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Gut microbiome of BA patients and normal controls

Metagenomic sequencing data of human gut microbiome

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The individuals at the User Institution to whom Dr. Jorge Bezerra and Dr. Shaotao Tang grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II.

1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use these Data for Research Purposes which are within the limitations (if any) set out in Appendix I. 2. The User Institution agrees to preserve, at all times, the confidentiality of these Data. In particular, it undertakes not to use, or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect these Data. 3. The User Institution agrees to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking all reasonable care to limit the possibility of identification. 4. The User Institution agrees not to link or combine these Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been formally granted to the User Institution or is freely available without restriction. 5. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate application for access to these Data. 6. The User Institution agrees that the Data Producers, and all other parties involved in the creation, funding or protection of these Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of these Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the Recipient that may arise (whether directly or indirectly) in any way whatsoever from the Recipient’s use of these Data or from the unavailability of, or break in access to, these Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of these Data. 7. The User Institution agrees to follow the Fort Lauderdale Guidelines ( ) and the Toronto Statement ( This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 8. The User Institution agrees to follow the Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 9. The User Institution agrees not to make intellectual property claims on these Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of these Data, or conclusion drawn directly from these Data. 10. The User Institution can elect to perform further research that would add intellectual and resource capital to these data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution agrees to implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) ( ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) ( ). 11. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the data for archival purposes in conformity with audit or legal requirements. 12. The User Institution will notify Dr. Jorge Bezerra and Dr. Shaotao Tang within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Dr. Jorge Bezerra and Dr. Shaotao Tang prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Dr. Jorge Bezerra and Dr. Shaotao Tang as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Dr. Jorge Bezerra and Dr. Shaotao Tang may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 16. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than Dr. Jorge Bezerra and Dr. Shaotao Tang. In the event that changes are required, the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 17. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorised Personnel. The User Institution will procure that the Authorised Personnel comply with the terms of this agreement. 19. This agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this agreement or its formation) shall be construed, interpreted and governed by the laws of England and Wales and shall be subject to the exclusive jurisdiction of the English courts. Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Jorge Bezerra Title: Director, Division of Gastroenterology, Hepatology and Nutrition; Medical Director, Pediatric Liver Care Center Date: Co-Principal Investigator Signature: Name: Shaotao Tang Title: Chief of Department of Pediatric Surgery Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) Name of project that created the dataset Human gut microbiome in babies with biliary atresia and normal controls File access: Data can be held in unencrypted files on an institutional compute system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should have password protected logins and screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. APPENDIX II – PROJECT DETAILS Details of dataset requested i.e., EGA Study and Dataset Accession Number Brief abstract of the Project in which the Data will be used (500 words max) The early onset of disease and the lack of genetic defects in most patients raise the possibility that other prenatal factors influence susceptibility of disease. Here, we test the hypothesis that the composition and function of the intestinal microbiome differs in biliary atresia patients and normal controls. All Individuals who the User Institution to be named as registered users Name of Registered User Email Job Title Supervisor* Li Yang Research associate Dr. Jorge Bezerra APPENDIX III – PUBLICATION POLICY Dr. Jorge Bezerra and Dr. Shaotao Tang intend to publish the results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. Dr. Jorge Bezerra and Dr. Shaotao Tang anticipate that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication should not occur unless Dr. Jorge Bezerra and Dr. Shaotao Tang has provided written consent to earlier submission. In any publications based on these data, please describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (e.g., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with Dr. Jorge Bezerra and Dr. Shaotao Tang.

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
EGAS00001005350 Metagenomics
ID File Type Size Located in
EGAF00005309095 fastq.gz 3.2 GB
EGAF00005309096 fastq.gz 3.4 GB
EGAF00005309097 fastq.gz 3.1 GB
EGAF00005309098 fastq.gz 3.2 GB
EGAF00005309099 fastq.gz 3.2 GB
EGAF00005309100 fastq.gz 3.4 GB
EGAF00005309101 fastq.gz 3.2 GB
EGAF00005309102 fastq.gz 3.3 GB
EGAF00005309103 fastq.gz 3.1 GB
EGAF00005309104 fastq.gz 3.1 GB
EGAF00005309105 fastq.gz 3.0 GB
EGAF00005309106 fastq.gz 3.1 GB
EGAF00005309107 fastq.gz 3.0 GB
EGAF00005309108 fastq.gz 3.1 GB
EGAF00005309109 fastq.gz 3.2 GB
EGAF00005309110 fastq.gz 3.2 GB
EGAF00005309111 fastq.gz 3.0 GB
EGAF00005309112 fastq.gz 3.1 GB
EGAF00005309113 fastq.gz 3.0 GB
EGAF00005309114 fastq.gz 3.1 GB
EGAF00005309115 fastq.gz 2.8 GB
EGAF00005309116 fastq.gz 2.8 GB
EGAF00005309117 fastq.gz 2.9 GB
EGAF00005309118 fastq.gz 3.0 GB
EGAF00005309119 fastq.gz 3.0 GB
EGAF00005309120 fastq.gz 3.0 GB
EGAF00005309121 fastq.gz 3.1 GB
EGAF00005309122 fastq.gz 3.2 GB
EGAF00005309123 fastq.gz 3.1 GB
EGAF00005309124 fastq.gz 3.2 GB
EGAF00005309125 fastq.gz 3.1 GB
EGAF00005309126 fastq.gz 3.2 GB
EGAF00005309127 fastq.gz 3.2 GB
EGAF00005309128 fastq.gz 3.3 GB
EGAF00005309129 fastq.gz 3.1 GB
EGAF00005309130 fastq.gz 3.2 GB
EGAF00005309131 fastq.gz 3.1 GB
EGAF00005309132 fastq.gz 3.1 GB
EGAF00005309133 fastq.gz 3.1 GB
EGAF00005309134 fastq.gz 3.2 GB
EGAF00005309135 fastq.gz 2.8 GB
EGAF00005309136 fastq.gz 3.0 GB
EGAF00005309137 fastq.gz 3.1 GB
EGAF00005309138 fastq.gz 3.2 GB
EGAF00005309139 fastq.gz 3.0 GB
EGAF00005309140 fastq.gz 3.1 GB
EGAF00005309141 fastq.gz 3.1 GB
EGAF00005309142 fastq.gz 3.2 GB
EGAF00005309143 fastq.gz 3.0 GB
EGAF00005309144 fastq.gz 3.0 GB
EGAF00005309145 fastq.gz 3.2 GB
EGAF00005309146 fastq.gz 3.2 GB
EGAF00005309147 fastq.gz 3.1 GB
EGAF00005309148 fastq.gz 3.2 GB
EGAF00005309149 fastq.gz 3.1 GB
EGAF00005309150 fastq.gz 3.2 GB
EGAF00005309151 fastq.gz 3.0 GB
EGAF00005309152 fastq.gz 3.2 GB
EGAF00005309153 fastq.gz 3.1 GB
EGAF00005309154 fastq.gz 3.1 GB
EGAF00005309155 fastq.gz 3.2 GB
EGAF00005309156 fastq.gz 3.5 GB
EGAF00005309157 fastq.gz 3.1 GB
EGAF00005309158 fastq.gz 3.2 GB
EGAF00005309159 fastq.gz 2.5 GB
EGAF00005309160 fastq.gz 2.6 GB
EGAF00005309161 fastq.gz 2.7 GB
EGAF00005309162 fastq.gz 2.8 GB
EGAF00005309163 fastq.gz 3.1 GB
EGAF00005309164 fastq.gz 3.2 GB
EGAF00005309165 fastq.gz 3.2 GB
EGAF00005309166 fastq.gz 3.3 GB
EGAF00005309167 fastq.gz 2.6 GB
EGAF00005309168 fastq.gz 2.6 GB
EGAF00005309169 fastq.gz 2.9 GB
EGAF00005309170 fastq.gz 2.9 GB
EGAF00005309171 fastq.gz 3.1 GB
EGAF00005309172 fastq.gz 3.2 GB
EGAF00005309173 fastq.gz 3.2 GB
EGAF00005309174 fastq.gz 3.2 GB
EGAF00005309175 fastq.gz 3.0 GB
EGAF00005309176 fastq.gz 3.1 GB
EGAF00005309177 fastq.gz 3.1 GB
EGAF00005309178 fastq.gz 3.3 GB
EGAF00005309179 fastq.gz 3.1 GB
EGAF00005309180 fastq.gz 3.3 GB
EGAF00005309181 fastq.gz 3.1 GB
EGAF00005309182 fastq.gz 3.3 GB
EGAF00005309183 fastq.gz 3.2 GB
EGAF00005309184 fastq.gz 3.2 GB
EGAF00005309185 fastq.gz 3.1 GB
EGAF00005309186 fastq.gz 3.1 GB
EGAF00005309187 fastq.gz 3.1 GB
EGAF00005309188 fastq.gz 3.2 GB
EGAF00005309189 fastq.gz 3.2 GB
EGAF00005309190 fastq.gz 3.3 GB
EGAF00005309191 fastq.gz 3.2 GB
EGAF00005309192 fastq.gz 3.2 GB
EGAF00005309193 fastq.gz 3.0 GB
EGAF00005309194 fastq.gz 3.1 GB
EGAF00005309195 fastq.gz 3.2 GB
EGAF00005309196 fastq.gz 3.2 GB
EGAF00005309197 fastq.gz 2.9 GB
EGAF00005309198 fastq.gz 3.0 GB
EGAF00005309199 fastq.gz 3.0 GB
EGAF00005309200 fastq.gz 3.0 GB
EGAF00005309201 fastq.gz 3.1 GB
EGAF00005309202 fastq.gz 3.1 GB
EGAF00005309203 fastq.gz 3.0 GB
EGAF00005309204 fastq.gz 3.1 GB
EGAF00005309205 fastq.gz 3.1 GB
EGAF00005309206 fastq.gz 3.2 GB
EGAF00005309207 fastq.gz 2.7 GB
EGAF00005309208 fastq.gz 2.8 GB
EGAF00005309209 fastq.gz 3.1 GB
EGAF00005309210 fastq.gz 3.2 GB
EGAF00005309211 fastq.gz 3.1 GB
EGAF00005309212 fastq.gz 3.2 GB
EGAF00005309213 fastq.gz 3.1 GB
EGAF00005309214 fastq.gz 3.1 GB
EGAF00005309215 fastq.gz 3.1 GB
EGAF00005309216 fastq.gz 3.2 GB
EGAF00005309217 fastq.gz 3.1 GB
EGAF00005309218 fastq.gz 3.2 GB
EGAF00005309219 fastq.gz 3.2 GB
EGAF00005309220 fastq.gz 3.4 GB
EGAF00005309221 fastq.gz 3.0 GB
EGAF00005309222 fastq.gz 3.1 GB
EGAF00005309223 fastq.gz 3.2 GB
EGAF00005309224 fastq.gz 3.4 GB
EGAF00005309225 fastq.gz 3.1 GB
EGAF00005309226 fastq.gz 3.2 GB
EGAF00005309227 fastq.gz 3.2 GB
EGAF00005309228 fastq.gz 3.3 GB
EGAF00005309229 fastq.gz 3.0 GB
EGAF00005309230 fastq.gz 3.0 GB
EGAF00005309231 fastq.gz 3.1 GB
EGAF00005309232 fastq.gz 3.1 GB
EGAF00005309233 fastq.gz 3.2 GB
EGAF00005309234 fastq.gz 3.3 GB
EGAF00005309235 fastq.gz 3.1 GB
EGAF00005309236 fastq.gz 3.1 GB
EGAF00005309237 fastq.gz 3.1 GB
EGAF00005309238 fastq.gz 3.1 GB
EGAF00005309239 fastq.gz 3.1 GB
EGAF00005309240 fastq.gz 3.2 GB
EGAF00005309241 fastq.gz 3.0 GB
EGAF00005309242 fastq.gz 3.1 GB
EGAF00005309243 fastq.gz 2.6 GB
EGAF00005309244 fastq.gz 2.6 GB
EGAF00005309245 fastq.gz 3.0 GB
EGAF00005309246 fastq.gz 3.1 GB
EGAF00005309247 fastq.gz 3.1 GB
EGAF00005309248 fastq.gz 3.1 GB
EGAF00005309249 fastq.gz 3.1 GB
EGAF00005309250 fastq.gz 3.2 GB
EGAF00005309251 fastq.gz 2.9 GB
EGAF00005309252 fastq.gz 2.9 GB
EGAF00005309253 fastq.gz 3.1 GB
EGAF00005309254 fastq.gz 3.1 GB
EGAF00005309255 fastq.gz 3.1 GB
EGAF00005309256 fastq.gz 3.1 GB
EGAF00005309257 fastq.gz 2.5 GB
EGAF00005309258 fastq.gz 2.6 GB
EGAF00005309259 fastq.gz 3.2 GB
EGAF00005309260 fastq.gz 3.3 GB
EGAF00005309261 fastq.gz 3.2 GB
EGAF00005309262 fastq.gz 3.3 GB
EGAF00005309263 fastq.gz 3.1 GB
EGAF00005309264 fastq.gz 3.2 GB
EGAF00005309265 fastq.gz 3.1 GB
EGAF00005309266 fastq.gz 3.2 GB
EGAF00005309267 fastq.gz 3.1 GB
EGAF00005309268 fastq.gz 3.2 GB
EGAF00005309269 fastq.gz 3.2 GB
EGAF00005309270 fastq.gz 3.3 GB
EGAF00005309271 fastq.gz 3.2 GB
EGAF00005309272 fastq.gz 3.3 GB
EGAF00005309273 fastq.gz 3.1 GB
EGAF00005309274 fastq.gz 3.2 GB
EGAF00005309275 fastq.gz 3.2 GB
EGAF00005309276 fastq.gz 3.3 GB
EGAF00005309277 fastq.gz 3.0 GB
EGAF00005309278 fastq.gz 3.0 GB
EGAF00005309279 fastq.gz 2.6 GB
EGAF00005309280 fastq.gz 2.6 GB
EGAF00005309281 fastq.gz 2.9 GB
EGAF00005309282 fastq.gz 3.1 GB
EGAF00005309283 fastq.gz 3.1 GB
EGAF00005309284 fastq.gz 3.1 GB
EGAF00005309285 fastq.gz 3.1 GB
EGAF00005309286 fastq.gz 3.1 GB
EGAF00005309287 fastq.gz 3.0 GB
EGAF00005309288 fastq.gz 3.0 GB
EGAF00005309289 fastq.gz 3.0 GB
EGAF00005309290 fastq.gz 3.1 GB
EGAF00005309291 fastq.gz 3.1 GB
EGAF00005309292 fastq.gz 3.2 GB
EGAF00005309293 fastq.gz 2.9 GB
EGAF00005309294 fastq.gz 2.9 GB
EGAF00005309295 fastq.gz 3.1 GB
EGAF00005309296 fastq.gz 3.2 GB
EGAF00005309297 fastq.gz 3.1 GB
EGAF00005309298 fastq.gz 3.1 GB
EGAF00005309299 fastq.gz 3.0 GB
EGAF00005309300 fastq.gz 3.1 GB
EGAF00005309301 fastq.gz 3.1 GB
EGAF00005309302 fastq.gz 3.2 GB
EGAF00005309303 fastq.gz 3.1 GB
EGAF00005309304 fastq.gz 3.2 GB
EGAF00005309305 fastq.gz 3.1 GB
EGAF00005309306 fastq.gz 3.2 GB
EGAF00005309307 fastq.gz 3.0 GB
EGAF00005309308 fastq.gz 3.0 GB
EGAF00005309309 fastq.gz 3.1 GB
EGAF00005309310 fastq.gz 3.1 GB
EGAF00005309311 fastq.gz 3.0 GB
EGAF00005309312 fastq.gz 3.0 GB
EGAF00005309313 fastq.gz 3.2 GB
EGAF00005309314 fastq.gz 3.5 GB
EGAF00005309315 fastq.gz 3.1 GB
EGAF00005309316 fastq.gz 3.2 GB
EGAF00005309317 fastq.gz 2.6 GB
EGAF00005309318 fastq.gz 2.7 GB
EGAF00005309319 fastq.gz 3.1 GB
EGAF00005309320 fastq.gz 3.3 GB
EGAF00005309321 fastq.gz 3.0 GB
EGAF00005309322 fastq.gz 3.1 GB
EGAF00005309323 fastq.gz 3.2 GB
EGAF00005309324 fastq.gz 3.2 GB
EGAF00005309325 fastq.gz 3.2 GB
EGAF00005309326 fastq.gz 3.4 GB
EGAF00005309327 fastq.gz 3.2 GB
EGAF00005309328 fastq.gz 3.2 GB
EGAF00005309329 fastq.gz 2.8 GB
EGAF00005309330 fastq.gz 2.8 GB
EGAF00005309331 fastq.gz 3.2 GB
EGAF00005309332 fastq.gz 3.3 GB
EGAF00005309333 fastq.gz 3.1 GB
EGAF00005309334 fastq.gz 3.1 GB
EGAF00005309335 fastq.gz 3.1 GB
EGAF00005309336 fastq.gz 3.2 GB
EGAF00005309337 fastq.gz 3.1 GB
EGAF00005309338 fastq.gz 3.3 GB
EGAF00005309339 fastq.gz 2.9 GB
EGAF00005309340 fastq.gz 3.0 GB
EGAF00005309341 fastq.gz 2.7 GB
EGAF00005309342 fastq.gz 2.8 GB
EGAF00005309343 fastq.gz 3.1 GB
EGAF00005309344 fastq.gz 3.2 GB
EGAF00005309345 fastq.gz 3.1 GB
EGAF00005309346 fastq.gz 3.2 GB
EGAF00005309347 fastq.gz 3.1 GB
EGAF00005309348 fastq.gz 3.1 GB
EGAF00005309349 fastq.gz 3.2 GB
EGAF00005309350 fastq.gz 3.3 GB
EGAF00005309351 fastq.gz 2.9 GB
EGAF00005309352 fastq.gz 3.0 GB
EGAF00005309353 fastq.gz 3.1 GB
EGAF00005309354 fastq.gz 3.2 GB
260 Files (803.6 GB)