarily provided either as supplemental data to the publication at the journal’s website. However, some of the databases mentioned above also accept processed data. In case of large processed-data files, these are co-submitted with the raw data to the public database. For instance, GEO has a flexible policy for accepting various file formats (flat-text, Excel). • For unpublished data, data is stored on the institutes’ infrastructure. For integrity reasons, raw data is kept at a designated partition that is write-protected (only writable by the system administrator). Data protection To prevent data loss in case of technical failures, the institutes’ data is stored: • On one of the public databases mentioned above (published data only) • At the institutes’ local infrastructure • In addition, raw sequencing data is mirrored at an independent physical location of the institute’s local infrastructure. • Raw data is write-protected (only writable by the system administrator). Maximum retention period • Both published and unpublished data is kept for a minimum of 10 years. • The public databases mentioned above do not explicitly state a restriction on preservation time of submitted data. Therefore, we regard this as ‘permanent’. Accessibility and re-use • Published data o Raw and processed data is publicly available through one of the databases mentioned above. o According current standards in our field, data of a published studies can be freely downloaded and re-used. Availability in databases is a prerequisite for acceptance of a manuscript; the journals request peer-reviewers to check the availability of both raw and published data. Databases such as GEO provide functionality such as ‘reviewer links’ that allow for anonymized download/viewing of submitted data, prior to publication. o The use of standardized data formats for DNA sequencing and mass-spectrometry (FASTQ, BAM, RAW), allows for re-analysis of the original data by others. • Unpublished data o Unpublished data is not publicly accessible, and is only available to researchers within the institutes’ departments. Privacy of sensitive data • Published data o Sensitive data containing identifiable information (DNA sequence data from donors, patients, healthy volunteers, etc.) is deposited under controlled access, depending on the informed consent of the corresponding project. Both EGA and dbGAP have controlled access mechanisms. As such they are appropriate databases for hosting sensitive patient data under secure standards. Access is controlled by a project-specific Data Access Committee (DAC) and applications are submitted to the Data Access and Compliance Office (DACO) or International Data Access Committee (IDAC). These ensure that potentially identifiable data will only be used by qualified scientists, taken into consideration access policies and restrictions on the purpose of data use. Procedures for identifiable data and controlled access are available via https://www.ebi.ac.uk/ega/about, https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/about.html • Unpublished data o Sensitive data containing identifiable information is not publicly available and not accessible to anyone outside of our institute.

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
EGAS00001006417 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
EGAF00006566262 fastq.gz 516.0 MB
EGAF00006566263 fastq.gz 520.7 MB
EGAF00006566264 fastq.gz 238.1 MB
EGAF00006566265 fastq.gz 239.9 MB
EGAF00006566266 fastq.gz 720.3 MB
EGAF00006566267 fastq.gz 731.6 MB
EGAF00006566268 fastq.gz 722.3 MB
EGAF00006566269 fastq.gz 732.3 MB
EGAF00006566270 fastq.gz 658.2 MB
EGAF00006566271 fastq.gz 660.9 MB
EGAF00006566272 fastq.gz 1.3 GB
EGAF00006566273 fastq.gz 1.3 GB
EGAF00006566274 fastq.gz 868.7 MB
EGAF00006566275 fastq.gz 919.7 MB
EGAF00006566276 fastq.gz 521.9 MB
EGAF00006566277 fastq.gz 525.5 MB
EGAF00006566278 fastq.gz 1.2 GB
EGAF00006566279 fastq.gz 1.2 GB
EGAF00006566280 fastq.gz 594.7 MB
EGAF00006566281 fastq.gz 598.6 MB
EGAF00006566282 fastq.gz 924.8 MB
EGAF00006566283 fastq.gz 937.1 MB
EGAF00006566284 fastq.gz 562.5 MB
EGAF00006566285 fastq.gz 563.2 MB
EGAF00006566286 fastq.gz 644.3 MB
EGAF00006566287 fastq.gz 650.8 MB
EGAF00006566288 fastq.gz 166.5 MB
EGAF00006566289 fastq.gz 169.0 MB
EGAF00006566290 fastq.gz 263.1 MB
EGAF00006566291 fastq.gz 266.9 MB
EGAF00006566292 fastq.gz 664.3 MB
EGAF00006566293 fastq.gz 692.6 MB
EGAF00006566294 fastq.gz 455.3 MB
EGAF00006566295 fastq.gz 458.6 MB
EGAF00006566296 fastq.gz 437.3 MB
EGAF00006566297 fastq.gz 441.6 MB
EGAF00006566298 fastq.gz 579.0 MB
EGAF00006566299 fastq.gz 608.2 MB
EGAF00006566300 fastq.gz 425.4 MB
EGAF00006566301 fastq.gz 427.4 MB
EGAF00006566302 fastq.gz 449.8 MB
EGAF00006566303 fastq.gz 451.1 MB
EGAF00006566304 fastq.gz 240.2 MB
EGAF00006566305 fastq.gz 242.8 MB
EGAF00006566306 fastq.gz 460.2 MB
EGAF00006566307 fastq.gz 460.9 MB
EGAF00006566308 fastq.gz 99.7 MB
EGAF00006566309 fastq.gz 100.1 MB
EGAF00006566310 fastq.gz 213.8 MB
EGAF00006566311 fastq.gz 216.2 MB
EGAF00006566312 fastq.gz 245.7 MB
EGAF00006566313 fastq.gz 247.1 MB
EGAF00006566314 fastq.gz 397.5 MB
EGAF00006566315 fastq.gz 399.2 MB
EGAF00006566316 fastq.gz 658.1 MB
EGAF00006566317 fastq.gz 661.2 MB
EGAF00006566318 fastq.gz 452.4 MB
EGAF00006566319 fastq.gz 454.0 MB
EGAF00006566320 fastq.gz 129.9 MB
EGAF00006566321 fastq.gz 129.9 MB
EGAF00006566322 fastq.gz 365.4 MB
EGAF00006566323 fastq.gz 367.9 MB
EGAF00006566324 fastq.gz 109.4 MB
EGAF00006566325 fastq.gz 109.9 MB
EGAF00006566326 fastq.gz 415.9 MB
EGAF00006566327 fastq.gz 416.2 MB
EGAF00006566328 fastq.gz 418.7 MB
EGAF00006566329 fastq.gz 416.5 MB
EGAF00006566330 fastq.gz 318.6 MB
EGAF00006566331 fastq.gz 320.6 MB
EGAF00006566332 fastq.gz 535.6 MB
EGAF00006566333 fastq.gz 534.4 MB
EGAF00006566334 fastq.gz 626.7 MB
EGAF00006566335 fastq.gz 628.6 MB
EGAF00006566336 fastq.gz 216.5 MB
EGAF00006566337 fastq.gz 218.9 MB
EGAF00006566338 fastq.gz 511.4 MB
EGAF00006566339 fastq.gz 511.9 MB
EGAF00006566340 fastq.gz 579.4 MB
EGAF00006566341 fastq.gz 582.1 MB
EGAF00006566342 fastq.gz 476.2 MB
EGAF00006566343 fastq.gz 481.6 MB
EGAF00006566344 fastq.gz 656.9 MB
EGAF00006566345 fastq.gz 664.9 MB
EGAF00006566346 fastq.gz 783.7 MB
EGAF00006566347 fastq.gz 791.8 MB
EGAF00006566348 fastq.gz 666.6 MB
EGAF00006566349 fastq.gz 667.5 MB
EGAF00006566350 fastq.gz 660.6 MB
EGAF00006566351 fastq.gz 659.4 MB
EGAF00006566352 fastq.gz 596.9 MB
EGAF00006566353 fastq.gz 600.5 MB
EGAF00006566354 fastq.gz 612.8 MB
EGAF00006566355 fastq.gz 614.5 MB
EGAF00006566356 fastq.gz 625.7 MB
EGAF00006566357 fastq.gz 624.8 MB
EGAF00006566358 fastq.gz 553.6 MB
EGAF00006566359 fastq.gz 554.8 MB
EGAF00006566360 fastq.gz 507.6 MB
EGAF00006566361 fastq.gz 509.9 MB
EGAF00006566362 fastq.gz 554.0 MB
EGAF00006566363 fastq.gz 556.2 MB
EGAF00006566364 fastq.gz 699.5 MB
EGAF00006566365 fastq.gz 698.0 MB
EGAF00006566366 fastq.gz 729.2 MB
EGAF00006566367 fastq.gz 745.8 MB
EGAF00006566368 fastq.gz 787.2 MB
EGAF00006566369 fastq.gz 806.1 MB
EGAF00006566370 fastq.gz 803.6 MB
EGAF00006566371 fastq.gz 818.7 MB
EGAF00006566372 fastq.gz 673.7 MB
EGAF00006566373 fastq.gz 688.1 MB
EGAF00006566374 fastq.gz 762.0 MB
EGAF00006566375 fastq.gz 777.6 MB
EGAF00006566376 fastq.gz 746.2 MB
EGAF00006566377 fastq.gz 760.1 MB
EGAF00006566378 fastq.gz 574.3 MB
EGAF00006566379 fastq.gz 579.1 MB
EGAF00006566380 fastq.gz 568.7 MB
EGAF00006566381 fastq.gz 579.8 MB
EGAF00006566382 fastq.gz 471.9 MB
EGAF00006566383 fastq.gz 479.2 MB
EGAF00006566384 fastq.gz 630.6 MB
EGAF00006566385 fastq.gz 629.4 MB
EGAF00006566386 fastq.gz 529.4 MB
EGAF00006566387 fastq.gz 528.8 MB
EGAF00006566388 fastq.gz 645.4 MB
EGAF00006566389 fastq.gz 644.2 MB
EGAF00006566390 fastq.gz 613.8 MB
EGAF00006566391 fastq.gz 618.9 MB
EGAF00006566392 fastq.gz 600.1 MB
EGAF00006566393 fastq.gz 605.9 MB
EGAF00006566394 fastq.gz 715.1 MB
EGAF00006566395 fastq.gz 720.5 MB
EGAF00006566396 fastq.gz 540.9 MB
EGAF00006566397 fastq.gz 541.6 MB
EGAF00006566398 fastq.gz 766.2 MB
EGAF00006566399 fastq.gz 766.7 MB
EGAF00006566400 fastq.gz 733.6 MB
EGAF00006566401 fastq.gz 734.8 MB
EGAF00006566402 fastq.gz 402.1 MB
EGAF00006566403 fastq.gz 400.2 MB
EGAF00006566404 fastq.gz 769.1 MB
EGAF00006566405 fastq.gz 785.2 MB
EGAF00006566406 fastq.gz 442.2 MB
EGAF00006566407 fastq.gz 445.5 MB
EGAF00006566408 fastq.gz 545.1 MB
EGAF00006566409 fastq.gz 546.4 MB
EGAF00006566410 fastq.gz 549.7 MB
EGAF00006566411 fastq.gz 552.6 MB
EGAF00006566412 fastq.gz 294.3 MB
EGAF00006566413 fastq.gz 296.3 MB
EGAF00006566414 fastq.gz 1.2 GB
EGAF00006566415 fastq.gz 1.2 GB
EGAF00006566416 fastq.gz 883.0 MB
EGAF00006566417 fastq.gz 887.0 MB
EGAF00006566418 fastq.gz 743.9 MB
EGAF00006566419 fastq.gz 748.4 MB
EGAF00006566420 fastq.gz 656.5 MB
EGAF00006566421 fastq.gz 660.5 MB
EGAF00006566422 fastq.gz 613.9 MB
EGAF00006566423 fastq.gz 618.4 MB
EGAF00006566424 fastq.gz 883.4 MB
EGAF00006566425 fastq.gz 921.2 MB
EGAF00006566426 fastq.gz 690.7 MB
EGAF00006566427 fastq.gz 696.6 MB
EGAF00006566428 fastq.gz 807.2 MB
EGAF00006566429 fastq.gz 812.2 MB
EGAF00006566430 fastq.gz 692.4 MB
EGAF00006566431 fastq.gz 709.2 MB
EGAF00006566432 fastq.gz 768.3 MB
EGAF00006566433 fastq.gz 777.0 MB
EGAF00006566434 fastq.gz 320.0 MB
EGAF00006566435 fastq.gz 322.9 MB
EGAF00006566436 fastq.gz 5.9 GB
EGAF00006566437 fastq.gz 5.9 GB
EGAF00006566438 fastq.gz 821.3 MB
EGAF00006566439 fastq.gz 841.7 MB
EGAF00006566440 fastq.gz 656.1 MB
EGAF00006566441 fastq.gz 661.3 MB
EGAF00006566442 fastq.gz 822.3 MB
EGAF00006566443 fastq.gz 826.3 MB
EGAF00006566444 fastq.gz 325.9 MB
EGAF00006566445 fastq.gz 333.2 MB
EGAF00006566446 fastq.gz 245.8 MB
EGAF00006566447 fastq.gz 247.6 MB
EGAF00006566448 fastq.gz 274.5 MB
EGAF00006566449 fastq.gz 277.0 MB
EGAF00006566450 fastq.gz 280.5 MB
EGAF00006566451 fastq.gz 284.4 MB
EGAF00006566452 fastq.gz 318.9 MB
EGAF00006566453 fastq.gz 321.9 MB
EGAF00006566454 fastq.gz 256.7 MB
EGAF00006566455 fastq.gz 258.8 MB
EGAF00006566456 fastq.gz 606.4 MB
EGAF00006566457 fastq.gz 618.2 MB
EGAF00006566458 fastq.gz 628.6 MB
EGAF00006566459 fastq.gz 642.4 MB
EGAF00006566460 fastq.gz 548.0 MB
EGAF00006566461 fastq.gz 559.6 MB
EGAF00006566462 fastq.gz 616.5 MB
EGAF00006566463 fastq.gz 628.5 MB
EGAF00006566464 fastq.gz 625.4 MB
EGAF00006566465 fastq.gz 638.3 MB
EGAF00006566466 fastq.gz 574.6 MB
EGAF00006566467 fastq.gz 582.8 MB
EGAF00006566468 fastq.gz 615.1 MB
EGAF00006566469 fastq.gz 631.2 MB
EGAF00006566470 fastq.gz 656.7 MB
EGAF00006566471 fastq.gz 667.2 MB
EGAF00006566472 fastq.gz 564.4 MB
EGAF00006566473 fastq.gz 575.4 MB
EGAF00006566474 fastq.gz 480.3 MB
EGAF00006566475 fastq.gz 490.8 MB
EGAF00006566476 fastq.gz 637.4 MB
EGAF00006566477 fastq.gz 652.6 MB
EGAF00006566478 fastq.gz 672.9 MB
EGAF00006566479 fastq.gz 674.6 MB
EGAF00006566480 fastq.gz 521.9 MB
EGAF00006566481 fastq.gz 522.5 MB
EGAF00006566482 fastq.gz 630.4 MB
EGAF00006566483 fastq.gz 629.4 MB
EGAF00006566484 fastq.gz 550.3 MB
EGAF00006566485 fastq.gz 553.4 MB
EGAF00006566486 fastq.gz 668.4 MB
EGAF00006566487 fastq.gz 668.6 MB
EGAF00006566488 fastq.gz 632.8 MB
EGAF00006566489 fastq.gz 655.7 MB
EGAF00006566490 fastq.gz 746.4 MB
EGAF00006566491 fastq.gz 750.0 MB
EGAF00006566492 fastq.gz 304.1 MB
EGAF00006566493 fastq.gz 306.4 MB
EGAF00006566494 fastq.gz 599.4 MB
EGAF00006566495 fastq.gz 606.5 MB
EGAF00006566496 fastq.gz 406.1 MB
EGAF00006566497 fastq.gz 407.3 MB
EGAF00006566498 fastq.gz 528.5 MB
EGAF00006566499 fastq.gz 525.5 MB
EGAF00006566500 fastq.gz 449.4 MB
EGAF00006566501 fastq.gz 450.9 MB
EGAF00006566502 fastq.gz 373.7 MB
EGAF00006566503 fastq.gz 388.3 MB
EGAF00006566504 fastq.gz 574.3 MB
EGAF00006566505 fastq.gz 579.1 MB
EGAF00006566506 fastq.gz 568.7 MB
EGAF00006566507 fastq.gz 579.8 MB
EGAF00006566508 fastq.gz 471.9 MB
EGAF00006566509 fastq.gz 479.2 MB
EGAF00006566510 fastq.gz 630.6 MB
EGAF00006566511 fastq.gz 629.4 MB
EGAF00006566512 fastq.gz 529.4 MB
EGAF00006566513 fastq.gz 528.8 MB
EGAF00006566514 fastq.gz 645.4 MB
EGAF00006566515 fastq.gz 644.2 MB
EGAF00006566516 fastq.gz 464.1 MB
EGAF00006566517 fastq.gz 469.3 MB
EGAF00006566518 fastq.gz 529.5 MB
EGAF00006566519 fastq.gz 538.9 MB
EGAF00006566520 fastq.gz 508.2 MB
EGAF00006566521 fastq.gz 513.4 MB
EGAF00006566522 fastq.gz 765.6 MB
EGAF00006566523 fastq.gz 767.6 MB
EGAF00006566524 fastq.gz 675.1 MB
EGAF00006566525 fastq.gz 676.7 MB
EGAF00006566526 fastq.gz 227.4 MB
EGAF00006566527 fastq.gz 228.5 MB
EGAF00006566528 fastq.gz 564.8 MB
EGAF00006566529 fastq.gz 572.0 MB
EGAF00006566530 fastq.gz 650.7 MB
EGAF00006566531 fastq.gz 654.2 MB
EGAF00006566532 fastq.gz 540.2 MB
EGAF00006566533 fastq.gz 542.2 MB
EGAF00006566534 fastq.gz 666.0 MB
EGAF00006566535 fastq.gz 666.8 MB
EGAF00006566536 fastq.gz 624.7 MB
EGAF00006566537 fastq.gz 626.5 MB
EGAF00006566538 fastq.gz 356.3 MB
EGAF00006566539 fastq.gz 358.5 MB
EGAF00006566540 fastq.gz 631.6 MB
EGAF00006566541 fastq.gz 635.7 MB
EGAF00006566542 fastq.gz 343.5 MB
EGAF00006566543 fastq.gz 348.1 MB
EGAF00006566544 fastq.gz 312.6 MB
EGAF00006566545 fastq.gz 313.9 MB
EGAF00006566546 fastq.gz 321.4 MB
EGAF00006566547 fastq.gz 323.8 MB
EGAF00006566548 fastq.gz 714.0 MB
EGAF00006566549 fastq.gz 717.7 MB
EGAF00006566550 fastq.gz 849.1 MB
EGAF00006566551 fastq.gz 853.8 MB
EGAF00006566552 fastq.gz 558.7 MB
EGAF00006566553 fastq.gz 562.8 MB
EGAF00006566554 fastq.gz 716.6 MB
EGAF00006566555 fastq.gz 722.1 MB
EGAF00006566556 fastq.gz 1.0 GB
EGAF00006566557 fastq.gz 1.0 GB
EGAF00006566558 fastq.gz 518.8 MB
EGAF00006566559 fastq.gz 522.6 MB
EGAF00006566560 fastq.gz 828.3 MB
EGAF00006566561 fastq.gz 835.1 MB
EGAF00006566562 fastq.gz 718.4 MB
EGAF00006566563 fastq.gz 720.5 MB
EGAF00006566564 fastq.gz 530.0 MB
EGAF00006566565 fastq.gz 538.7 MB
EGAF00006566566 fastq.gz 653.9 MB
EGAF00006566567 fastq.gz 658.0 MB
EGAF00006566568 fastq.gz 770.1 MB
EGAF00006566569 fastq.gz 774.9 MB
EGAF00006566570 fastq.gz 691.0 MB
EGAF00006566571 fastq.gz 697.7 MB
EGAF00006566572 fastq.gz 630.3 MB
EGAF00006566573 fastq.gz 636.7 MB
EGAF00006566574 fastq.gz 935.0 MB
EGAF00006566575 fastq.gz 939.6 MB
EGAF00006566576 csv 8.9 kB
315 Files (192.3 GB)