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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Spatial transcriptomics reveals immune and tissue remodeling, highlighting diverse host responses across mycobacterial granuloma types

Granulomas are the hallmark of Mycobacterium infections, forming structured immune environments that drive disease persistence. However, their spatial and functional organization remains unclear. Using spatial RNA sequencing on 33 patient explants, we try to reveal the detailed gene expression and cell composition landscape of granulomas.

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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 Data belonging to research published in peer-reviewed journals  Unpublished data. Data belonging to unpublished research.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
EGAS50000000998 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
EGAF50000369228 fastq.gz 1.3 GB
EGAF50000369229 fastq.gz 1.1 GB
EGAF50000369230 fastq.gz 3.7 GB
EGAF50000369231 fastq.gz 5.4 GB
EGAF50000369232 fastq.gz 878.2 MB
EGAF50000369233 fastq.gz 873.4 MB
EGAF50000369234 fastq.gz 2.6 GB
EGAF50000369235 fastq.gz 3.8 GB
EGAF50000369236 fastq.gz 755.7 MB
EGAF50000369237 fastq.gz 865.1 MB
EGAF50000369238 fastq.gz 2.7 GB
EGAF50000369239 fastq.gz 3.8 GB
EGAF50000369240 fastq.gz 847.0 MB
EGAF50000369241 fastq.gz 964.0 MB
EGAF50000369242 fastq.gz 2.9 GB
EGAF50000369243 fastq.gz 4.0 GB
EGAF50000369244 fastq.gz 827.4 MB
EGAF50000369245 fastq.gz 914.0 MB
EGAF50000369246 fastq.gz 2.9 GB
EGAF50000369247 fastq.gz 3.7 GB
EGAF50000369248 fastq.gz 925.6 MB
EGAF50000369249 fastq.gz 1.0 GB
EGAF50000369250 fastq.gz 2.9 GB
EGAF50000369251 fastq.gz 4.2 GB
EGAF50000369252 fastq.gz 706.7 MB
EGAF50000369253 fastq.gz 793.2 MB
EGAF50000369254 fastq.gz 2.3 GB
EGAF50000369255 fastq.gz 3.4 GB
EGAF50000369256 fastq.gz 881.6 MB
EGAF50000369257 fastq.gz 870.4 MB
EGAF50000369258 fastq.gz 2.8 GB
EGAF50000369259 fastq.gz 3.9 GB
EGAF50000369260 fastq.gz 811.1 MB
EGAF50000369261 fastq.gz 872.5 MB
EGAF50000369262 fastq.gz 2.5 GB
EGAF50000369263 fastq.gz 3.6 GB
EGAF50000369264 fastq.gz 812.9 MB
EGAF50000369265 fastq.gz 1.1 GB
EGAF50000369266 fastq.gz 3.0 GB
EGAF50000369267 fastq.gz 4.3 GB
EGAF50000369268 fastq.gz 705.6 MB
EGAF50000369269 fastq.gz 839.9 MB
EGAF50000369270 fastq.gz 2.4 GB
EGAF50000369271 fastq.gz 3.6 GB
EGAF50000369272 fastq.gz 546.1 MB
EGAF50000369273 fastq.gz 622.6 MB
EGAF50000369274 fastq.gz 1.9 GB
EGAF50000369275 fastq.gz 2.8 GB
EGAF50000369276 fastq.gz 818.3 MB
EGAF50000369277 fastq.gz 932.8 MB
EGAF50000369278 fastq.gz 3.0 GB
EGAF50000369279 fastq.gz 4.4 GB
EGAF50000369280 fastq.gz 1.1 GB
EGAF50000369281 fastq.gz 1.0 GB
EGAF50000369282 fastq.gz 3.1 GB
EGAF50000369283 fastq.gz 4.4 GB
EGAF50000369284 fastq.gz 946.1 MB
EGAF50000369285 fastq.gz 1.1 GB
EGAF50000369286 fastq.gz 3.2 GB
EGAF50000369287 fastq.gz 4.8 GB
EGAF50000369288 fastq.gz 1.5 GB
EGAF50000369289 fastq.gz 1.7 GB
EGAF50000369290 fastq.gz 5.6 GB
EGAF50000369291 fastq.gz 8.2 GB
EGAF50000369292 fastq.gz 486.5 MB
EGAF50000369293 fastq.gz 619.8 MB
EGAF50000369294 fastq.gz 1.7 GB
EGAF50000369295 fastq.gz 2.4 GB
EGAF50000369296 fastq.gz 1.2 GB
EGAF50000369297 fastq.gz 1.3 GB
EGAF50000369298 fastq.gz 4.1 GB
EGAF50000369299 fastq.gz 5.7 GB
EGAF50000369300 fastq.gz 1.1 GB
EGAF50000369301 fastq.gz 1.1 GB
EGAF50000369302 fastq.gz 3.2 GB
EGAF50000369303 fastq.gz 4.4 GB
EGAF50000369304 fastq.gz 810.4 MB
EGAF50000369305 fastq.gz 878.0 MB
EGAF50000369306 fastq.gz 2.7 GB
EGAF50000369307 fastq.gz 3.8 GB
EGAF50000369308 fastq.gz 1.3 GB
EGAF50000369309 fastq.gz 1.5 GB
EGAF50000369310 fastq.gz 4.6 GB
EGAF50000369311 fastq.gz 6.7 GB
EGAF50000369312 fastq.gz 816.5 MB
EGAF50000369313 fastq.gz 951.9 MB
EGAF50000369314 fastq.gz 2.9 GB
EGAF50000369315 fastq.gz 4.3 GB
EGAF50000369316 fastq.gz 715.8 MB
EGAF50000369317 fastq.gz 854.8 MB
EGAF50000369318 fastq.gz 2.3 GB
EGAF50000369319 fastq.gz 3.4 GB
EGAF50000369320 fastq.gz 1.8 GB
EGAF50000369321 fastq.gz 2.2 GB
EGAF50000369322 fastq.gz 6.9 GB
EGAF50000369323 fastq.gz 9.7 GB
EGAF50000369324 fastq.gz 695.7 MB
EGAF50000369325 fastq.gz 827.8 MB
EGAF50000369326 fastq.gz 2.7 GB
EGAF50000369327 fastq.gz 3.8 GB
EGAF50000369328 fastq.gz 1.2 GB
EGAF50000369329 fastq.gz 1.2 GB
EGAF50000369330 fastq.gz 4.1 GB
EGAF50000369331 fastq.gz 6.0 GB
EGAF50000369332 fastq.gz 949.4 MB
EGAF50000369333 fastq.gz 1.0 GB
EGAF50000369334 fastq.gz 3.2 GB
EGAF50000369335 fastq.gz 4.4 GB
EGAF50000369336 fastq.gz 948.1 MB
EGAF50000369337 fastq.gz 1.1 GB
EGAF50000369338 fastq.gz 3.4 GB
EGAF50000369339 fastq.gz 5.0 GB
EGAF50000369340 fastq.gz 745.1 MB
EGAF50000369341 fastq.gz 788.6 MB
EGAF50000369342 fastq.gz 2.5 GB
EGAF50000369343 fastq.gz 3.5 GB
EGAF50000369344 fastq.gz 975.2 MB
EGAF50000369345 fastq.gz 1.1 GB
EGAF50000369346 fastq.gz 3.2 GB
EGAF50000369347 fastq.gz 4.8 GB
EGAF50000369348 fastq.gz 733.4 MB
EGAF50000369349 fastq.gz 813.2 MB
EGAF50000369350 fastq.gz 2.6 GB
EGAF50000369351 fastq.gz 3.8 GB
EGAF50000369352 fastq.gz 736.9 MB
EGAF50000369353 fastq.gz 770.6 MB
EGAF50000369354 fastq.gz 2.6 GB
EGAF50000369355 fastq.gz 3.6 GB
EGAF50000369356 fastq.gz 784.2 MB
EGAF50000369357 fastq.gz 908.6 MB
EGAF50000369358 fastq.gz 2.7 GB
EGAF50000369359 fastq.gz 3.9 GB
132 Files (314.3 GB)