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Single-cell omics data for COVID-19 patients

Single-cell RNA-seq, single-cell ATAC-seq, and genotypes used in the analysis for the study "Altered and allele-specific open chromatin landscape reveal epigenetic and genetic regulators of innate immunity in COVID-19". The RNA-seq and ATAC-seq are raw data in FASTQ format while the genotypes are in the VCF format which was filtered and imputed (more details are available in the main text of the study).

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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 Data belonging to research published in peer-reviewed journals  Unpublished data. Data belonging to unpublished research.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
EGAS00001006559 Other
EGAS00001006560 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
EGAF00007019834 vcf.gz 309.4 MB
EGAF00007019835 fastq.gz 2.3 GB
EGAF00007019836 fastq.gz 11.1 GB
EGAF00007019837 fastq.gz 5.8 GB
EGAF00007019838 fastq.gz 11.1 GB
EGAF00007019839 fastq.gz 2.0 GB
EGAF00007019840 fastq.gz 9.5 GB
EGAF00007019841 fastq.gz 5.0 GB
EGAF00007019842 fastq.gz 9.5 GB
EGAF00007019843 fastq.gz 1.9 GB
EGAF00007019844 fastq.gz 8.4 GB
EGAF00007019845 fastq.gz 4.4 GB
EGAF00007019846 fastq.gz 8.4 GB
EGAF00007019847 fastq.gz 1.8 GB
EGAF00007019848 fastq.gz 8.4 GB
EGAF00007019849 fastq.gz 4.3 GB
EGAF00007019850 fastq.gz 8.4 GB
EGAF00007019851 fastq.gz 2.0 GB
EGAF00007019852 fastq.gz 8.6 GB
EGAF00007019853 fastq.gz 4.5 GB
EGAF00007019854 fastq.gz 8.8 GB
EGAF00007019855 fastq.gz 1.7 GB
EGAF00007019856 fastq.gz 7.8 GB
EGAF00007019857 fastq.gz 4.1 GB
EGAF00007019858 fastq.gz 7.7 GB
EGAF00007019859 fastq.gz 1.6 GB
EGAF00007019860 fastq.gz 7.6 GB
EGAF00007019861 fastq.gz 4.0 GB
EGAF00007019862 fastq.gz 7.5 GB
EGAF00007019863 fastq.gz 1.9 GB
EGAF00007019864 fastq.gz 8.7 GB
EGAF00007019865 fastq.gz 4.5 GB
EGAF00007019866 fastq.gz 8.7 GB
EGAF00007019867 fastq.gz 1.8 GB
EGAF00007019868 fastq.gz 8.5 GB
EGAF00007019869 fastq.gz 4.4 GB
EGAF00007019870 fastq.gz 8.6 GB
EGAF00007019871 fastq.gz 1.8 GB
EGAF00007019872 fastq.gz 8.5 GB
EGAF00007019873 fastq.gz 4.5 GB
EGAF00007019874 fastq.gz 8.6 GB
EGAF00007019875 fastq.gz 1.9 GB
EGAF00007019876 fastq.gz 8.5 GB
EGAF00007019877 fastq.gz 4.5 GB
EGAF00007019878 fastq.gz 8.5 GB
EGAF00007019879 fastq.gz 1.9 GB
EGAF00007019880 fastq.gz 8.8 GB
EGAF00007019881 fastq.gz 4.6 GB
EGAF00007019882 fastq.gz 8.8 GB
EGAF00007019883 fastq.gz 2.0 GB
EGAF00007019884 fastq.gz 8.7 GB
EGAF00007019885 fastq.gz 4.5 GB
EGAF00007019886 fastq.gz 8.7 GB
EGAF00007019887 fastq.gz 3.2 GB
EGAF00007019888 fastq.gz 15.3 GB
EGAF00007019889 fastq.gz 7.9 GB
EGAF00007019890 fastq.gz 15.5 GB
EGAF00007019891 fastq.gz 1.7 GB
EGAF00007019892 fastq.gz 8.3 GB
EGAF00007019893 fastq.gz 4.3 GB
EGAF00007019894 fastq.gz 8.3 GB
EGAF00007019895 fastq.gz 3.7 GB
EGAF00007019896 fastq.gz 18.6 GB
EGAF00007019897 fastq.gz 9.5 GB
EGAF00007019898 fastq.gz 18.7 GB
EGAF00007019899 fastq.gz 3.4 GB
EGAF00007019900 fastq.gz 3.4 GB
EGAF00007019901 fastq.gz 12.8 GB
EGAF00007019902 fastq.gz 27.8 GB
EGAF00007019903 fastq.gz 3.4 GB
EGAF00007019904 fastq.gz 3.5 GB
EGAF00007019905 fastq.gz 13.0 GB
EGAF00007019906 fastq.gz 28.3 GB
EGAF00007019907 fastq.gz 2.6 GB
EGAF00007019908 fastq.gz 2.9 GB
EGAF00007019909 fastq.gz 9.3 GB
EGAF00007019910 fastq.gz 21.0 GB
EGAF00007019911 fastq.gz 3.1 GB
EGAF00007019912 fastq.gz 3.2 GB
EGAF00007019913 fastq.gz 11.6 GB
EGAF00007019914 fastq.gz 25.9 GB
EGAF00007019915 fastq.gz 2.6 GB
EGAF00007019916 fastq.gz 3.0 GB
EGAF00007019917 fastq.gz 9.8 GB
EGAF00007019918 fastq.gz 21.0 GB
EGAF00007019919 fastq.gz 3.3 GB
EGAF00007019920 fastq.gz 3.2 GB
EGAF00007019921 fastq.gz 11.4 GB
EGAF00007019922 fastq.gz 24.7 GB
EGAF00007019923 fastq.gz 3.5 GB
EGAF00007019924 fastq.gz 3.2 GB
EGAF00007019925 fastq.gz 11.4 GB
EGAF00007019926 fastq.gz 25.4 GB
EGAF00007019927 fastq.gz 3.2 GB
EGAF00007019928 fastq.gz 3.5 GB
EGAF00007019929 fastq.gz 12.3 GB
EGAF00007019930 fastq.gz 27.3 GB
EGAF00007019931 fastq.gz 3.5 GB
EGAF00007019932 fastq.gz 3.5 GB
EGAF00007019933 fastq.gz 12.5 GB
EGAF00007019934 fastq.gz 27.0 GB
EGAF00007019935 fastq.gz 2.6 GB
EGAF00007019936 fastq.gz 2.9 GB
EGAF00007019937 fastq.gz 10.2 GB
EGAF00007019938 fastq.gz 21.9 GB
EGAF00007019939 fastq.gz 1.6 GB
EGAF00007019940 fastq.gz 1.8 GB
EGAF00007019941 fastq.gz 5.6 GB
EGAF00007019942 fastq.gz 12.3 GB
EGAF00007019943 fastq.gz 3.3 GB
EGAF00007019944 fastq.gz 3.3 GB
EGAF00007019945 fastq.gz 11.6 GB
EGAF00007019946 fastq.gz 25.5 GB
EGAF00007019947 fastq.gz 3.2 GB
EGAF00007019948 fastq.gz 3.2 GB
EGAF00007019949 fastq.gz 11.8 GB
EGAF00007019950 fastq.gz 25.2 GB
EGAF00007019951 fastq.gz 2.5 GB
EGAF00007019952 fastq.gz 2.7 GB
EGAF00007019953 fastq.gz 8.7 GB
EGAF00007019954 fastq.gz 18.5 GB
EGAF00007019955 fastq.gz 3.4 GB
EGAF00007019956 fastq.gz 3.4 GB
EGAF00007019957 fastq.gz 12.5 GB
EGAF00007019958 fastq.gz 28.2 GB
EGAF00007019959 fastq.gz 3.4 GB
EGAF00007019960 fastq.gz 3.6 GB
EGAF00007019961 fastq.gz 13.3 GB
EGAF00007019962 fastq.gz 28.4 GB
129 Files (1.1 TB)