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Dynamics of individual T cell repertoires: from cord blood to centenarians

Genomics of Adaptive Immunity Laboratory


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  <identifier identifierType="DOI">10.5281/zenodo.826447</identifier>
  <creators>
    <creator>
      <creatorName>Genomics of Adaptive Immunity Laboratory</creatorName>
      <affiliation>Institute of Bioorganic Chemistry, Russian Academy of Sciences</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Dynamics of individual T cell repertoires: from cord blood to centenarians</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2017</publicationYear>
  <subjects>
    <subject>t-cell</subject>
    <subject>immune repertoire</subject>
    <subject>sequencing</subject>
    <subject>immunology</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2017-07-13</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/826447</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.826446</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;The dataset contains processed T-cell receptor repertoire sequencing data from 79 individuals of different sex and age, originally published in [1] and [2]. Note that [1] describes only a subset of samples, while [2] describes the full cohort.&lt;/p&gt;

&lt;p&gt;The libraries were prepared using a 5'RACE protocol and sequenced on HiSEQ. The libraries incorporate unique molecular identifier (UMI) tags that were mainly used for counting cDNA molecules. Preprocessing was performed using the MIGEC software [3] as follows: all UMI tags represented by a single sequencing read were discarded, the remaining UMI tags were used to assemble cDNA consensus sequences. Note that this procedure eliminates most of cross-sample contamination (batch effect) as described in [2]. VDJ partitioning and CDR3 extraction was performed using MiTCR software [4], sequencing error correction was performed using ETE option in MiTCR. All datasets are converted into VDJtools [5] format, see http://vdjtools-doc.readthedocs.io/en/latest/input.html#vdjtools-format.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Sample description:&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;The A* in sample identifier is the batch ID.&lt;/li&gt;
	&lt;li&gt;Age and sex data is provided in the metadata.txt file.&lt;/li&gt;
	&lt;li&gt;Samples having age "0" are umbilical cord blood samples.&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;Contributors:&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;The T-cell repertoire aging study was a project ran in the Genomics of Adaptive Immunity Lab (Prof. Dmitry Chudakov)&lt;/li&gt;
	&lt;li&gt;The samples were acquired, prepared and sequenced by Dr. Olga Britanova&lt;/li&gt;
	&lt;li&gt;The data was analyzed and uploaded by Dr. Mikhail Shugay&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;Citations:&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;[1] OV Britanova, EV Putintseva, M Shugay, EM Merzlyak, MA Turchaninova, et al. Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling. The Journal of Immunology 2014; 192 (6), 2689-2698&lt;/li&gt;
	&lt;li&gt;[2] OV Britanova, M Shugay, EM Merzlyak, DB Staroverov, EV Putintseva, et al. Dynamics of individual T cell repertoires: from cord blood to centenarians. The Journal of Immunology 2016; 196 (12), 5005-5013&lt;/li&gt;
	&lt;li&gt;[3] M Shugay, OV Britanova, EM Merzlyak, MA Turchaninova, IZ Mamedov, et al. Towards error-free profiling of immune repertoires. Nature methods 2014; 11 (6), 653-655&lt;/li&gt;
	&lt;li&gt;[4] DA Bolotin, M Shugay, IZ Mamedov, EV Putintseva, MA Turchaninova, et al. MiTCR: software for T-cell receptor sequencing data analysis. Nature methods 2013; 10 (9), 813-814&lt;/li&gt;
	&lt;li&gt;[5] M Shugay, DV Bagaev, MA Turchaninova, DA Bolotin, OV Britanova, et al. VDJtools: unifying post-analysis of T cell receptor repertoires. PLoS computational biology 2015; 11 (11), e1004503&lt;/li&gt;
&lt;/ul&gt;</description>
  </descriptions>
</resource>
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