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RNAseq and ATACseq data

RNAseq and ATACseq data for the FMF patients and healthy control. The RNAseq data was sequenced on a BGI MGI G400 machine, with PE100 reads. ATAC-seq libraries were prepared with Illumina Nextera primers and sequenced on NovaSeq 6000 platform with 50bp paired-end sequencing, where each sample was sequenced to approximate 60 million reads.

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Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud university medical center.

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 Data belonging to research published in peer-reviewed journals  Unpublished data. Data belonging to unpublished research.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 ( for DNA sequencing and array data (USA), open access o dbGAP ( for DNA sequencing and array data (USA), controlled access o ENA ( for DNA sequencing and array data (EU), open access o EGA ( for DNA sequencing and array data (EU), controlled access o 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, • 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
EGAS00001007165 Other
EGAS00001007166 Other
ID File Type Size Located in
EGAF00008034240 fastq.gz 1.7 GB
EGAF00008034241 fastq.gz 1.7 GB
EGAF00008034242 fastq.gz 1.5 GB
EGAF00008034243 fastq.gz 1.6 GB
EGAF00008034244 fastq.gz 1.8 GB
EGAF00008034245 fastq.gz 1.9 GB
EGAF00008034246 fastq.gz 2.1 GB
EGAF00008034247 fastq.gz 2.1 GB
EGAF00008034248 fastq.gz 2.0 GB
EGAF00008034249 fastq.gz 2.0 GB
EGAF00008034250 fastq.gz 1.7 GB
EGAF00008034251 fastq.gz 1.7 GB
EGAF00008034252 fastq.gz 1.7 GB
EGAF00008034253 fastq.gz 1.8 GB
EGAF00008034254 fastq.gz 1.5 GB
EGAF00008034255 fastq.gz 1.4 GB
EGAF00008034256 fastq.gz 1.8 GB
EGAF00008034257 fastq.gz 1.6 GB
EGAF00008034258 fastq.gz 2.0 GB
EGAF00008034259 fastq.gz 2.0 GB
EGAF00008034260 fastq.gz 1.6 GB
EGAF00008034261 fastq.gz 1.7 GB
EGAF00008034262 fastq.gz 1.6 GB
EGAF00008034263 fastq.gz 1.6 GB
EGAF00008034264 fastq.gz 1.5 GB
EGAF00008034265 fastq.gz 1.6 GB
EGAF00008034266 fastq.gz 1.9 GB
EGAF00008034267 fastq.gz 2.0 GB
EGAF00008034268 fastq.gz 1.7 GB
EGAF00008034269 fastq.gz 1.8 GB
EGAF00008034270 fastq.gz 1.5 GB
EGAF00008034271 fastq.gz 1.4 GB
EGAF00008034272 fastq.gz 1.8 GB
EGAF00008034273 fastq.gz 1.8 GB
EGAF00008034274 fastq.gz 1.7 GB
EGAF00008034275 fastq.gz 1.7 GB
EGAF00008034276 fastq.gz 2.0 GB
EGAF00008034277 fastq.gz 2.1 GB
EGAF00008034278 fastq.gz 1.9 GB
EGAF00008034279 fastq.gz 2.0 GB
EGAF00008034280 fastq.gz 1.8 GB
EGAF00008034281 fastq.gz 1.9 GB
EGAF00008034282 fq.gz 3.0 GB
EGAF00008034283 fq.gz 3.0 GB
EGAF00008034284 fq.gz 3.0 GB
EGAF00008034285 fq.gz 3.1 GB
EGAF00008034286 fq.gz 3.0 GB
EGAF00008034287 fq.gz 3.0 GB
EGAF00008034288 fq.gz 2.9 GB
EGAF00008034289 fq.gz 2.9 GB
EGAF00008034290 fq.gz 3.0 GB
EGAF00008034291 fq.gz 3.0 GB
EGAF00008034292 fq.gz 3.0 GB
EGAF00008034293 fq.gz 3.0 GB
EGAF00008034294 fq.gz 3.0 GB
EGAF00008034295 fq.gz 3.0 GB
EGAF00008034296 fq.gz 3.0 GB
EGAF00008034297 fq.gz 3.0 GB
EGAF00008034298 fq.gz 3.0 GB
EGAF00008034299 fq.gz 3.0 GB
EGAF00008034300 fq.gz 3.2 GB
EGAF00008034301 fq.gz 3.2 GB
EGAF00008034302 fq.gz 3.0 GB
EGAF00008034303 fq.gz 3.0 GB
EGAF00008034304 fq.gz 3.0 GB
EGAF00008034305 fq.gz 3.0 GB
EGAF00008034306 fq.gz 3.0 GB
EGAF00008034307 fq.gz 3.0 GB
EGAF00008034308 fq.gz 2.9 GB
EGAF00008034309 fq.gz 2.9 GB
EGAF00008034310 fq.gz 2.9 GB
EGAF00008034311 fq.gz 2.9 GB
EGAF00008034312 fq.gz 3.0 GB
EGAF00008034313 fq.gz 3.0 GB
EGAF00008034314 fq.gz 3.0 GB
EGAF00008034315 fq.gz 3.1 GB
EGAF00008034316 fq.gz 3.0 GB
EGAF00008034317 fq.gz 3.1 GB
EGAF00008034318 fq.gz 2.8 GB
EGAF00008034319 fq.gz 2.9 GB
EGAF00008034320 fq.gz 2.6 GB
EGAF00008034321 fq.gz 2.7 GB
EGAF00008034322 fq.gz 2.6 GB
EGAF00008034323 fq.gz 2.6 GB
EGAF00008034324 fq.gz 3.1 GB
EGAF00008034325 fq.gz 3.2 GB
EGAF00008034326 fq.gz 3.1 GB
EGAF00008034327 fq.gz 3.2 GB
EGAF00008034328 fq.gz 3.0 GB
EGAF00008034329 fq.gz 3.1 GB
EGAF00008034330 fq.gz 3.0 GB
EGAF00008034331 fq.gz 3.1 GB
EGAF00008034332 fq.gz 2.8 GB
EGAF00008034333 fq.gz 2.9 GB
EGAF00008034334 fq.gz 3.2 GB
EGAF00008034335 fq.gz 3.2 GB
EGAF00008034336 fq.gz 3.2 GB
EGAF00008034337 fq.gz 3.2 GB
EGAF00008034338 fq.gz 3.0 GB
EGAF00008034339 fq.gz 3.1 GB
EGAF00008034340 fq.gz 2.8 GB
EGAF00008034341 fq.gz 2.9 GB
EGAF00008034342 fq.gz 3.0 GB
EGAF00008034343 fq.gz 3.0 GB
EGAF00008034344 fq.gz 3.0 GB
EGAF00008034345 fq.gz 3.0 GB
EGAF00008034346 fq.gz 3.0 GB
EGAF00008034347 fq.gz 3.0 GB
EGAF00008034348 fq.gz 3.0 GB
EGAF00008034349 fq.gz 3.0 GB
EGAF00008034350 fq.gz 3.1 GB
EGAF00008034351 fq.gz 3.1 GB
EGAF00008034352 fq.gz 3.1 GB
EGAF00008034353 fq.gz 3.1 GB
EGAF00008034354 fq.gz 3.0 GB
EGAF00008034355 fq.gz 3.1 GB
EGAF00008034356 fq.gz 3.0 GB
EGAF00008034357 fq.gz 3.0 GB
EGAF00008034358 fq.gz 3.0 GB
EGAF00008034359 fq.gz 3.1 GB
EGAF00008034360 fq.gz 3.1 GB
EGAF00008034361 fq.gz 3.1 GB
EGAF00008034362 fq.gz 3.0 GB
EGAF00008034363 fq.gz 3.1 GB
EGAF00008034364 fq.gz 3.0 GB
EGAF00008034365 fq.gz 3.0 GB
126 Files (326.5 GB)