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RNAseq and T cell receptor (TCR) profiling of PBMC cells 3 months post Omicron exposure

This dataset contains RNA-seq and T cell receptor (TCR) sequencing files from a cohort (n=20) 3 months post positive PCR for SARS-CoV-2. A total of 10 hospitalised (samples H1-10) and 10 non-hospitalised (samples NH1-10) are contained within this dataset. RNA sequencing was performed using the Illumina Stranded mRNA Prep Ligation kit to investigate the protein coding transcriptome of PBMC cells. T cell receptor (TCR) repertoire profiling was performed with the TakaraBio SMART-Seq Human TCR (with UMIs) on PBMC cells to investigate the depth and persistence of SARS-CoV-2 targeting TCRs.

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COVRES-2 Data Access Policy

COVID Response Study 2 (COVRES-2) COVRES-2 Data Access Agreement Section I: Contact and Project Information A. Data Recipient (including contact details) Please ensure that a full postal address and a valid Institutional email address are included Name: Institution’s Legal Name: Institutional Postal Address: Institutional E-mail Address: Website of the Institution: B. Authorised Representative of the Data Recipient Name: Position: Affiliation: Institutional Postal Address: Institutional E-mail Address: C. Data Controller(s) (including contact details) Please ensure that a full postal address and a valid Institutional email address are included Name: Institution’s Legal Name: Institutional Postal Address: Institutional E-mail Address: Website of the Institution: D. Authorised Representative of the Data Controller(s) Name: Position: Affiliation: Institutional Postal Address: Institutional E-mail Address: E. Title of the Proposed Research Project F. Research Project (Scientific Abstract): Please provide a clear description of the Project, its stakeholders, its main question and its relevance to the research domain addressed, its specific aims, and duration. Note that any use of the Data, if approved, must fall under the framework of the described Project (300 words max): G. Research Credentials Please provide a list of three Publications, relevant to the Project description, of which the Data Recipient is author or co-author, and, also, attach their (Data Recipient’s) short CV. If the Data Recipient has not authored or co-authored three relevant Publications, please describe their relevant expertise or experience in no more than 150 words; also, notify how the research project will be carried out (e.g. available funding, infrastructure and so on). Section II: Data Access Agreement (DAA) Definitions GDPR: This DAA makes both parties compliant with the Regulation (EU) 2016/679 of the European Parliament and of the Council, that is, the General Data Protection Regulation (herein referred to as the ‘GDPR’) and the UK General Data Protection Regulation (‘UK GDPR’). ,2 Data: Refers to controlled access data (the Data). Under this Agreement, the Data is pseudonymised. Data Access/Transfer: Refers to an Institution’s right to request access to the Data and retrieve them from the Data Controller’s Institution upon approval of this DAA by the corresponding Data Access Committee (DAC) within the Data Controller’s Institution. Data Handling: Refers to an Institution’s ability to analyse and manipulate the Data within its own computer network. Data Controller(s): Refers to an Institution, responsible for the generation of the Data and its pseudonymisation. A key-code permitting relinkage to Data Subjects is kept by the Data Controller(s). Data Subject: Refers to any individual who is the source of any Data covered by this Agreement. Data Recipient (‘You’): Refers to the Institution who requests Access to the Data through this Agreement. Authorised Personnel: The individual(s) at the Institution requesting Access to the Data. Research Project: The Project for which You have requested Access to the Data. Publications: Refers, without limitation, to any and all articles published in print journals, electronic journals, reviews, books, posters, and other written and verbal presentations of Research that have been accepted by peer review. EU-STANDS4PM: This DAA was adapted from the harmonised data access agreement (hDAA) developed by the EU-STANDS4PM, https://www.eu-stands4pm.eu/ Terms and Conditions In signing this Agreement: 1. You, the Data Recipient, agree to only use the Data for the Purpose of the Project. 2. You agree to preserve, at all times, the confidentiality of information and Data pertaining to Data Subjects. You undertake not to use or attempt to use the Data to compromise or otherwise infringe the confidentiality of information on Data Subjects and their data protection rights. 3. You agree to comply with your obligations pursuant to GDPR and UK GDPR in your processing of the Data. 4. You agree not to attempt to identify Data Subjects. 5. You and your Authorised Personnel agree to take into consideration any usage restrictions (if any), stemming from consent, i.e. the appropriate lawful basis for processing the Data, as well as any usage restrictions stemming from any applicable internal policies of your Institution. 6. You agree that in handling this Data You will follow an up-to-date information technology (IT) policy that must include, at a minimum, the following items: a. Logging and auditing of Access to the Data and to the computer network; b. Password protection to computer network and/or strong data encryption; c. Virus and malware protection to computers on the computer network; d. Secure backup procedure; 7. You acknowledge that Access to the Data is granted for the duration of the Project described in Section I, as well as any new Project under the same research field or area. Any use of the Data for a Project of another research field or area will need to be approved under a new Agreement. 8. You recognize that nothing in this Agreement shall operate to transfer to You any intellectual property rights to the Data. 9. You agree not to make intellectual property claims on the Data and not to use intellectual property protection in ways that would prevent or block Access to, or use of, any element of the Data. 10. You can elect to perform further Research that would add intellectual and resource capital to the Data, and decide to obtain intellectual property rights on these downstream discoveries. In this case, You agree to implement licensing policies that will not obstruct further Research, following the Organisation for Economic Co-operation and Development Guidelines. 11. You agree that the Research Project 1) bears no legal responsibility for the accuracy or comprehensiveness of the Data; 2) accepts no liability for indirect, consequential, or incidental damages or losses arising from use of the Data; and 3) bears no responsibility for the further analysis or interpretation of these Data over and above that published by the Controller(s). 12. You agree to hold the Data Subject(s) and Data Controller(s) harmless and to defend and indemnify all these parties against all liabilities, demands, damages, expenses, and losses arising out of Your use for any Purpose of the Data. 13. You agree to a moratorium on publishing global analyses of the dataset until the Data Controller(s) have published their own global analysis or twelve (12) months, the maximum, have passed from the time the Data were deposited, whichever occurs first. You acknowledge that prompt publication or public disclosure of the results of the Research Project is encouraged. You also agree that by publishing Your global analyses of the Data, you will not disclose any results generated from the Data. 14. You agree to acknowledge the contribution of the Data Controller(s) in all oral and written presentations, disclosures, and Publications resulting from all analyses of the Data. 15. You agree to use the Data in Your laboratory. Any Authorised Personnel shall work under Your direct supervision. You agree to distribute a copy of these terms to the Authorised Personnel. 16. You may not transfer any information included in the Data to anyone unless specifically designated in the Research Project, or by prior specific or general written authorisation of the Data Controller(s) responsible for the generation of the original Data in each case. 17. You may not transfer the Data itself to anyone outside the Institution, unless the Controller(s) has (have) approved such transfer and its terms in writing. 18. Should You wish to share the Data with an external collaborator, the external collaborator must complete a separate Data Access Agreement. 19. You shall ensure that ‘all’ who have Access to the Data, namely You and Your Authorised Personnel, will be listed out, and are made aware and be bound by the terms of this Agreement. You remain solely and fully responsible for Your Authorised Personnel’s non-compliance with the provision of the Agreement and/or applicable laws. 20. In case of a breach of security resulting from ‘accidental’ use of Data by You and Your Authorised Personnel, which leads to disclosure of Data, then You must report this to Data Controller(s) within 48 hours maximum, and follow any requirements provided by the GDPR and UK GDPR. 21. In case of a ‘non-accidental or minor’ breach of hDAA by You, You will further be required to destroy any Data held. 22. You accept that this Agreement will terminate immediately upon ‘any’ breach by You, or its termination (see Section I). 23. You endeavour to settle any dispute with the Data Controller(s) amicably. If you are unable to reach an Agreement, you will meet and negotiate in good faith in an effort to resolve the issue. If the issue has not been resolved within a reasonable period (e.g. 30 calendar days), you are both entitled to submit it for resolution by an arbitrator. 24. Further, the language of the proceedings will be ‘English’ if not otherwise agreed. The award of the arbitration will be final and binding upon the parties concerned. 25. This Agreement (and any dispute, controversy, proceedings, or claim of whatever nature arising out of it or its formation) shall be interpreted, governed by and construed in accordance with the Laws of Northern Ireland, and shall be subject to the exclusive jurisdiction of the Courts of Northern Ireland. Agreement I have read, understood and agree to abide by the terms and conditions stipulated in this Data Access Agreement. Data Recipient or Authorised Representative of the Data Recipient: Name: Title and position (if applicable): Affiliation (if applicable): Signature: _____________________________________Date: _____________________ Data Controller(s) or Authorised Representative of the Data Controller(s): Name: Title and position (if applicable): Affiliation (if applicable): Signature: _____________________________________Date: ______________________

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
EGAS50000000926 RNASeq

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
EGAF50000330170 fastq.gz 173.7 MB
EGAF50000330171 fastq.gz 157.9 MB
EGAF50000330172 fastq.gz 379.4 MB
EGAF50000330173 fastq.gz 414.2 MB
EGAF50000330174 fastq.gz 451.1 MB
EGAF50000330175 fastq.gz 501.3 MB
EGAF50000330176 fastq.gz 1.1 GB
EGAF50000330177 fastq.gz 116.0 MB
EGAF50000330178 fastq.gz 126.7 MB
EGAF50000330179 fastq.gz 1.2 GB
EGAF50000330180 fastq.gz 857.0 MB
EGAF50000330181 fastq.gz 913.4 MB
EGAF50000330182 fastq.gz 261.2 MB
EGAF50000330183 fastq.gz 287.1 MB
EGAF50000330184 fastq.gz 624.4 MB
EGAF50000330185 fastq.gz 673.0 MB
EGAF50000330186 fastq.gz 894.1 MB
EGAF50000330187 fastq.gz 938.4 MB
EGAF50000330188 fastq.gz 849.6 MB
EGAF50000330189 fastq.gz 909.3 MB
EGAF50000330190 fastq.gz 808.0 MB
EGAF50000330191 fastq.gz 285.0 MB
EGAF50000330192 fastq.gz 300.1 MB
EGAF50000330193 fastq.gz 29.4 MB
EGAF50000330194 fastq.gz 32.4 MB
EGAF50000330195 fastq.gz 52.1 MB
EGAF50000330196 fastq.gz 59.5 MB
EGAF50000330197 fastq.gz 855.4 MB
EGAF50000330198 fastq.gz 88.8 MB
EGAF50000330199 fastq.gz 98.4 MB
EGAF50000330200 fastq.gz 128.9 MB
EGAF50000330201 fastq.gz 68.4 MB
EGAF50000330202 fastq.gz 76.6 MB
EGAF50000330203 fastq.gz 142.5 MB
EGAF50000330204 fastq.gz 413.5 MB
EGAF50000330205 fastq.gz 451.5 MB
EGAF50000330206 fastq.gz 728.0 MB
EGAF50000330207 fastq.gz 784.3 MB
EGAF50000330208 fastq.gz 53.8 MB
EGAF50000330209 fastq.gz 59.5 MB
EGAF50000330210 fastq.gz 239.6 MB
EGAF50000330211 fastq.gz 238.8 MB
EGAF50000330212 fastq.gz 299.8 MB
EGAF50000330213 fastq.gz 303.7 MB
EGAF50000330214 fastq.gz 526.0 MB
EGAF50000330215 fastq.gz 510.3 MB
EGAF50000330216 fastq.gz 87.4 MB
EGAF50000330217 fastq.gz 86.8 MB
EGAF50000330218 fastq.gz 608.0 MB
EGAF50000330219 fastq.gz 619.1 MB
EGAF50000330220 fastq.gz 143.8 MB
EGAF50000330221 fastq.gz 142.1 MB
EGAF50000330222 fastq.gz 205.0 MB
EGAF50000330223 fastq.gz 202.7 MB
EGAF50000330224 fastq.gz 1.0 GB
EGAF50000330225 fastq.gz 992.4 MB
EGAF50000330226 fastq.gz 583.7 MB
EGAF50000330227 fastq.gz 574.5 MB
EGAF50000330228 fastq.gz 665.9 MB
EGAF50000330229 fastq.gz 209.0 MB
EGAF50000330230 fastq.gz 651.8 MB
EGAF50000330231 fastq.gz 116.3 MB
EGAF50000330232 fastq.gz 209.3 MB
EGAF50000330233 fastq.gz 115.4 MB
EGAF50000330234 fastq.gz 138.9 MB
EGAF50000330235 fastq.gz 138.3 MB
EGAF50000330236 fastq.gz 202.1 MB
EGAF50000330237 fastq.gz 205.9 MB
EGAF50000330238 fastq.gz 193.7 MB
EGAF50000330239 fastq.gz 192.8 MB
EGAF50000330240 fastq.gz 102.8 MB
EGAF50000330241 fastq.gz 102.3 MB
EGAF50000330242 fastq.gz 596.0 MB
EGAF50000330243 fastq.gz 579.5 MB
EGAF50000330244 fastq.gz 1.1 GB
EGAF50000330245 fastq.gz 124.1 MB
EGAF50000330246 fastq.gz 1.1 GB
EGAF50000330247 fastq.gz 123.0 MB
EGAF50000330248 bai 2.7 MB
EGAF50000330249 md5sum 184 Bytes
EGAF50000330250 bam 464.1 MB
EGAF50000330251 md5sum 184 Bytes
EGAF50000330252 bai 3.9 MB
EGAF50000330253 bam 659.4 MB
EGAF50000330254 bai 4.5 MB
EGAF50000330255 md5sum 184 Bytes
EGAF50000330256 bam 179.9 MB
EGAF50000330257 bai 2.4 MB
EGAF50000330258 md5sum 184 Bytes
EGAF50000330259 bam 1.3 GB
EGAF50000330260 bai 4.4 MB
EGAF50000330261 md5sum 184 Bytes
EGAF50000330262 bam 313.3 MB
EGAF50000330263 md5sum 184 Bytes
EGAF50000330264 bai 2.9 MB
EGAF50000330265 bam 1.4 GB
EGAF50000330266 md5sum 184 Bytes
EGAF50000330267 bai 3.3 MB
EGAF50000330268 bam 464.2 MB
EGAF50000330269 bai 5.3 MB
EGAF50000330270 md5sum 184 Bytes
EGAF50000330271 bam 1.3 GB
EGAF50000330272 md5sum 184 Bytes
EGAF50000330273 bai 4.4 MB
EGAF50000330274 bam 2.4 GB
EGAF50000330275 bai 4.7 MB
EGAF50000330276 md5sum 184 Bytes
EGAF50000330277 bam 448.4 MB
EGAF50000330278 md5sum 184 Bytes
EGAF50000330279 bai 3.5 MB
EGAF50000330280 bam 1.6 GB
EGAF50000330281 bai 2.0 MB
EGAF50000330282 bam 247.0 MB
EGAF50000330283 md5sum 184 Bytes
EGAF50000330284 bai 2.4 MB
EGAF50000330285 md5sum 184 Bytes
EGAF50000330286 bam 291.9 MB
EGAF50000330287 bai 2.8 MB
EGAF50000330288 md5sum 184 Bytes
EGAF50000330289 bai 2.6 MB
EGAF50000330290 md5sum 184 Bytes
EGAF50000330291 bam 393.4 MB
EGAF50000330292 bam 197.2 MB
EGAF50000330293 bai 2.7 MB
EGAF50000330294 md5sum 184 Bytes
EGAF50000330295 bam 379.4 MB
EGAF50000330296 bai 5.1 MB
EGAF50000330297 md5sum 184 Bytes
EGAF50000330298 bam 1.5 GB
EGAF50000330299 bai 5.5 MB
EGAF50000330300 md5sum 184 Bytes
EGAF50000330301 bam 250.4 MB
EGAF50000330302 bai 3.1 MB
EGAF50000330303 md5sum 184 Bytes
EGAF50000330304 bam 2.7 GB
135 Files (48.2 GB)