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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300BCG trained immunity scRNAseq

We have paired 39 individuals in 4 conditions: T0_RPMI (baseline, before BCG and without LPS); T0_LPS (before BCG and with LPS); T3m_RPMI (3 months after BCG, without LPS); T3m_LPS (3 months after BCG, with LPS).

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

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 Data belonging to research published in peer-reviewed journals  Unpublished data. Data belonging to unpublished research.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
EGAS00001006990 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
EGAF00007930834 vcf 116.6 MB
EGAF00007930835 fastq.gz 959.9 MB Report
EGAF00007930836 fastq.gz 945.3 MB Report
EGAF00007930837 fastq.gz 3.1 GB Report
EGAF00007930838 fastq.gz 7.0 GB Report
EGAF00007930839 fastq.gz 15.6 GB Report
EGAF00007930840 fastq.gz 37.0 GB Report
EGAF00007930841 fastq.gz 4.2 GB Report
EGAF00007930842 fastq.gz 9.8 GB Report
EGAF00007930843 fastq.gz 2.0 GB Report
EGAF00007930844 fastq.gz 2.3 GB Report
EGAF00007930845 fastq.gz 7.5 GB Report
EGAF00007930846 fastq.gz 17.4 GB Report
EGAF00007930847 fastq.gz 2.0 GB Report
EGAF00007930848 fastq.gz 2.0 GB Report
EGAF00007930849 fastq.gz 6.4 GB Report
EGAF00007930850 fastq.gz 14.9 GB Report
EGAF00007930851 fastq.gz 1.8 GB Report
EGAF00007930852 fastq.gz 2.0 GB Report
EGAF00007930853 fastq.gz 6.6 GB Report
EGAF00007930854 fastq.gz 15.5 GB Report
EGAF00007930855 fastq.gz 1.8 GB Report
EGAF00007930856 fastq.gz 2.2 GB Report
EGAF00007930857 fastq.gz 6.6 GB Report
EGAF00007930858 fastq.gz 15.3 GB Report
EGAF00007930859 fastq.gz 1.9 GB Report
EGAF00007930860 fastq.gz 2.2 GB Report
EGAF00007930861 fastq.gz 6.6 GB Report
EGAF00007930862 fastq.gz 15.4 GB Report
EGAF00007930863 fastq.gz 1.9 GB Report
EGAF00007930864 fastq.gz 2.1 GB Report
EGAF00007930865 fastq.gz 6.4 GB Report
EGAF00007930866 fastq.gz 14.8 GB Report
EGAF00007930867 fastq.gz 2.2 GB Report
EGAF00007930868 fastq.gz 1.8 GB Report
EGAF00007930869 fastq.gz 6.3 GB Report
EGAF00007930870 fastq.gz 14.5 GB Report
EGAF00007930871 fastq.gz 1.8 GB Report
EGAF00007930872 fastq.gz 1.9 GB Report
EGAF00007930873 fastq.gz 6.3 GB Report
EGAF00007930874 fastq.gz 14.1 GB Report
EGAF00007930875 fastq.gz 1.9 GB Report
EGAF00007930876 fastq.gz 2.1 GB Report
EGAF00007930877 fastq.gz 6.6 GB Report
EGAF00007930878 fastq.gz 15.5 GB Report
EGAF00007930879 fastq.gz 1.7 GB Report
EGAF00007930880 fastq.gz 1.6 GB Report
EGAF00007930881 fastq.gz 5.8 GB Report
EGAF00007930882 fastq.gz 13.4 GB Report
EGAF00007930883 fastq.gz 2.0 GB Report
EGAF00007930884 fastq.gz 2.1 GB Report
EGAF00007930885 fastq.gz 7.4 GB Report
EGAF00007930886 fastq.gz 17.1 GB Report
EGAF00007930887 fastq.gz 1.6 GB Report
EGAF00007930888 fastq.gz 1.6 GB Report
EGAF00007930889 fastq.gz 5.4 GB Report
EGAF00007930890 fastq.gz 12.5 GB Report
EGAF00007930891 fastq.gz 1.8 GB Report
EGAF00007930892 fastq.gz 1.9 GB Report
EGAF00007930893 fastq.gz 6.8 GB Report
EGAF00007930894 fastq.gz 15.5 GB Report
EGAF00007930895 fastq.gz 2.3 GB Report
EGAF00007930896 fastq.gz 2.4 GB Report
EGAF00007930897 fastq.gz 8.3 GB Report
EGAF00007930898 fastq.gz 19.3 GB Report
EGAF00007930899 fastq.gz 1.8 GB Report
EGAF00007930900 fastq.gz 2.1 GB Report
EGAF00007930901 fastq.gz 6.6 GB Report
EGAF00007930902 fastq.gz 15.5 GB Report
EGAF00007930903 fastq.gz 2.0 GB Report
EGAF00007930904 fastq.gz 1.9 GB Report
EGAF00007930905 fastq.gz 6.3 GB Report
EGAF00007930906 fastq.gz 14.3 GB Report
EGAF00007930907 fastq.gz 2.6 GB Report
EGAF00007930908 fastq.gz 2.7 GB Report
EGAF00007930909 fastq.gz 9.6 GB Report
EGAF00007930910 fastq.gz 21.6 GB Report
EGAF00007930911 fastq.gz 2.6 GB Report
EGAF00007930912 fastq.gz 2.3 GB Report
EGAF00007930913 fastq.gz 8.3 GB Report
EGAF00007930914 fastq.gz 19.4 GB Report
EGAF00007930915 fastq.gz 2.1 GB Report
EGAF00007930916 fastq.gz 2.2 GB Report
EGAF00007930917 fastq.gz 7.1 GB Report
EGAF00007930918 fastq.gz 16.8 GB Report
EGAF00007930919 fastq.gz 2.0 GB Report
EGAF00007930920 fastq.gz 1.8 GB Report
EGAF00007930921 fastq.gz 5.8 GB Report
EGAF00007930922 fastq.gz 13.6 GB Report
EGAF00007930923 fastq.gz 2.0 GB Report
EGAF00007930924 fastq.gz 2.1 GB Report
EGAF00007930925 fastq.gz 7.1 GB Report
EGAF00007930926 fastq.gz 16.7 GB Report
EGAF00007930927 fastq.gz 1.9 GB Report
EGAF00007930928 fastq.gz 2.1 GB Report
EGAF00007930929 fastq.gz 7.1 GB Report
EGAF00007930930 fastq.gz 16.6 GB Report
EGAF00007930931 fastq.gz 2.2 GB Report
EGAF00007930932 fastq.gz 2.1 GB Report
EGAF00007930933 fastq.gz 7.2 GB Report
EGAF00007930934 fastq.gz 16.6 GB Report
EGAF00007930935 fastq.gz 2.8 GB Report
EGAF00007930936 fastq.gz 2.8 GB Report
EGAF00007930937 fastq.gz 10.5 GB Report
EGAF00007930938 fastq.gz 24.5 GB Report
EGAF00007930939 fastq.gz 2.1 GB Report
EGAF00007930940 fastq.gz 2.4 GB Report
EGAF00007930941 fastq.gz 7.9 GB Report
EGAF00007930942 fastq.gz 18.7 GB Report
EGAF00007930943 fastq.gz 2.2 GB Report
EGAF00007930944 fastq.gz 2.5 GB Report
EGAF00007930945 fastq.gz 8.3 GB Report
EGAF00007930946 fastq.gz 19.6 GB Report
EGAF00007930947 fastq.gz 2.0 GB Report
EGAF00007930948 fastq.gz 2.3 GB Report
EGAF00007930949 fastq.gz 7.5 GB Report
EGAF00007930950 fastq.gz 17.3 GB Report
EGAF00007930951 fastq.gz 1.9 GB Report
EGAF00007930952 fastq.gz 2.2 GB Report
EGAF00007930953 fastq.gz 7.0 GB Report
EGAF00007930954 fastq.gz 16.5 GB Report
EGAF00007930955 fastq.gz 2.3 GB Report
EGAF00007930956 fastq.gz 2.6 GB Report
EGAF00007930957 fastq.gz 8.6 GB Report
EGAF00007930958 fastq.gz 20.3 GB Report
EGAF00007937969 fastq.gz 3.9 GB Report
EGAF00007937970 fastq.gz 4.6 GB Report
EGAF00007937971 fastq.gz 1.3 GB Report
EGAF00007937972 fastq.gz 1.2 GB Report
129 Files (902.6 GB)