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The BNT162b2 mRNA COVID-19 vaccine induces long-term effects on both adaptive and innate immune responses

This dataset contains bulk RNA sequencing at different timepoints post-BNT162b2 mRNA COVID-19 vaccination. Stimulation experiments were performed at each of the timepoints (RPMI, Influenza, R848 and Influenza stimuli), resulting in 242 libraries distributed over 4 stimulations and 4 timepoints. Libraries were sequenced on the DBNSEQ platform.

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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 Data belonging to research published in peer-reviewed journals  Unpublished data. Data belonging to unpublished research.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
EGAS00001006818 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
EGAF00008093951 fq.gz 2.0 GB
EGAF00008093952 fq.gz 2.0 GB
EGAF00008093953 fq.gz 1.6 GB
EGAF00008093954 fq.gz 1.7 GB
EGAF00008093955 fq.gz 1.9 GB
EGAF00008093956 fq.gz 2.0 GB
EGAF00008093957 fq.gz 1.9 GB
EGAF00008093958 fq.gz 2.0 GB
EGAF00008093959 fq.gz 1.9 GB
EGAF00008093960 fq.gz 2.0 GB
EGAF00008093961 fq.gz 1.9 GB
EGAF00008093962 fq.gz 2.0 GB
EGAF00008093963 fq.gz 1.9 GB
EGAF00008093964 fq.gz 2.0 GB
EGAF00008093965 fq.gz 2.1 GB
EGAF00008093966 fq.gz 2.1 GB
EGAF00008093967 fq.gz 2.0 GB
EGAF00008093968 fq.gz 2.1 GB
EGAF00008093969 fq.gz 2.1 GB
EGAF00008093970 fq.gz 2.2 GB
EGAF00008093971 fq.gz 1.9 GB
EGAF00008093972 fq.gz 2.0 GB
EGAF00008093973 fq.gz 2.0 GB
EGAF00008093974 fq.gz 2.1 GB
EGAF00008093975 fq.gz 1.9 GB
EGAF00008093976 fq.gz 2.0 GB
EGAF00008093977 fq.gz 1.9 GB
EGAF00008093978 fq.gz 2.0 GB
EGAF00008093979 fq.gz 1.9 GB
EGAF00008093980 fq.gz 2.0 GB
EGAF00008093981 fq.gz 1.9 GB
EGAF00008093982 fq.gz 2.0 GB
EGAF00008093983 fq.gz 1.9 GB
EGAF00008093984 fq.gz 2.0 GB
EGAF00008093985 fq.gz 1.9 GB
EGAF00008093986 fq.gz 2.0 GB
EGAF00008093987 fq.gz 1.9 GB
EGAF00008093988 fq.gz 2.0 GB
EGAF00008093989 fq.gz 1.9 GB
EGAF00008093990 fq.gz 2.0 GB
EGAF00008093991 fq.gz 1.9 GB
EGAF00008093992 fq.gz 2.0 GB
EGAF00008093993 fq.gz 1.9 GB
EGAF00008093994 fq.gz 2.0 GB
EGAF00008093995 fq.gz 1.9 GB
EGAF00008093996 fq.gz 2.0 GB
EGAF00008093997 fq.gz 1.9 GB
EGAF00008093998 fq.gz 2.0 GB
EGAF00008093999 fq.gz 1.9 GB
EGAF00008094000 fq.gz 2.0 GB
EGAF00008094001 fq.gz 1.9 GB
EGAF00008094002 fq.gz 2.0 GB
EGAF00008094003 fq.gz 1.9 GB
EGAF00008094004 fq.gz 2.0 GB
EGAF00008094005 fq.gz 1.9 GB
EGAF00008094006 fq.gz 2.0 GB
EGAF00008094007 fq.gz 1.9 GB
EGAF00008094008 fq.gz 2.0 GB
EGAF00008094009 fq.gz 1.9 GB
EGAF00008094010 fq.gz 1.9 GB
EGAF00008094011 fq.gz 1.9 GB
EGAF00008094012 fq.gz 2.0 GB
EGAF00008094013 fq.gz 1.9 GB
EGAF00008094014 fq.gz 1.9 GB
EGAF00008094015 fq.gz 1.9 GB
EGAF00008094016 fq.gz 2.0 GB
EGAF00008094017 fq.gz 1.9 GB
EGAF00008094018 fq.gz 2.1 GB
EGAF00008094019 fq.gz 1.9 GB
EGAF00008094020 fq.gz 2.0 GB
EGAF00008094021 fq.gz 1.9 GB
EGAF00008094022 fq.gz 2.1 GB
EGAF00008094023 fq.gz 1.9 GB
EGAF00008094024 fq.gz 2.0 GB
EGAF00008094025 fq.gz 1.9 GB
EGAF00008094026 fq.gz 2.0 GB
EGAF00008094027 fq.gz 1.9 GB
EGAF00008094028 fq.gz 2.0 GB
EGAF00008094029 fq.gz 1.9 GB
EGAF00008094030 fq.gz 2.0 GB
EGAF00008094031 fq.gz 1.9 GB
EGAF00008094032 fq.gz 2.0 GB
EGAF00008094033 fq.gz 1.9 GB
EGAF00008094034 fq.gz 2.0 GB
EGAF00008094035 fq.gz 1.9 GB
EGAF00008094036 fq.gz 2.0 GB
EGAF00008094037 fq.gz 1.9 GB
EGAF00008094038 fq.gz 2.0 GB
EGAF00008094039 fq.gz 1.9 GB
EGAF00008094040 fq.gz 2.0 GB
EGAF00008094041 fq.gz 1.9 GB
EGAF00008094042 fq.gz 2.0 GB
EGAF00008094043 fq.gz 1.9 GB
EGAF00008094044 fq.gz 2.0 GB
EGAF00008094045 fq.gz 1.9 GB
EGAF00008094046 fq.gz 2.0 GB
EGAF00008094047 fq.gz 1.9 GB
EGAF00008094048 fq.gz 2.0 GB
EGAF00008094049 fq.gz 1.9 GB
EGAF00008094050 fq.gz 2.0 GB
EGAF00008094051 fq.gz 1.9 GB
EGAF00008094052 fq.gz 2.0 GB
EGAF00008094053 fq.gz 1.9 GB
EGAF00008094054 fq.gz 2.0 GB
EGAF00008094055 fq.gz 1.9 GB
EGAF00008094056 fq.gz 2.0 GB
EGAF00008094057 fq.gz 1.9 GB
EGAF00008094058 fq.gz 2.0 GB
EGAF00008094059 fq.gz 1.9 GB
EGAF00008094060 fq.gz 2.0 GB
EGAF00008094061 fq.gz 1.9 GB
EGAF00008094062 fq.gz 2.0 GB
EGAF00008094063 fq.gz 1.9 GB
EGAF00008094064 fq.gz 2.0 GB
EGAF00008094065 fq.gz 1.9 GB
EGAF00008094066 fq.gz 2.0 GB
EGAF00008094067 fq.gz 1.9 GB
EGAF00008094068 fq.gz 2.0 GB
EGAF00008094069 fq.gz 1.9 GB
EGAF00008094070 fq.gz 2.0 GB
EGAF00008094071 fq.gz 1.9 GB
EGAF00008094072 fq.gz 2.1 GB
EGAF00008094073 fq.gz 1.9 GB
EGAF00008094074 fq.gz 2.0 GB
EGAF00008094075 fq.gz 1.9 GB
EGAF00008094076 fq.gz 2.0 GB
EGAF00008094077 fq.gz 2.0 GB
EGAF00008094078 fq.gz 2.0 GB
EGAF00008094079 fq.gz 1.9 GB
EGAF00008094080 fq.gz 2.0 GB
EGAF00008094081 fq.gz 1.9 GB
EGAF00008094082 fq.gz 2.0 GB
EGAF00008094083 fq.gz 1.9 GB
EGAF00008094084 fq.gz 2.0 GB
EGAF00008094085 fq.gz 1.9 GB
EGAF00008094086 fq.gz 2.0 GB
EGAF00008094087 fq.gz 2.0 GB
EGAF00008094088 fq.gz 2.0 GB
EGAF00008094089 fq.gz 276.8 MB
EGAF00008094090 fq.gz 295.4 MB
EGAF00008094091 fq.gz 1.9 GB
EGAF00008094092 fq.gz 2.0 GB
EGAF00008094093 fq.gz 1.9 GB
EGAF00008094094 fq.gz 2.0 GB
EGAF00008094095 fq.gz 1.9 GB
EGAF00008094096 fq.gz 2.0 GB
EGAF00008094097 fq.gz 1.9 GB
EGAF00008094098 fq.gz 2.0 GB
EGAF00008094099 fq.gz 1.9 GB
EGAF00008094100 fq.gz 2.0 GB
EGAF00008094101 fq.gz 1.9 GB
EGAF00008094102 fq.gz 2.0 GB
EGAF00008094103 fq.gz 1.9 GB
EGAF00008094104 fq.gz 2.0 GB
EGAF00008094105 fq.gz 112.3 MB
EGAF00008094106 fq.gz 118.3 MB
EGAF00008094107 fq.gz 1.9 GB
EGAF00008094108 fq.gz 2.0 GB
EGAF00008094109 fq.gz 1.9 GB
EGAF00008094110 fq.gz 2.0 GB
EGAF00008094111 fq.gz 1.9 GB
EGAF00008094112 fq.gz 2.0 GB
EGAF00008094113 fq.gz 1.9 GB
EGAF00008094114 fq.gz 2.0 GB
EGAF00008094115 fq.gz 1.9 GB
EGAF00008094116 fq.gz 2.0 GB
EGAF00008094117 fq.gz 1.9 GB
EGAF00008094118 fq.gz 2.0 GB
EGAF00008094119 fq.gz 1.9 GB
EGAF00008094120 fq.gz 2.0 GB
EGAF00008094121 fq.gz 1.9 GB
EGAF00008094122 fq.gz 2.0 GB
EGAF00008094123 fq.gz 1.9 GB
EGAF00008094124 fq.gz 2.0 GB
EGAF00008094125 fq.gz 1.9 GB
EGAF00008094126 fq.gz 2.0 GB
EGAF00008094127 fq.gz 1.9 GB
EGAF00008094128 fq.gz 2.0 GB
EGAF00008094129 fq.gz 1.9 GB
EGAF00008094130 fq.gz 2.0 GB
EGAF00008094131 fq.gz 1.9 GB
EGAF00008094132 fq.gz 2.0 GB
EGAF00008094133 fq.gz 1.9 GB
EGAF00008094134 fq.gz 2.0 GB
EGAF00008094135 fq.gz 1.8 GB
EGAF00008094136 fq.gz 1.8 GB
EGAF00008094137 fq.gz 1.9 GB
EGAF00008094138 fq.gz 2.0 GB
EGAF00008094139 fq.gz 1.9 GB
EGAF00008094140 fq.gz 2.0 GB
EGAF00008094141 fq.gz 1.9 GB
EGAF00008094142 fq.gz 2.0 GB
EGAF00008094143 fq.gz 1.9 GB
EGAF00008094144 fq.gz 2.1 GB
EGAF00008094145 fq.gz 1.9 GB
EGAF00008094146 fq.gz 2.0 GB
EGAF00008094147 fq.gz 1.9 GB
EGAF00008094148 fq.gz 2.0 GB
EGAF00008094149 fq.gz 1.9 GB
EGAF00008094150 fq.gz 2.0 GB
EGAF00008094151 fq.gz 1.9 GB
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EGAF00008094158 fq.gz 2.0 GB
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EGAF00008094161 fq.gz 1.9 GB
EGAF00008094162 fq.gz 2.0 GB
EGAF00008094163 fq.gz 1.9 GB
EGAF00008094164 fq.gz 2.0 GB
EGAF00008094165 fq.gz 1.9 GB
EGAF00008094166 fq.gz 2.0 GB
EGAF00008094167 fq.gz 1.9 GB
EGAF00008094168 fq.gz 2.0 GB
EGAF00008094169 fq.gz 1.9 GB
EGAF00008094170 fq.gz 2.0 GB
EGAF00008094171 fq.gz 1.9 GB
EGAF00008094172 fq.gz 2.0 GB
EGAF00008094173 fq.gz 1.9 GB
EGAF00008094174 fq.gz 2.0 GB
EGAF00008094175 fq.gz 2.1 GB
EGAF00008094176 fq.gz 2.1 GB
EGAF00008094177 fq.gz 1.9 GB
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EGAF00008094179 fq.gz 1.9 GB
EGAF00008094180 fq.gz 2.0 GB
EGAF00008094181 fq.gz 1.9 GB
EGAF00008094182 fq.gz 2.0 GB
EGAF00008094183 fq.gz 2.0 GB
EGAF00008094184 fq.gz 2.0 GB
EGAF00008094185 fq.gz 1.9 GB
EGAF00008094186 fq.gz 2.0 GB
EGAF00008094187 fq.gz 2.0 GB
EGAF00008094188 fq.gz 2.0 GB
EGAF00008094189 fq.gz 1.9 GB
EGAF00008094190 fq.gz 2.0 GB
EGAF00008094191 fq.gz 2.0 GB
EGAF00008094192 fq.gz 2.0 GB
EGAF00008094193 fq.gz 2.0 GB
EGAF00008094194 fq.gz 2.0 GB
EGAF00008094195 fq.gz 1.9 GB
EGAF00008094196 fq.gz 2.1 GB
EGAF00008094197 fq.gz 1.9 GB
EGAF00008094198 fq.gz 2.1 GB
EGAF00008094199 fq.gz 2.0 GB
EGAF00008094200 fq.gz 2.1 GB
EGAF00008094201 fq.gz 1.9 GB
EGAF00008094202 fq.gz 2.1 GB
EGAF00008094203 fq.gz 1.9 GB
EGAF00008094204 fq.gz 2.0 GB
EGAF00008094205 fq.gz 2.0 GB
EGAF00008094206 fq.gz 2.0 GB
EGAF00008094207 fq.gz 1.9 GB
EGAF00008094208 fq.gz 2.0 GB
EGAF00008094209 fq.gz 2.0 GB
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EGAF00008094211 fq.gz 2.0 GB
EGAF00008094212 fq.gz 2.1 GB
EGAF00008094213 fq.gz 1.5 GB
EGAF00008094214 fq.gz 1.6 GB
EGAF00008094215 fq.gz 1.9 GB
EGAF00008094216 fq.gz 2.0 GB
EGAF00008094217 fq.gz 176.9 MB
EGAF00008094218 fq.gz 187.2 MB
EGAF00008094219 fq.gz 1.9 GB
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EGAF00008094223 fq.gz 1.9 GB
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EGAF00008094252 fq.gz 2.0 GB
EGAF00008094253 fq.gz 1.9 GB
EGAF00008094254 fq.gz 2.0 GB
EGAF00008094255 fq.gz 2.0 GB
EGAF00008094256 fq.gz 2.0 GB
EGAF00008094257 fq.gz 1.9 GB
EGAF00008094258 fq.gz 1.9 GB
EGAF00008094259 fq.gz 2.0 GB
EGAF00008094260 fq.gz 2.0 GB
EGAF00008094261 fq.gz 2.1 GB
EGAF00008094262 fq.gz 2.1 GB
EGAF00008094263 fq.gz 1.9 GB
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EGAF00008094267 fq.gz 2.1 GB
EGAF00008094268 fq.gz 2.1 GB
EGAF00008094269 fq.gz 1.9 GB
EGAF00008094270 fq.gz 2.0 GB
EGAF00008094271 fq.gz 2.0 GB
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EGAF00008094273 fq.gz 1.9 GB
EGAF00008094274 fq.gz 2.0 GB
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EGAF00008094277 fq.gz 1.9 GB
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EGAF00008094283 fq.gz 1.9 GB
EGAF00008094284 fq.gz 2.0 GB
EGAF00008094285 fq.gz 1.9 GB
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EGAF00008094287 fq.gz 1.9 GB
EGAF00008094288 fq.gz 1.9 GB
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EGAF00008094290 fq.gz 1.9 GB
EGAF00008094291 fq.gz 137.7 MB
EGAF00008094292 fq.gz 143.0 MB
EGAF00008094293 fq.gz 1.5 GB
EGAF00008094294 fq.gz 1.5 GB
EGAF00008094295 fq.gz 177.8 MB
EGAF00008094296 fq.gz 182.1 MB
EGAF00008094297 fq.gz 190.0 MB
EGAF00008094298 fq.gz 199.4 MB
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EGAF00008094300 fq.gz 186.2 MB
EGAF00008094301 fq.gz 63.3 MB
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EGAF00008094303 fq.gz 232.7 MB
EGAF00008094304 fq.gz 242.9 MB
EGAF00008094305 fq.gz 1.8 GB
EGAF00008094306 fq.gz 1.9 GB
EGAF00008094307 fq.gz 1.8 GB
EGAF00008094308 fq.gz 1.9 GB
EGAF00008094309 fq.gz 173.2 MB
EGAF00008094310 fq.gz 182.8 MB
EGAF00008094311 fq.gz 137.9 MB
EGAF00008094312 fq.gz 143.7 MB
EGAF00008094313 fq.gz 1.8 GB
EGAF00008094314 fq.gz 1.9 GB
EGAF00008094315 fq.gz 1.9 GB
EGAF00008094316 fq.gz 2.0 GB
EGAF00008094317 fq.gz 1.9 GB
EGAF00008094318 fq.gz 1.9 GB
EGAF00008094319 fq.gz 1.9 GB
EGAF00008094320 fq.gz 2.0 GB
EGAF00008094321 fq.gz 1.9 GB
EGAF00008094322 fq.gz 1.9 GB
EGAF00008094323 fq.gz 1.5 GB
EGAF00008094324 fq.gz 1.5 GB
EGAF00008094325 fq.gz 1.8 GB
EGAF00008094326 fq.gz 1.8 GB
EGAF00008094327 fq.gz 1.9 GB
EGAF00008094328 fq.gz 1.9 GB
EGAF00008094329 fq.gz 1.9 GB
EGAF00008094330 fq.gz 1.9 GB
EGAF00008094331 fq.gz 1.9 GB
EGAF00008094332 fq.gz 1.9 GB
EGAF00008094333 fq.gz 1.8 GB
EGAF00008094334 fq.gz 1.9 GB
EGAF00008094335 fq.gz 1.8 GB
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484 Files (893.6 GB)