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run_metadata

302 rows where experiment.library_layout = "PAIRED", experiment.library_strategy = "AMPLICON" and technology = "unknown"

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tissue_curation 5

devstage_curation 5

experiment.library_selection 3

devstage_curation_coarse 3

technology 1

  • unknown · 302 ✖

experiment.platform 1

experiment.library_strategy 1

  • AMPLICON · 302 ✖

experiment.library_source 1

experiment.library_layout 1

  • PAIRED · 302 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
28514 28514 SRR26502432 SRX22206245 SRS19261598 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the TNP KLH via IP injection. Zebrafish AB IP TNP KLH 28d IPTNP 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP TNP KLH|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgZ2 at 28 days post the TNP KLH via IP injection: adult kidney fish2 zebrafish AB Kidney IP TNPKLH IgZ2 Fish2 zebrafish AB Kidney IP TNPKLH IgZ2 Fish2 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish2 kidneys were harvested 28 days post IP injected TNP KLH to construct an IgZ2 library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPTNP_28d_AB_Ki_Z2_Fish2_clean_R1.fastq.gz IPTNP_28d_AB_Ki_Z2_Fish2_clean_R2.fastq.gz fastq fastq 223722000.0 372870.0 IPTNP 28d AB Ki Z2 Fish2 clean R1.fastq.gz 0:300 1:300 A:60349354;C:49977478;G:49698065;T:63696951;N:152 300 300     60349354 49977478 49698065 63696951 152 SRX22206245 SRS19261598 SRA1738863 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.00039 0.56274 0.0 0.03514 0.99977 0.99977 0.13793 0.0001 300 300 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28515 28515 SRR26502433 SRX22206244 SRS19261598 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the TNP KLH via IP injection. Zebrafish AB IP TNP KLH 28d IPTNP 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP TNP KLH|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgM at 28 days post the TNP KLH via IP injection: adult kidney fish2 zebrafish AB Kidney IP TNPKLH IgM Fish2 zebrafish AB Kidney IP TNPKLH IgM Fish2 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish2 kidneys were harvested 28 days post IP injected TNP KLH to construct an IgM library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPTNP_28d_AB_Ki_M_Fish2_clean_R2.fastq.gz IPTNP_28d_AB_Ki_M_Fish2_clean_R1.fastq.gz fastq fastq 1296356400.0 2160594.0 IPTNP 28d AB Ki M Fish2 clean R1.fastq.gz 0:300 1:300 A:345599628;C:292675523;G:307032178;T:351048163;N:908 300 300     345599628 292675523 307032178 351048163 908 SRX22206244 SRS19261598 SRA1738863 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.13277 0.493 0.0 0.0538 0.99997 0.99983 0.0 0.00016 300 300 B B mate1-mate2 similar by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28516 28516 SRR26502438 SRX22206239 SRS19261598 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the TNP KLH via IP injection. Zebrafish AB IP TNP KLH 28d IPTNP 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP TNP KLH|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgZ2 at 28 days post the TNP KLH via IP injection: adult kidney fish6 zebrafish AB Kidney IP TNPKLH IgZ2 Fish6 zebrafish AB Kidney IP TNPKLH IgZ2 Fish6 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish6 kidneys were harvested 28 days post IP injected TNP KLH to construct an IgZ2 library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPTNP_28d_AB_Ki_Z2_Fish6_clean_R1.fastq.gz IPTNP_28d_AB_Ki_Z2_Fish6_clean_R2.fastq.gz fastq fastq 36927000.0 61545.0 IPTNP 28d AB Ki Z2 Fish6 clean R1.fastq.gz 0:300 1:300 A:10692726;C:8421425;G:7948050;T:9864799;N:0 300 300     10692726 8421425 7948050 9864799 0 SRX22206239 SRS19261598 SRA1738863 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.00217 0.43144 0.00031 0.04455 0.99902 0.99926 0.46153 0.00207 300 300 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28517 28517 SRR26502439 SRX22206238 SRS19261598 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the TNP KLH via IP injection. Zebrafish AB IP TNP KLH 28d IPTNP 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP TNP KLH|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgM at 28 days post the TNP KLH via IP injection: adult kidney fish6 zebrafish AB Kidney IP TNPKLH IgM Fish6 zebrafish AB Kidney IP TNPKLH IgM Fish6 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish6 kidneys were harvested 28 days post IP injected TNP KLH to construct an IgM library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPTNP_28d_AB_Ki_M_Fish6_clean_R1.fastq.gz IPTNP_28d_AB_Ki_M_Fish6_clean_R2.fastq.gz fastq fastq 579266400.0 965444.0 IPTNP 28d AB Ki M Fish6 clean R1.fastq.gz 0:300 1:300 A:155729386;C:133391465;G:134161096;T:155984401;N:52 300 300     155729386 133391465 134161096 155984401 52 SRX22206238 SRS19261598 SRA1738863 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.10691 0.50696 0.0 0.06888 0.99989 0.99975 0.00022 0.00014 300 300 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28518 28518 SRR26502440 SRX22206237 SRS19261598 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the TNP KLH via IP injection. Zebrafish AB IP TNP KLH 28d IPTNP 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP TNP KLH|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgZ2 at 28 days post the TNP KLH via IP injection: adult kidney fish5 zebrafish AB Kidney IP TNPKLH IgZ2 Fish5 zebrafish AB Kidney IP TNPKLH IgZ2 Fish5 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish5 kidneys were harvested 28 days post IP injected TNP KLH to construct an IgZ2 library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPTNP_28d_AB_Ki_Z2_Fish5_clean_R1.fastq.gz IPTNP_28d_AB_Ki_Z2_Fish5_clean_R2.fastq.gz fastq fastq 72321600.0 120536.0 IPTNP 28d AB Ki Z2 Fish5 clean R1.fastq.gz 0:300 1:300 A:20213882;C:16497376;G:15762001;T:19848333;N:8 300 300     20213882 16497376 15762001 19848333 8 SRX22206237 SRS19261598 SRA1738863 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.00248 0.52445 0.00015 0.04429 0.99902 0.99918 0.13142 0.00403 300 300 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28519 28519 SRR26502441 SRX22206236 SRS19261598 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the TNP KLH via IP injection. Zebrafish AB IP TNP KLH 28d IPTNP 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP TNP KLH|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgM at 28 days post the TNP KLH via IP injection: adult kidney fish5 zebrafish AB Kidney IP TNPKLH IgM Fish5 zebrafish AB Kidney IP TNPKLH IgM Fish5 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish5 kidneys were harvested 28 days post IP injected TNP KLH to construct an IgM library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPTNP_28d_AB_Ki_M_Fish5_clean_R1.fastq.gz IPTNP_28d_AB_Ki_M_Fish5_clean_R2.fastq.gz fastq fastq 627508800.0 1045848.0 IPTNP 28d AB Ki M Fish5 clean R1.fastq.gz 0:300 1:300 A:166970849;C:144788459;G:146254051;T:169495382;N:59 300 300     166970849 144788459 146254051 169495382 59 SRX22206236 SRS19261598 SRA1738863 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.14044 0.5736 0.0 0.07097 0.99997 0.99983 0.0 0.00011 300 300 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28520 28520 SRR26502442 SRX22206235 SRS19261598 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the TNP KLH via IP injection. Zebrafish AB IP TNP KLH 28d IPTNP 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP TNP KLH|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgZ2 at 28 days post the TNP KLH via IP injection: adult kidney fish4 zebrafish AB Kidney IP TNPKLH IgZ2 Fish4 zebrafish AB Kidney IP TNPKLH IgZ2 Fish4 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish4 kidneys were harvested 28 days post IP injected TNP KLH to construct an IgZ2 library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPTNP_28d_AB_Ki_Z2_Fish4_clean_R1.fastq.gz IPTNP_28d_AB_Ki_Z2_Fish4_clean_R2.fastq.gz fastq fastq 84922800.0 141538.0 IPTNP 28d AB Ki Z2 Fish4 clean R1.fastq.gz 0:300 1:300 A:24137795;C:19238356;G:18271192;T:23275452;N:5 300 300     24137795 19238356 18271192 23275452 5 SRX22206235 SRS19261598 SRA1738863 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.00273 0.51115 7e-05 0.05752 0.99924 0.99939 0.14655 0.00062 300 300 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28521 28521 SRR26502443 SRX22206234 SRS19261598 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the TNP KLH via IP injection. Zebrafish AB IP TNP KLH 28d IPTNP 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP TNP KLH|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgM at 28 days post the TNP KLH via IP injection: adult kidney fish4 zebrafish AB Kidney IP TNPKLH IgM Fish4 zebrafish AB Kidney IP TNPKLH IgM Fish4 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish4 kidneys were harvested 28 days post IP injected TNP KLH to construct an IgM library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPTNP_28d_AB_Ki_M_Fish4_clean_R1.fastq.gz IPTNP_28d_AB_Ki_M_Fish4_clean_R2.fastq.gz fastq fastq 538648200.0 897747.0 IPTNP 28d AB Ki M Fish4 clean R1.fastq.gz 0:300 1:300 A:144890138;C:124184645;G:124940661;T:144632730;N:26 300 300     144890138 124184645 124940661 144632730 26 SRX22206234 SRS19261598 SRA1738863 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.17776 0.53894 0.0 0.07275 0.99991 0.99975 7e-05 0.00013 300 300 B B mate1-mate2 similar by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28522 28522 SRR26502444 SRX22206233 SRS19261598 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the TNP KLH via IP injection. Zebrafish AB IP TNP KLH 28d IPTNP 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP TNP KLH|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgZ2 at 28 days post the TNP KLH via IP injection: adult kidney fish3 zebrafish AB Kidney IP TNPKLH IgZ2 Fish3 zebrafish AB Kidney IP TNPKLH IgZ2 Fish3 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish3 kidneys were harvested 28 days post IP injected TNP KLH to construct an IgZ2 library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPTNP_28d_AB_Ki_Z2_Fish3_clean_R1.fastq.gz IPTNP_28d_AB_Ki_Z2_Fish3_clean_R2.fastq.gz fastq fastq 130978800.0 218298.0 IPTNP 28d AB Ki Z2 Fish3 clean R1.fastq.gz 0:300 1:300 A:36642819;C:29649925;G:28560355;T:36125688;N:13 300 300     36642819 29649925 28560355 36125688 13 SRX22206233 SRS19261598 SRA1738863 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.00233 0.44747 4e-05 0.05829 0.99933 0.99939 0.07443 0.00038 300 300 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28523 28523 SRR26502445 SRX22206232 SRS19261598 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the TNP KLH via IP injection. Zebrafish AB IP TNP KLH 28d IPTNP 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP TNP KLH|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgM at 28 days post the TNP KLH via IP injection: adult kidney fish3 zebrafish AB Kidney IP TNPKLH IgM Fish3 zebrafish AB Kidney IP TNPKLH IgM Fish3 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish3 kidneys were harvested 28 days post IP injected TNP KLH to construct an IgM library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPTNP_28d_AB_Ki_M_Fish3_clean_R1.fastq.gz IPTNP_28d_AB_Ki_M_Fish3_clean_R2.fastq.gz fastq fastq 771168000.0 1285280.0 IPTNP 28d AB Ki M Fish3 clean R1.fastq.gz 0:300 1:300 A:208307845;C:178771404;G:179327317;T:204761363;N:71 300 300     208307845 178771404 179327317 204761363 71 SRX22206232 SRS19261598 SRA1738863 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.10754 0.46893 1e-05 0.06264 0.99993 0.99985 0.00015 7e-05 300 300 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28524 28524 SRR26502448 SRX22206229 SRS19261598 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the TNP KLH via IP injection. Zebrafish AB IP TNP KLH 28d IPTNP 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP TNP KLH|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgZ2 at 28 days post the TNP KLH via IP injection: adult kidney fish1 zebrafish AB Kidney IP TNPKLH IgZ2 Fish1 zebrafish AB Kidney IP TNPKLH IgZ2 Fish1 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish1 kidneys were harvested 28 days post IP injected TNP KLH to construct an IgZ2 library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPTNP_28d_AB_Ki_Z2_Fish1_clean_R1.fastq.gz IPTNP_28d_AB_Ki_Z2_Fish1_clean_R2.fastq.gz fastq fastq 542712000.0 904520.0 IPTNP 28d AB Ki Z2 Fish1 clean R1.fastq.gz 0:300 1:300 A:146626751;C:121353093;G:120763062;T:153968769;N:325 300 300     146626751 121353093 120763062 153968769 325 SRX22206229 SRS19261598 SRA1738863 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.00068 0.42171 0.0 0.03977 0.99991 0.99987 0.0196 6e-05 300 300 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28525 28525 SRR26502449 SRX22206228 SRS19261598 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the TNP KLH via IP injection. Zebrafish AB IP TNP KLH 28d IPTNP 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP TNP KLH|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgM at 28 days post the TNP KLH via IP injection: adult kidney fish1 zebrafish AB Kidney IP TNPKLH IgM Fish1 zebrafish AB Kidney IP TNPKLH IgM Fish1 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish1 kidneys were harvested 28 days post IP injected TNP KLH to construct an IgM library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPTNP_28d_AB_Ki_M_Fish1_clean_R1.fastq.gz IPTNP_28d_AB_Ki_M_Fish1_clean_R2.fastq.gz fastq fastq 1346198400.0 2243664.0 IPTNP 28d AB Ki M Fish1 clean R1.fastq.gz 0:300 1:300 A:363410047;C:305388036;G:321604982;T:355794421;N:914 300 300     363410047 305388036 321604982 355794421 914 SRX22206228 SRS19261598 SRA1738863 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.12792 0.47382 2e-05 0.04534 0.99991 0.99981 0.00019 8e-05 300 300 B B mate1-mate2 similar by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28526 28526 SRR26502105 SRX22205912 SRS19261295 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the Vibrio anguillarum via IP injection. Zebrafish AB IP Va 28d IPVa 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP Vibrio anguillarum|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgZ2 at 28 days post the Vibrio anguillarum via IP injection: adult kidney fish2 zebrafish AB Kidney IP Va IgZ2 Fish2 zebrafish AB Kidney IP Va IgZ2 Fish2 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish2 kidneys were harvested 28 days post IP injected Vibrio anguillarum to construct an IgZ2 library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPVa_28d_AB_Ki_Z2_Fish2_clean_R1.fastq.gz IPVa_28d_AB_Ki_Z2_Fish2_clean_R2.fastq.gz fastq fastq 148917000.0 248195.0 IPVa 28d AB Ki Z2 Fish2 clean R1.fastq.gz 0:300 1:300 A:40902871;C:33748474;G:32788902;T:41456104;N:20649 300 300     40902871 33748474 32788902 41456104 20649 SRX22205912 SRS19261295 SRA1738828 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.00127 0.21671 4e-05 0.02384 0.99939 0.99953 0.14285 0.00065 300 300 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28527 28527 SRR26502106 SRX22205911 SRS19261295 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the Vibrio anguillarum via IP injection. Zebrafish AB IP Va 28d IPVa 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP Vibrio anguillarum|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgM at 28 days post the Vibrio anguillarum via IP injection: adult kidney fish2 zebrafish AB Kidney IP Va IgM Fish2 zebrafish AB Kidney IP Va IgM Fish2 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish2 kidneys were harvested 28 days post IP injected Vibrio anguillarum to construct an IgM library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPVa_28d_AB_Ki_M_Fish2_clean_R1.fastq.gz IPVa_28d_AB_Ki_M_Fish2_clean_R2.fastq.gz fastq fastq 1400700000.0 2334500.0 IPVa 28d AB Ki M Fish2 clean R1.fastq.gz 0:300 1:300 A:382658780;C:319810107;G:330740047;T:367285987;N:205079 300 300     382658780 319810107 330740047 367285987 205079 SRX22205911 SRS19261295 SRA1738828 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.12814 0.36107 0.0 0.0523 0.99997 0.99985 0.0 0.00014 300 300 B B mate1-mate2 similar by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28528 28528 SRR26502115 SRX22205902 SRS19261295 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the Vibrio anguillarum via IP injection. Zebrafish AB IP Va 28d IPVa 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP Vibrio anguillarum|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgZ2 at 28 days post the Vibrio anguillarum via IP injection: adult kidney fish1 zebrafish AB Kidney IP Va IgZ2 Fish1 zebrafish AB Kidney IP Va IgZ2 Fish1 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish1 kidneys were harvested 28 days post IP injected Vibrio anguillarum to construct an IgZ2 library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPVa_28d_AB_Ki_Z2_Fish1_clean_R1.fastq.gz IPVa_28d_AB_Ki_Z2_Fish1_clean_R2.fastq.gz fastq fastq 96198600.0 160331.0 IPVa 28d AB Ki Z2 Fish1 clean R1.fastq.gz 0:300 1:300 A:26939421;C:21370857;G:21135801;T:26737674;N:14847 300 300     26939421 21370857 21135801 26737674 14847 SRX22205902 SRS19261295 SRA1738828 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.00209 0.50064 5e-05 0.05156 0.99955 0.99969 0.06435 0.00015 300 300 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28529 28529 SRR26502116 SRX22205901 SRS19261295 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     AB strain zebrafish was used to collect a library of IgM and IgZ2 at 28 days post the Vibrio anguillarum via IP injection. Zebrafish AB IP Va 28d IPVa 28d AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:IP Vibrio anguillarum|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgM at 28 days post the Vibrio anguillarum via IP injection: adult kidney fish1 zebrafish AB Kidney IP Va IgM Fish1 zebrafish AB Kidney IP Va IgM Fish1 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. Fish1 kidneys were harvested 28 days post IP injected Vibrio anguillarum to construct an IgM library.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     IPVa_28d_AB_Ki_M_Fish1_clean_R1.fastq.gz IPVa_28d_AB_Ki_M_Fish1_clean_R2.fastq.gz fastq fastq 1208007000.0 2013345.0 IPVa 28d AB Ki M Fish1 clean R1.fastq.gz 0:300 1:300 A:333262499;C:274287635;G:285027652;T:315252859;N:176355 300 300     333262499 274287635 285027652 315252859 176355 SRX22205901 SRS19261295 SRA1738828 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.11556 0.31221 0.0 0.04066 0.99993 0.99985 0.00017 0.00028 300 300 B B mate1-mate2 similar by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-25 Adult Adult Multi-tissue Multi-system
28530 28530 SRR26488229 SRX22192101 SRS19248767 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     Kidney tissue from AB strain zebrafish was used to collect a library of IgM and IgZ2 without xxx. Zebrafish AB Kidney Unimmunization UI AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:Unimmunization|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgZ2 without xxx: adult kidney fish4 zebrafish AB Kidney Unimmunization IgZ2 Fish4 zebrafish AB Kidney Unimmunization IgZ2 Fish4 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. In the 11 nave individuals without xxx a single AB zebrafish kidney was utilized to construct a library of fish4 IgZ2.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     UI_AB_Ki_Z2_Fish4_clean_R1.fastq.gz UI_AB_Ki_Z2_Fish4_clean_R2.fastq.gz fastq fastq 452866800.0 754778.0 UI AB Ki Z2 Fish4 clean R1.fastq.gz 0:300 1:300 A:119823464;C:102645888;G:102371143;T:127641629;N:384676 300 300     119823464 102645888 102371143 127641629 384676 SRX22192101 SRS19248767 SRA1738037 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.00081 0.39173 0.0 0.16017 0.99981 0.99979 0.04273 0.00056 300 300 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-24 Adult Adult Multi-tissue Multi-system
28531 28531 SRR26488230 SRX22192100 SRS19248767 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     Kidney tissue from AB strain zebrafish was used to collect a library of IgM and IgZ2 without xxx. Zebrafish AB Kidney Unimmunization UI AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:Unimmunization|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgM without xxx: adult kidney fish4 zebrafish AB Kidney Unimmunization IgM Fish4 zebrafish AB Kidney Unimmunization IgM Fish4 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. In the 11 nave individuals without xxx a single AB zebrafish kidney was utilized to construct a library of fish4 IgM.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     UI_AB_Ki_M_Fish4_clean_R2.fastq.gz UI_AB_Ki_M_Fish4_clean_R1.fastq.gz fastq fastq 1175273400.0 1958789.0 UI AB Ki M Fish4 clean R1.fastq.gz 0:300 1:300 A:320768072;C:266946605;G:278763949;T:307641532;N:1153242 300 300     320768072 266946605 278763949 307641532 1153242 SRX22192100 SRS19248767 SRA1738037 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.36646 0.48405 0.0 0.0978 0.99993 0.99981 3e-05 7e-05 300 300 B B biological fallback assumption illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-24 Adult Adult Multi-tissue Multi-system
28532 28532 SRR26488233 SRX22192097 SRS19248767 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     Kidney tissue from AB strain zebrafish was used to collect a library of IgM and IgZ2 without xxx. Zebrafish AB Kidney Unimmunization UI AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:Unimmunization|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgZ2 without xxx: adult kidney fish2 zebrafish AB Kidney Unimmunization IgZ2 Fish2 zebrafish AB Kidney Unimmunization IgZ2 Fish2 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. In the 11 nave individuals without xxx a single AB zebrafish kidney was utilized to construct a library of fish2 IgZ2.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     UI_AB_Ki_Z2_Fish2_clean_R2.fastq.gz UI_AB_Ki_Z2_Fish2_clean_R1.fastq.gz fastq fastq 180337528.0 299564.0 UI AB Ki Z2 Fish2 clean R1.fastq.gz 0:301 1:301 A:50544268;C:41015792;G:40132471;T:48636308;N:8689 301 301     50544268 41015792 40132471 48636308 8689 SRX22192097 SRS19248767 SRA1738037 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.00202 0.27435 0.00016 0.05953 0.99736 0.99866 0.41224 0.00434 301 301 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-24 Adult Adult Multi-tissue Multi-system
28533 28533 SRR26488236 SRX22192094 SRS19248767 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     Kidney tissue from AB strain zebrafish was used to collect a library of IgM and IgZ2 without xxx. Zebrafish AB Kidney Unimmunization UI AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:Unimmunization|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgM without xxx: adult kidney fish2 zebrafish AB Kidney Unimmunization IgM Fish2 zebrafish AB Kidney Unimmunization IgM Fish2 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. In the 11 nave individuals without xxx a single AB zebrafish kidney was utilized to construct a library of fish2 IgM.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     UI_AB_Ki_M_Fish2_clean_R1.fastq.gz UI_AB_Ki_M_Fish2_clean_R2.fastq.gz fastq fastq 235187554.0 390677.0 UI AB Ki M Fish2 clean R1.fastq.gz 0:301 1:301 A:63276642;C:54233985;G:55195713;T:62481210;N:4 301 301     63276642 54233985 55195713 62481210 4 SRX22192094 SRS19248767 SRA1738037 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.12903 0.42746 0.0 0.0323 0.99995 0.99987 0.0 9e-05 301 301 B B mate1-mate2 similar by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-24 Adult Adult Multi-tissue Multi-system
28534 28534 SRR26488237 SRX22192093 SRS19248767 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     Kidney tissue from AB strain zebrafish was used to collect a library of IgM and IgZ2 without xxx. Zebrafish AB Kidney Unimmunization UI AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:Unimmunization|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgZ2 without xxx: adult kidney fish10 zebrafish AB Kidney Unimmunization IgZ2 Fish10 zebrafish AB Kidney Unimmunization IgZ2 Fish10 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. In the 11 nave individuals without xxx a single AB zebrafish kidney was utilized to construct a library of fish10 IgZ2.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     UI_AB_Ki_Z2_Fish10_clean_R1.fastq.gz UI_AB_Ki_Z2_Fish10_clean_R2.fastq.gz fastq fastq 187774200.0 312957.0 UI AB Ki Z2 Fish10 clean R1.fastq.gz 0:300 1:300 A:51941827;C:41824457;G:42259702;T:51589508;N:158706 300 300     51941827 41824457 42259702 51589508 158706 SRX22192093 SRS19248767 SRA1738037 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.00197 0.48348 4e-05 0.02602 0.99981 0.99985 0.02049 4e-05 300 300 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-24 Adult Adult Multi-tissue Multi-system
28535 28535 SRR26488238 SRX22192092 SRS19248767 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     Kidney tissue from AB strain zebrafish was used to collect a library of IgM and IgZ2 without xxx. Zebrafish AB Kidney Unimmunization UI AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:Unimmunization|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgM without xxx: adult kidney fish10 zebrafish AB Kidney Unimmunization IgM Fish10 zebrafish AB Kidney Unimmunization IgM Fish10 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. In the 11 nave individuals without xxx a single AB zebrafish kidney was utilized to construct a library of fish10 IgM.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     UI_AB_Ki_M_Fish10_clean_R1.fastq.gz UI_AB_Ki_M_Fish10_clean_R2.fastq.gz fastq fastq 1348929600.0 2248216.0 UI AB Ki M Fish10 clean R1.fastq.gz 0:300 1:300 A:372533980;C:296280069;G:315957178;T:362830159;N:1328214 300 300     372533980 296280069 315957178 362830159 1328214 SRX22192092 SRS19248767 SRA1738037 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.04106 0.65457 0.0 0.01839 0.99995 0.99987 0.00017 2e-05 300 300 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-24 Adult Adult Multi-tissue Multi-system
28536 28536 SRR26488247 SRX22192083 SRS19248767 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     Kidney tissue from AB strain zebrafish was used to collect a library of IgM and IgZ2 without xxx. Zebrafish AB Kidney Unimmunization UI AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:Unimmunization|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgZ2 without xxx: adult kidney fish1 zebrafish AB Kidney Unimmunization IgZ2 Fish1 zebrafish AB Kidney Unimmunization IgZ2 Fish1 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. In the 11 nave individuals without xxx a single AB zebrafish kidney was utilized to construct a library of fish1 IgZ2.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     UI_AB_Ki_Z2_Fish1_clean_R1.fastq.gz UI_AB_Ki_Z2_Fish1_clean_R2.fastq.gz fastq fastq 74076702.0 123051.0 UI AB Ki Z2 Fish1 clean R1.fastq.gz 0:301 1:301 A:21163846;C:16505697;G:16394698;T:20009432;N:3029 301 301     21163846 16505697 16394698 20009432 3029 SRX22192083 SRS19248767 SRA1738037 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.00345 0.35918 0.00037 0.01229 0.99797 0.99888 0.46913 0.00408 301 301 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-24 Adult Adult Multi-tissue Multi-system
28537 28537 SRR26488248 SRX22192082 SRS19248767 SRP468057 PRJNA1027976 Danio rerio BCR rep seq Raw sequence reads PRJNA1027976 Other A library of B cell receptors including IgM and IgZ2 was constructed using the SMARTer Human BCR Profiling Kit to understand its expression in the AB strain of zebrafish.     Kidney tissue from AB strain zebrafish was used to collect a library of IgM and IgZ2 without xxx. Zebrafish AB Kidney Unimmunization UI AB   strain:AB|dev stage:adult|sex:not determined|tissue:kidney gill Intestines|collection date:2022|geo loc name:not applicable|health state:health|treatment:Unimmunization|BioSampleModel:Model organism or animal                 Rep Seq of zebrafish AB IgM without xxx: adult kidney fish1 zebrafish AB Kidney Unimmunization IgM Fish1 zebrafish AB Kidney Unimmunization IgM Fish1 A method was designed for constructing a AB strain zebrafish B cell receptor BCR library based on the SMARTer Human BCR IgG IgM HKL Profiling Kit. In the 11 nave individuals without xxx a single AB zebrafish kidney was utilized to construct a library of fish1 IgM.     AMPLICON TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   SRP468057     UI_AB_Ki_M_Fish1_clean_R1.fastq.gz UI_AB_Ki_M_Fish1_clean_R2.fastq.gz fastq fastq 237047132.0 393766.0 UI AB Ki M Fish1 clean R1.fastq.gz 0:301 1:301 A:64821499;C:55151969;G:56692025;T:60381634;N:5 301 301     64821499 55151969 56692025 60381634 5 SRX22192082 SRS19248767 SRA1738037 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.11965 0.51034 0.0 0.01727 0.99995 0.99987 8e-05 2e-05 301 301 T B mate1 technical by mapping diff illumina miseq full_length poly_a smarter bulk unknown unknown   China 2023-10-24 Adult Adult Multi-tissue Multi-system
40376 40376 SRR3166964 SRX1583817 SRS1295580 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRA library 28d Calm4   breed:AB|chain:alpha|index:26|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 28d Calm4 116 28d Calm4 alpha 116 28d Calm4 alpha five prime RACE amplification of TCRa transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_116_28d_Calm4_alpha.fq.gz read2_116_28d_Calm4_alpha.fq.gz fastq fastq 12052440600.0 40174802.0 116 28d Calm4 alpha files 0:150 1:150 A:3274476247;C:2324807837;G:3578878507;T:2848354560;N:25923449 150 150     3274476247 2324807837 3578878507 2848354560 25923449 SRX1583817 SRS1295580 SRA353254 SRA Bar-Ilan University 2 0.00096 0.22917 0.00017 0.19822 0.99906 0.99762 0.35172 0.6189 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40377 40377 SRR3166963 SRX1583816 SRS1295581 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRA library 28d Calm2   breed:AB|chain:alpha|index:25|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 28d Calm2 114 28d Calm2 alpha 114 28d Calm2 alpha five prime RACE amplification of TCRa transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_114_28d_Calm2_alpha.fq.gz read2_114_28d_Calm2_alpha.fq.gz fastq fastq 4957122900.0 16523743.0 114 28d Calm2 alpha files 0:150 1:150 A:1398510544;C:988027281;G:1244120221;T:1316350204;N:10114650 150 150     1398510544 988027281 1244120221 1316350204 10114650 SRX1583816 SRS1295581 SRA353254 SRA Bar-Ilan University 2 0.00167 0.03332 0.00146 0.028 0.99967 0.99896 0.15789 0.60731 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40378 40378 SRR3166962 SRX1583815 SRS1295582 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRA library 28d KLH6   breed:AB|chain:alpha|index:21|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 28d KLH6 110 28d KLH6 alpha 110 28d KLH6 alpha five prime RACE amplification of TCRa transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_110_28d_KLH6_alpha.fq.gz read2_110_28d_KLH6_alpha.fq.gz fastq fastq 6270530700.0 20901769.0 110 28d KLH6 alpha files 0:150 1:150 A:1802311183;C:1236560108;G:1561615962;T:1659163742;N:10879705 150 150     1802311183 1236560108 1561615962 1659163742 10879705 SRX1583815 SRS1295582 SRA353254 SRA Bar-Ilan University 2 0.00179 0.13512 0.00073 0.11592 0.99967 0.99855 0.21568 0.87835 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40379 40379 SRR3166961 SRX1583814 SRS1295583 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRA library 28d PHA6   breed:AB|chain:alpha|index:32|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 28d PHA6 102 28d PHA6 alpha 102 28d PHA6 alpha five prime RACE amplification of TCRa transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_102_28d_PHA6_alpha.fq.gz read2_102_28d_PHA6_alpha.fq.gz fastq fastq 10067723700.0 33559079.0 102 28d PHA6 alpha files 0:150 1:150 A:2803515995;C:2027880463;G:2649055724;T:2566963260;N:20308258 150 150     2803515995 2027880463 2649055724 2566963260 20308258 SRX1583814 SRS1295583 SRA353254 SRA Bar-Ilan University 2 0.00158 0.04576 0.00056 0.03839 0.99922 0.99831 0.3246 0.40078 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2016-02-14 Undetermined Undetermined Whole Organism All anatomical structures
40380 40380 SRR3166960 SRX1583813 SRS1295584 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRA library 7d KLH2   breed:AB|chain:alpha|index:34|sex:male|time point:7d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 7d KLH2 16 7d KLH2 alpha 16 7d KLH2 alpha five prime RACE amplification of TCRa transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_16_7d_KLH2_alpha.fq.gz read2_16_7d_KLH2_alpha.fq.gz fastq fastq 2783317500.0 9277725.0 16 7d KLH2 alpha files 0:150 1:150 A:761370556;C:556705024;G:719835894;T:727504605;N:17901421 150 150     761370556 556705024 719835894 727504605 17901421 SRX1583813 SRS1295584 SRA353254 SRA Bar-Ilan University 2 0.00143 0.13658 0.0008 0.11879 0.99935 0.99876 0.25409 0.87567 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2016-02-14 Undetermined Undetermined Whole Organism All anatomical structures
40381 40381 SRR3166959 SRX1583812 SRS1295585 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRA library 21d KLH6   breed:AB|chain:alpha|index:24|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 21d KLH6 78 21d KLH6 alpha 78 21d KLH6 alpha five prime RACE amplification of TCRa transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_78_21d_KLH6_alpha.fq.gz read2_78_21d_KLH6_alpha.fq.gz fastq fastq 7720614900.0 25735383.0 78 21d KLH6 alpha files 0:150 1:150 A:2163229607;C:1591913203;G:1963558161;T:1998596363;N:3317566 150 150     2163229607 1591913203 1963558161 1998596363 3317566 SRX1583812 SRS1295585 SRA353254 SRA Bar-Ilan University 2 0.00105 0.04913 0.00036 0.04186 0.99937 0.99835 0.14393 0.4819 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40382 40382 SRR3166958 SRX1583811 SRS1295586 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRA library 7d Calm6   breed:AB|chain:alpha|index:33|sex:male|time point:7d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 7d Calm6 27 7d Calm6 alpha 27 7d Calm6 alpha five prime RACE amplification of TCRa transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_27_7d_Calm6_alpha.fq.gz read2_27_7d_Calm6_alpha.fq.gz fastq fastq 4337226600.0 14457422.0 27 7d Calm6 alpha files 0:150 1:150 A:1174401516;C:871068073;G:1145864920;T:1118174763;N:27717328 150 150     1174401516 871068073 1145864920 1118174763 27717328 SRX1583811 SRS1295586 SRA353254 SRA Bar-Ilan University 2 0.002 0.032 0.0007 0.02494 0.99924 0.99912 0.38 0.38606 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2016-02-14 Undetermined Undetermined Whole Organism All anatomical structures
40383 40383 SRR3166957 SRX1583810 SRS1295587 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRA library 7d PHA7   breed:AB|chain:alpha|index:36|sex:male|time point:7d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 7d PHA7 14 7d PHA7 alpha 14 7d PHA7 alpha five prime RACE amplification of TCRa transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_14_7d_PHA7_alpha.fq.gz read2_14_7d_PHA7_alpha.fq.gz fastq fastq 3401366100.0 11337887.0 14 7d PHA7 alpha files                       SRX1583810 SRS1295587 SRA353254 SRA Bar-Ilan University 2 0.00357 0.02242 0.00202 0.01952 0.99902 0.99811 0.35016 0.5424 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40384 40384 SRR3166956 SRX1583809 SRS1295588 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRA library 7d PHA3   breed:AB|chain:alpha|index:35|sex:male|time point:7d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRa sequencing of zebrafish: whole zebrafish: Sample TCRA library 7d PHA3 10 7d PHA3 alpha 10 7d PHA3 alpha five prime RACE amplification of TCRa transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read2_10_7d_PHA3_alpha.fq.gz read1_10_7d_PHA3_alpha.fq.gz fastq fastq 4293459300.0 14311531.0 10 7d PHA3 alpha files 0:150 1:150 A:1208054755;C:855800391;G:1072212534;T:1129932131;N:27459489 150 150     1208054755 855800391 1072212534 1129932131 27459489 SRX1583809 SRS1295588 SRA353254 SRA Bar-Ilan University 2 0.00174 0.05155 0.0009 0.0472 0.99937 0.9989 0.2256 0.60714 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40385 40385 SRR3166955 SRX1583808 SRS1295589 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 28d Calm7   breed:AB|chain:beta|index:56|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d Calm7 119 28d Calm7 beta 119 28d Calm7 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_119_28d_Calm7_beta.fq.gz read2_119_28d_Calm7_beta.fq.gz fastq fastq 3494941800.0 11649806.0 119 28d Calm7 beta files 0:150 1:150 A:1262121526;C:602497563;G:790544892;T:738346792;N:101431027 150 150     1262121526 602497563 790544892 738346792 101431027 SRX1583808 SRS1295589 SRA353254 SRA Bar-Ilan University 2 3e-05 0.00179 0.0 7e-05 0.99997 0.99831 0.0 0.42009 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40386 40386 SRR3166954 SRX1583807 SRS1295590 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 28d Calm5   breed:AB|chain:beta|index:55|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d Calm5 117 28d Calm5 beta 117 28d Calm5 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read2_117_28d_Calm5_beta.fq.gz read1_117_28d_Calm5_beta.fq.gz fastq fastq 2950876200.0 9836254.0 117 28d Calm5 beta files 0:150 1:150 A:1025845698;C:505599350;G:688977765;T:634738210;N:95715177 150 150     1025845698 505599350 688977765 634738210 95715177 SRX1583807 SRS1295590 SRA353254 SRA Bar-Ilan University 2 0.0 0.00023 0.0 0.0 1.0 0.99987   0.07692 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2016-03-02 Undetermined Undetermined Whole Organism All anatomical structures
40387 40387 SRR3166953 SRX1583806 SRS1295591 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 28d Calm3   breed:AB|chain:beta|index:54|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d Calm3 115 28d Calm3 beta 115 28d Calm3 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_115_28d_Calm3_beta.fq.gz read2_115_28d_Calm3_beta.fq.gz fastq fastq 1913218200.0 6377394.0 115 28d Calm3 beta files 0:150 1:150 A:637646003;C:349779874;G:435732113;T:430619528;N:59440682 150 150     637646003 349779874 435732113 430619528 59440682 SRX1583806 SRS1295591 SRA353254 SRA Bar-Ilan University 2 0.0 0.02438 0.0 0.00184 1.0 0.99908   0.01511 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40388 40388 SRR3166952 SRX1583805 SRS1295592 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 28d KLH6   breed:AB|chain:beta|index:27|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d KLH6 110 28d KLH6 beta 110 28d KLH6 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_110_28d_KLH6_beta.fq.gz read2_110_28d_KLH6_beta.fq.gz fastq fastq 2689206600.0 8964022.0 110 28d KLH6 beta files 0:150 1:150 A:807762783;C:503825062;G:585283183;T:703818890;N:88516682 150 150     807762783 503825062 585283183 703818890 88516682 SRX1583805 SRS1295592 SRA353254 SRA Bar-Ilan University 2 0.00014 0.3078 0.0 0.02202 0.99975 0.99095 0.38888 0.10297 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40389 40389 SRR3166951 SRX1583804 SRS1295593 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 28d KLH2   breed:AB|chain:beta|index:23|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d KLH2 106 28d KLH2 beta 106 28d KLH2 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read2_106_28d_KLH2_beta.fq.gz read1_106_28d_KLH2_beta.fq.gz fastq fastq 2795086200.0 9316954.0 106 28d KLH2 beta files 0:150 1:150 A:897420089;C:470460508;G:621809014;T:712999451;N:92397138 150 150     897420089 470460508 621809014 712999451 92397138 SRX1583804 SRS1295593 SRA353254 SRA Bar-Ilan University 2 0.0 0.05106 0.0 0.00859 1.0 0.99943   0.01388 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2016-03-02 Undetermined Undetermined Whole Organism All anatomical structures
40390 40390 SRR3166950 SRX1583803 SRS1295594 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 28d KLH1   breed:AB|chain:beta|index:22|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d KLH1 105 28d KLH1 beta 105 28d KLH1 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_105_28d_KLH1_beta.fq.gz read2_105_28d_KLH1_beta.fq.gz fastq fastq 1768628700.0 5895429.0 105 28d KLH1 beta files 0:150 1:150 A:486366963;C:366398128;G:389871583;T:478235213;N:47756813 150 150     486366963 366398128 389871583 478235213 47756813 SRX1583803 SRS1295594 SRA353254 SRA Bar-Ilan University 2 4e-05 0.09054 3e-05 0.01597 1.0 0.99931   0.00767 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40391 40391 SRR3166949 SRX1583802 SRS1295595 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 28d PHA7   breed:AB|chain:beta|index:30|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d PHA7 103 28d PHA7 beta 103 28d PHA7 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_103_28d_PHA7_beta.fq.gz read2_103_28d_PHA7_beta.fq.gz fastq fastq 2234344500.0 7447815.0 103 28d PHA7 beta files 0:150 1:150 A:628358242;C:462371909;G:526170885;T:548473987;N:68969477 150 150     628358242 462371909 526170885 548473987 68969477 SRX1583802 SRS1295595 SRA353254 SRA Bar-Ilan University 2 0.00104 0.68691 5e-05 0.01999 0.99894 0.97281 0.23076 0.44172 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2016-03-02 Undetermined Undetermined Whole Organism All anatomical structures
40392 40392 SRR3166948 SRX1583801 SRS1295596 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 28d PHA5   breed:AB|chain:beta|index:29|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d PHA5 101 28d PHA5 beta 101 28d PHA5 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_101_28d_PHA5_beta.fq.gz read2_101_28d_PHA5_beta.fq.gz fastq fastq 1356278400.0 4520928.0 101 28d PHA5 beta files 0:150 1:150 A:372190640;C:278464953;G:294268430;T:378226253;N:33128124 150 150     372190640 278464953 294268430 378226253 33128124 SRX1583801 SRS1295596 SRA353254 SRA Bar-Ilan University 2 0.00254 0.10913 0.0001 0.01715 0.99995 0.99904 0.01106 0.01084 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40393 40393 SRR3166947 SRX1583800 SRS1295597 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 28d PHA2   breed:AB|chain:beta|index:28|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d PHA2 98 28d PHA2 beta 98 28d PHA2 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read2_98_28d_PHA2_beta.fq.gz read1_98_28d_PHA2_beta.fq.gz fastq fastq 4533755400.0 15112518.0 98 28d PHA2 beta files 0:150 1:150 A:1508096116;C:749853448;G:1051562277;T:1142392486;N:81851073 150 150     1508096116 749853448 1051562277 1142392486 81851073 SRX1583800 SRS1295597 SRA353254 SRA Bar-Ilan University 2 0.0 0.33493 0.0 0.02388 1.0 0.99758   0.15819 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40394 40394 SRR3166946 SRX1583799 SRS1295598 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 28d IFA 5   breed:AB|chain:beta|index:11|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d IFA 5 93 28d IFA 5 beta 93 28d IFA 5 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_93_28d_IFA_5_beta.fq.gz read2_93_28d_IFA_5_beta.fq.gz fastq fastq 1526394600.0 5087982.0 93 28d IFA 5 beta files 0:150 1:150 A:431910708;C:323148774;G:334806769;T:417586287;N:18942062 150 150     431910708 323148774 334806769 417586287 18942062 SRX1583799 SRS1295598 SRA353254 SRA Bar-Ilan University 2 0.00039 0.31457 0.00015 0.00771 0.99963 0.98468 0.28947 0.16209 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40395 40395 SRR3166945 SRX1583798 SRS1295599 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 28d IFA 2   breed:AB|chain:beta|index:10|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d IFA 2 90 28d IFA 2 beta 90 28d IFA 2 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_90_28d_IFA_2_beta.fq.gz read2_90_28d_IFA_2_beta.fq.gz fastq fastq 2345298300.0 7817661.0 90 28d IFA 2 beta files 0:150 1:150 A:753823005;C:419081900;G:516233583;T:613533931;N:42625881 150 150     753823005 419081900 516233583 613533931 42625881 SRX1583798 SRS1295599 SRA353254 SRA Bar-Ilan University 2 0.00015 0.38592 3e-05 0.00508 0.99985 0.99385 0.33333 0.06202 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40396 40396 SRR3166944 SRX1583797 SRS1295600 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 28d IFA 1   breed:AB|chain:beta|index:28|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 28d IFA 1 89 28d IFA 1 beta 89 28d IFA 1 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_89_28d_IFA_1_beta.fq.gz read2_89_28d_IFA_1_beta.fq.gz fastq fastq 2029349400.0 6764498.0 89 28d IFA 1 beta files 0:150 1:150 A:714287901;C:360307311;G:472841677;T:446872160;N:35040351 150 150     714287901 360307311 472841677 446872160 35040351 SRX1583797 SRS1295600 SRA353254 SRA Bar-Ilan University 2 0.0 0.06313 0.0 0.01031 1.0 0.99703   0.15591 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40397 40397 SRR3166943 SRX1583796 SRS1295601 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 21d Calm6   breed:AB|chain:beta|index:44|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d Calm6 86 21d Calm6 beta 86 21d Calm6 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read2_86_21d_Calm6_beta.fq.gz read1_86_21d_Calm6_beta.fq.gz fastq fastq 2610499200.0 8701664.0 86 21d Calm6 beta files 0:150 1:150 A:764524163;C:544491001;G:601533912;T:654396223;N:45553901 150 150     764524163 544491001 601533912 654396223 45553901 SRX1583796 SRS1295601 SRA353254 SRA Bar-Ilan University 2 0.00108 0.63356 0.00012 0.12284 0.99837 0.96193 0.21768 0.38237 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2016-03-02 Undetermined Undetermined Whole Organism All anatomical structures
40398 40398 SRR3166942 SRX1583795 SRS1295602 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 21d Calm5   breed:AB|chain:beta|index:43|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d Calm5 85 21d Calm5 beta 85 21d Calm5 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_85_21d_Calm5_beta.fq.gz read2_85_21d_Calm5_beta.fq.gz fastq fastq 2700056100.0 9000187.0 85 21d Calm5 beta files 0:150 1:150 A:755011216;C:593419169;G:623123170;T:688658373;N:39844172 150 150     755011216 593419169 623123170 688658373 39844172 SRX1583795 SRS1295602 SRA353254 SRA Bar-Ilan University 2 0.00244 0.68155 0.00026 0.01492 0.99766 0.96597 0.24863 0.31823 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40399 40399 SRR3166941 SRX1583794 SRS1295603 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 21d Calm1   breed:AB|chain:beta|index:42|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d Calm1 81 21d Calm1 beta 81 21d Calm1 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_81_21d_Calm1_beta.fq.gz read2_81_21d_Calm1_beta.fq.gz fastq fastq 2296683900.0 7655613.0 81 21d Calm1 beta files 0:150 1:150 A:776751441;C:430253074;G:528909259;T:525320137;N:35449989 150 150     776751441 430253074 528909259 525320137 35449989 SRX1583794 SRS1295603 SRA353254 SRA Bar-Ilan University 2 2e-05 0.0464 0.0 0.00091 0.99997 0.99882 0.0 0.0134 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2016-03-02 Undetermined Undetermined Whole Organism All anatomical structures
40400 40400 SRR3166940 SRX1583793 SRS1295604 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 21d KLH6   breed:AB|chain:beta|index:50|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d KLH6 78 21d KLH6 beta 78 21d KLH6 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_78_21d_KLH6_beta.fq.gz read2_78_21d_KLH6_beta.fq.gz fastq fastq 1500221100.0 5000737.0 78 21d KLH6 beta files 0:150 1:150 A:435807096;C:294707078;G:337922064;T:361615328;N:70169534 150 150     435807096 294707078 337922064 361615328 70169534 SRX1583793 SRS1295604 SRA353254 SRA Bar-Ilan University 2 5e-05 0.37212 3e-05 0.03128 0.99997 0.99358 0.0 0.11962 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40401 40401 SRR3166939 SRX1583792 SRS1295605 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 21d KLH5   breed:AB|chain:beta|index:49|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d KLH5 77 21d KLH5 beta 77 21d KLH5 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_77_21d_KLH5_beta.fq.gz read2_77_21d_KLH5_beta.fq.gz fastq fastq 2106732600.0 7022442.0 77 21d KLH5 beta files 0:150 1:150 A:696373936;C:376059887;G:465978414;T:465485185;N:102835178 150 150     696373936 376059887 465978414 465485185 102835178 SRX1583792 SRS1295605 SRA353254 SRA Bar-Ilan University 2 0.0 0.04625 0.0 0.00381 1.0 0.99979   0.00123 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40402 40402 SRR3166938 SRX1583791 SRS1295606 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 21d KLH1   breed:AB|chain:beta|index:48|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d KLH1 73 21d KLH1 beta 73 21d KLH1 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read2_73_21d_KLH1_beta.fq.gz read1_73_21d_KLH1_beta.fq.gz fastq fastq 3554391900.0 11847973.0 73 21d KLH1 beta files 0:150 1:150 A:1312477977;C:598886813;G:787337227;T:686894043;N:168795840 150 150     1312477977 598886813 787337227 686894043 168795840 SRX1583791 SRS1295606 SRA353254 SRA Bar-Ilan University 2 6e-05 0.00136 5e-05 0.00019 1.0 0.99983   0.0303 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40403 40403 SRR3166937 SRX1583790 SRS1295607 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 21d PHA6   breed:AB|chain:beta|index:53|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d PHA6 70 21d PHA6 beta 70 21d PHA6 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read2_70_21d_PHA6_beta.fq.gz read1_70_21d_PHA6_beta.fq.gz fastq fastq 4238076900.0 14126923.0 70 21d PHA6 beta files 0:150 1:150 A:1519543327;C:710498920;G:932091678;T:844220454;N:231722521 150 150     1519543327 710498920 932091678 844220454 231722521 SRX1583790 SRS1295607 SRA353254 SRA Bar-Ilan University 2 0.00023 0.00772 7e-05 0.00068 0.99991 0.99851 0.25 0.08615 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40404 40404 SRR3166936 SRX1583789 SRS1295608 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 21d PHA4   breed:AB|chain:beta|index:52|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d PHA4 68 21d PHA4 beta 68 21d PHA4 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_68_21d_PHA4_beta.fq.gz read2_68_21d_PHA4_beta.fq.gz fastq fastq 2030511600.0 6768372.0 68 21d PHA4 beta files 0:150 1:150 A:659873688;C:307551211;G:388669539;T:566328083;N:108089079 150 150     659873688 307551211 388669539 566328083 108089079 SRX1583789 SRS1295608 SRA353254 SRA Bar-Ilan University 2 0.00029 0.24246 3e-05 0.05929 0.99971 0.99214 0.4 0.16492 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40405 40405 SRR3166935 SRX1583788 SRS1295609 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 21d PHA1   breed:AB|chain:beta|index:51|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d PHA1 65 21d PHA1 beta 65 21d PHA1 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_65_21d_PHA1_beta.fq.gz read2_65_21d_PHA1_beta.fq.gz fastq fastq 930240600.0 3100802.0 65 21d PHA1 beta files 0:150 1:150 A:259486434;C:184043790;G:197463162;T:250422190;N:38825024 150 150     259486434 184043790 197463162 250422190 38825024 SRX1583788 SRS1295609 SRA353254 SRA Bar-Ilan University 2 0.00012 0.14868 0.0 0.02051 0.99963 0.99111 0.36842 0.258 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40406 40406 SRR3166934 SRX1583787 SRS1295610 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 21d IFA 8   breed:AB|chain:beta|index:47|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d IFA 8 64 21d IFA 8 beta 64 21d IFA 8 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_64_21d_IFA_8_beta.fq.gz read2_64_21d_IFA_8_beta.fq.gz fastq fastq 1461868800.0 4872896.0 64 21d IFA 8 beta files 0:150 1:150 A:462418747;C:247121586;G:284662907;T:394116911;N:73548649 150 150     462418747 247121586 284662907 394116911 73548649 SRX1583787 SRS1295610 SRA353254 SRA Bar-Ilan University 2 0.0001 0.17532 0.0 0.04988 0.99983 0.99843 0.25 0.01908 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40407 40407 SRR3166933 SRX1583786 SRS1295611 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 21d IFA 4   breed:AB|chain:beta|index:46|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d IFA 4 60 21d IFA 4 beta 60 21d IFA 4 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read2_60_21d_IFA_4_beta.fq.gz read1_60_21d_IFA_4_beta.fq.gz fastq fastq 4128399900.0 13761333.0 60 21d IFA 4 beta files 0:150 1:150 A:1332478795;C:800389451;G:937176538;T:950735272;N:107619844 150 150     1332478795 800389451 937176538 950735272 107619844 SRX1583786 SRS1295611 SRA353254 SRA Bar-Ilan University 2 0.00043 0.19668 5e-05 0.00597 0.99953 0.9782 0.2647 0.35656 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40408 40408 SRR3166932 SRX1583785 SRS1295612 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 21d IFA 2   breed:AB|chain:beta|index:45|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 21d IFA 2 58 21d IFA 2 beta 58 21d IFA 2 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read2_58_21d_IFA_2_beta.fq.gz read1_58_21d_IFA_2_beta.fq.gz fastq fastq 5035078800.0 16783596.0 58 21d IFA 2 beta files 0:150 1:150 A:1714919930;C:839542402;G:1121993893;T:1220614755;N:138007820 150 150     1714919930 839542402 1121993893 1220614755 138007820 SRX1583785 SRS1295612 SRA353254 SRA Bar-Ilan University 2 0.0 0.17551 0.0 0.00318 1.0 0.99833   0.10802 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2016-03-02 Undetermined Undetermined Whole Organism All anatomical structures
40409 40409 SRR3166931 SRX1583784 SRS1295613 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 14d Calm6   breed:AB|chain:beta|index:37|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 14d Calm6 55 14d Calm6 beta 55 14d Calm6 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_55_14d_Calm6_beta.fq.gz read2_55_14d_Calm6_beta.fq.gz fastq fastq 1028012700.0 3426709.0 55 14d Calm6 beta files 0:150 1:150 A:295958360;C:207583542;G:216651025;T:284035600;N:23784173 150 150     295958360 207583542 216651025 284035600 23784173 SRX1583784 SRS1295613 SRA353254 SRA Bar-Ilan University 2 5e-05 0.16498 0.0 0.01748 0.99989 0.99253 0.33333 0.12385 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2016-03-02 Undetermined Undetermined Whole Organism All anatomical structures
40410 40410 SRR3166930 SRX1583783 SRS1295614 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library Naive6   breed:AB|chain:beta|index:31|sex:male|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library Naive6 126 Naive6 beta 126 Naive6 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read2_126_Naive6_beta.fq.gz read1_126_Naive6_beta.fq.gz fastq fastq 1984909800.0 6616366.0 126 Naive6 beta files 0:150 1:150 A:574002364;C:411972224;G:452963561;T:493883048;N:52088603 150 150     574002364 411972224 452963561 493883048 52088603 SRX1583783 SRS1295614 SRA353254 SRA Bar-Ilan University 2 0.0007 0.73767 5e-05 0.01562 0.99928 0.9754 0.16 0.44061 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40411 40411 SRR3166929 SRX1583782 SRS1295615 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 14d IFA1   breed:AB|chain:beta|index:38|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 14d IFA1 36 14d IFA1 beta 36 14d IFA1 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read2_36_14d_IFA1_beta.fq.gz read1_36_14d_IFA1_beta.fq.gz fastq fastq 2641709400.0 8805698.0 36 14d IFA1 beta files 0:150 1:150 A:828430279;C:516389015;G:603137557;T:652458512;N:41294037 150 150     828430279 516389015 603137557 652458512 41294037 SRX1583782 SRS1295615 SRA353254 SRA Bar-Ilan University 2 6e-05 0.17777 1e-05 0.00441 0.99991 0.99243 0.5 0.07212 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40412 40412 SRR3166928 SRX1583781 SRS1295616 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 14d PHA7   breed:AB|chain:beta|index:41|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 14d PHA7 35 14d PHA7 beta 35 14d PHA7 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read2_35_14d_PHA7_beta.fq.gz read1_35_14d_PHA7_beta.fq.gz fastq fastq 2481744900.0 8272483.0 35 14d PHA7 beta files 0:150 1:150 A:684148801;C:534638425;G:555073374;T:671216692;N:36667608 150 150     684148801 534638425 555073374 671216692 36667608 SRX1583781 SRS1295616 SRA353254 SRA Bar-Ilan University 2 0.00054 0.3447 8e-05 0.03511 0.9991 0.97049 0.29411 0.37357 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2017-02-12 Undetermined Undetermined Whole Organism All anatomical structures
40413 40413 SRR3166927 SRX1583780 SRS1295617 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 14d PHA6   breed:AB|chain:beta|index:40|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 14d PHA6 34 14d PHA6 beta 34 14d PHA6 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_34_14d_PHA6_beta.fq.gz read2_34_14d_PHA6_beta.fq.gz fastq fastq 2149899000.0 7166330.0 34 14d PHA6 beta files 0:150 1:150 A:603640552;C:452244383;G:474826068;T:587177894;N:32010103 150 150     603640552 452244383 474826068 587177894 32010103 SRX1583780 SRS1295617 SRA353254 SRA Bar-Ilan University 2 4e-05 0.16994 0.0 0.14727 0.99991 0.99342 0.0 0.31047 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2016-03-02 Undetermined Undetermined Whole Organism All anatomical structures
40414 40414 SRR3166926 SRX1583779 SRS1295618 SRP070056 PRJNA309588 Analysis of the T cell response in Zebrafish PRJNA309588 Other Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.         TCRB library 14d PHA5   breed:AB|chain:beta|index:39|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal                 TCRb sequencing of zebrafish: whole zebrafish: Sample TCRB library 14d PHA5 33 14d PHA5 beta 33 14d PHA5 beta five prime RACE amplification of TCRb transcript     AMPLICON TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070056     read1_33_14d_PHA5_beta.fq.gz read2_33_14d_PHA5_beta.fq.gz fastq fastq 4781329500.0 15937765.0 33 14d PHA5 beta files 0:150 1:150 A:1564269921;C:790001191;G:1015752339;T:1331170138;N:80135911 150 150     1564269921 790001191 1015752339 1331170138 80135911 SRX1583779 SRS1295618 SRA353254 SRA Bar-Ilan University 2 0.00034 0.20127 0.00018 0.00887 0.99989 0.99567 0.05263 0.08667 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Israel 2016-03-02 Undetermined Undetermined Whole Organism All anatomical structures
48726 48726 SRR7789580 SRX4644423 SRS3742493 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 12hpf 3 S18   strain:5D|isolate:108|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 12hpf 3 S18 TDCIPP 12hpf 3 S18 TDCIPP 12hpf 3 S18 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-12hpf-3_S18_L001_R2_001.fastq.gz TDCIPP-12hpf-3_S18_L001_R1_001.fastq.gz fastq fastq 103340472.0 472844.0 TDCIPP 12hpf 3 S18 L001 R1 001.fastq.gz 0:109.23 1:109.32 A:26737838;C:24795090;G:24934613;T:26529096;N:343835 109 109     26737838 24795090 24934613 26529096 343835 SRX4644423 SRS3742493 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.95154 0.95221 0.00019 0.00019 0.99922 0.99924 0.41074 0.41244 121 121 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48727 48727 SRR7789581 SRX4644422 SRS3742492 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 12hpf 2 S17   strain:5D|isolate:107|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 12hpf 2 S17 TDCIPP 12hpf 2 S17 TDCIPP 12hpf 2 S17 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-12hpf-2_S17_L001_R1_001.fastq.gz TDCIPP-12hpf-2_S17_L001_R2_001.fastq.gz fastq fastq 127382315.0 575073.0 TDCIPP 12hpf 2 S17 L001 R1 001.fastq.gz 0:110.70 1:110.81 A:32604644;C:30882861;G:31076792;T:32385804;N:432214 110 110     32604644 30882861 31076792 32385804 432214 SRX4644422 SRS3742492 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.94383 0.94386 0.00021 0.00022 0.99926 0.99926 0.41023 0.38711 151 151 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48728 48728 SRR7789582 SRX4644421 SRS3742490 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 12hpf 1 S16   strain:5D|isolate:106|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 12hpf 1 S16 TDCIPP 12hpf 1 S16 TDCIPP 12hpf 1 S16 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-12hpf-1_S16_L001_R1_001.fastq.gz TDCIPP-12hpf-1_S16_L001_R2_001.fastq.gz fastq fastq 106771425.0 482515.0 TDCIPP 12hpf 1 S16 L001 R1 001.fastq.gz 0:110.59 1:110.69 A:27853264;C:25384933;G:25518809;T:27629968;N:384451 110 110     27853264 25384933 25518809 27629968 384451 SRX4644421 SRS3742490 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.95913 0.95873 0.00021 0.00025 0.99928 0.99928 0.4122 0.39928 79 79 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48729 48729 SRR7789583 SRX4644420 SRS3742491 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DMSO 12hpf 3 S9x   strain:5D|isolate:105|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 12hpf 3 S9x DMSO 12hpf 3 S9x DMSO 12hpf 3 S9x Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     DMSO-12hpf-3_S9x_L001_R2_001.fastq.gz DMSO-12hpf-3_S9x_L001_R1_001.fastq.gz fastq fastq 106526213.0 483892.0 DMSO 12hpf 3 S9x L001 R2 001.fastq.gz 0:110.00 1:110.14 A:27523846;C:25609135;G:25786277;T:27228622;N:378333 110 110     27523846 25609135 25786277 27228622 378333 SRX4644420 SRS3742491 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.95736 0.95668 0.00013 0.00011 0.99924 0.99926 0.45348 0.45617 77 77 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48730 48730 SRR7789584 SRX4644419 SRS3742489 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DMSO 12hpf 2 S8   strain:5D|isolate:104|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 12hpf 2 S8 DMSO 12hpf 2 S8 DMSO 12hpf 2 S8 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     DMSO-12hpf-2_S8_L001_R1_001.fastq.gz DMSO-12hpf-2_S8_L001_R2_001.fastq.gz fastq fastq 126754105.0 599652.0 DMSO 12hpf 2 S8 L001 R1 001.fastq.gz 0:105.62 1:105.76 A:32875248;C:30352965;G:30543115;T:32575671;N:407106 105 105     32875248 30352965 30543115 32575671 407106 SRX4644419 SRS3742489 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.9631 0.96229 0.00019 0.00019 0.99928 0.99928 0.45939 0.44598 92 92 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48731 48731 SRR7789585 SRX4644418 SRS3742488 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DMSO 12hpf 1 S7   strain:5D|isolate:103|dev stage:12 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 12hpf 1 S7 DMSO 12hpf 1 S7 DMSO 12hpf 1 S7 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     DMSO-12hpf-1_S7_L001_R2_001.fastq.gz DMSO-12hpf-1_S7_L001_R1_001.fastq.gz fastq fastq 133973234.0 626692.0 DMSO 12hpf 1 S7 L001 R1 001.fastq.gz 0:106.86 1:106.92 A:34741794;C:32048895;G:32233963;T:34368689;N:579893 106 106     34741794 32048895 32233963 34368689 579893 SRX4644418 SRS3742488 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.961 0.9606 0.0002 0.00021 0.99928 0.99928 0.47357 0.45763 74 74 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Segmentation Embryo Embryo Imprecise All anatomical structures
48732 48732 SRR7789586 SRX4644417 SRS3742487 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 6hpf 5 S15   strain:5D|isolate:102|dev stage:6 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 6hpf 5 S15 TDCIPP 6hpf 5 S15 TDCIPP 6hpf 5 S15 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-6hpf-5_S15_L001_R1_001.fastq.gz TDCIPP-6hpf-5_S15_L001_R2_001.fastq.gz fastq fastq 103436592.0 515633.0 TDCIPP 6hpf 5 S15 L001 R2 001.fastq.gz 0:100.23 1:100.37 A:26213221;C:25393681;G:25395332;T:25877353;N:557005 100 100     26213221 25393681 25395332 25877353 557005 SRX4644417 SRS3742487 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.9545 0.9544 0.00043 0.0004 0.99898 0.99904 0.33908 0.3596 64 151 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Gastrula Embryo Embryo Imprecise All anatomical structures
48733 48733 SRR7789587 SRX4644416 SRS3742486 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 6hpf 3 S14   strain:5D|isolate:101|dev stage:6 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 6hpf 3 S14 TDCIPP 6hpf 3 S14 TDCIPP 6hpf 3 S14 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-6hpf-3_S14_L001_R1_001.fastq.gz TDCIPP-6hpf-3_S14_L001_R2_001.fastq.gz fastq fastq 99767681.0 500238.0 TDCIPP 6hpf 3 S14 L001 R2 001.fastq.gz 0:99.64 1:99.80 A:25255312;C:24464400;G:24481390;T:25002218;N:564361 99 99     25255312 24464400 24481390 25002218 564361 SRX4644416 SRS3742486 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.96117 0.96052 0.00028 0.00028 0.99924 0.99922 0.35418 0.35375 148 149 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Gastrula Embryo Embryo Imprecise All anatomical structures
48752 48752 SRR7789606 SRX4644397 SRS3742467 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DMSO 6hpf 5 S6   strain:5D|isolate:99|dev stage:6 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 6hpf 5 S6 DMSO 6hpf 5 S6 DMSO 6hpf 5 S6 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     DMSO-6hpf-5_S6_L001_R1_001.fastq.gz DMSO-6hpf-5_S6_L001_R2_001.fastq.gz fastq fastq 107736291.0 525615.0 DMSO 6hpf 5 S6 L001 R2 001.fastq.gz 0:102.38 1:102.59 A:27251903;C:26520518;G:26567935;T:26878661;N:517274 102 102     27251903 26520518 26567935 26878661 517274 SRX4644397 SRS3742467 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.96019 0.95982 0.00045 0.00043 0.99918 0.99916 0.37174 0.3343 151 148 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Gastrula Embryo Embryo Imprecise All anatomical structures
48753 48753 SRR7789607 SRX4644396 SRS3742466 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 6hpf 1 S13   strain:5D|isolate:100|dev stage:6 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 6hpf 1 S13 TDCIPP 6hpf 1 S13 TDCIPP 6hpf 1 S13 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-6hpf-1_S13_L001_R2_001.fastq.gz TDCIPP-6hpf-1_S13_L001_R1_001.fastq.gz fastq fastq 91271391.0 448917.0 TDCIPP 6hpf 1 S13 L001 R2 001.fastq.gz 0:101.61 1:101.71 A:23269221;C:22266290;G:22291849;T:22983659;N:460372 101 101     23269221 22266290 22291849 22983659 460372 SRX4644396 SRS3742466 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.96069 0.96135 0.0005 0.00051 0.99916 0.99916 0.34621 0.3774 76 76 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Gastrula Embryo Embryo Imprecise All anatomical structures
48754 48754 SRR7789608 SRX4644395 SRS3742465 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DMSO 3hpf 2 S1   strain:5D|isolate:91|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 3hpf 2 S1 DMSO 3hpf 2 S1 DMSO 3hpf 2 S1 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     DMSO-3hpf-2_S1_L001_R1_001.fastq.gz DMSO-3hpf-2_S1_L001_R2_001.fastq.gz fastq fastq 143035914.0 673342.0 DMSO 3hpf 2 S1 L001 R2 001.fastq.gz 0:106.19 1:106.24 A:37104542;C:34199194;G:34286529;T:36802368;N:643281 106 106     37104542 34199194 34286529 36802368 643281 SRX4644395 SRS3742465 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.97329 0.97288 0.00018 0.00017 0.99931 0.99931 0.41042 0.4514 39 39 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Blastula Embryo Embryo Imprecise All anatomical structures
48755 48755 SRR7789609 SRX4644394 SRS3742464 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DMSO 3hpf 3 S2   strain:5D|isolate:92|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 3hpf 3 S2 DMSO 3hpf 3 S2 DMSO 3hpf 3 S2 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     DMSO-3hpf-3_S2_L001_R2_001.fastq.gz DMSO-3hpf-3_S2_L001_R1_001.fastq.gz fastq fastq 121995763.0 560778.0 DMSO 3hpf 3 S2 L001 R2 001.fastq.gz 0:108.73 1:108.82 A:31569811;C:29316325;G:29402755;T:31346545;N:360327 108 108     31569811 29316325 29402755 31346545 360327 SRX4644394 SRS3742464 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.96945 0.96871 0.00029 0.00031 0.99924 0.99924 0.3498 0.37356 134 134 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Blastula Embryo Embryo Imprecise All anatomical structures
48756 48756 SRR7789610 SRX4644393 SRS3742463 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DMSO 3hpf 4 S3   strain:5D|isolate:93|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 3hpf 4 S3 DMSO 3hpf 4 S3 DMSO 3hpf 4 S3 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     DMSO-3hpf-4_S3_L001_R1_001.fastq.gz DMSO-3hpf-4_S3_L001_R2_001.fastq.gz fastq fastq 131169421.0 625415.0 DMSO 3hpf 4 S3 L001 R2 001.fastq.gz 0:104.81 1:104.92 A:33973430;C:31403379;G:31490054;T:33651313;N:651245 104 104     33973430 31403379 31490054 33651313 651245 SRX4644393 SRS3742463 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.98214 0.98232 0.00039 0.00042 0.99931 0.99928 0.43853 0.43838 94 94 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Blastula Embryo Embryo Imprecise All anatomical structures
48757 48757 SRR7789611 SRX4644392 SRS3742462 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 3hpf 1 S10   strain:5D|isolate:94|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 3hpf 1 S10 TDCIPP 3hpf 1 S10 TDCIPP 3hpf 1 S10 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-3hpf-1_S10_L001_R2_001.fastq.gz TDCIPP-3hpf-1_S10_L001_R1_001.fastq.gz fastq fastq 142472001.0 675614.0 TDCIPP 3hpf 1 S10 L001 R2 001.fastq.gz 0:105.40 1:105.48 A:37237954;C:33780885;G:33866153;T:36894511;N:692498 105 105     37237954 33780885 33866153 36894511 692498 SRX4644392 SRS3742462 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.98448 0.98456 3e-05 5e-05 0.99928 0.99926 0.44535 0.45235 89 89 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Blastula Embryo Embryo Imprecise All anatomical structures
48758 48758 SRR7789612 SRX4644391 SRS3742461 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 3hpf 2 S11   strain:5D|isolate:95|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 3hpf 2 S11 TDCIPP 3hpf 2 S11 TDCIPP 3hpf 2 S11 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-3hpf-2_S11_L001_R1_001.fastq.gz TDCIPP-3hpf-2_S11_L001_R2_001.fastq.gz fastq fastq 135473127.0 649900.0 TDCIPP 3hpf 2 S11 L001 R2 001.fastq.gz 0:104.20 1:104.25 A:35005838;C:32424512;G:32538931;T:34827379;N:676467 104 104     35005838 32424512 32538931 34827379 676467 SRX4644391 SRS3742461 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.98266 0.98245 0.0 0.0 0.99933 0.99933 0.49436 0.49577 59 59 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Blastula Embryo Embryo Imprecise All anatomical structures
48759 48759 SRR7789613 SRX4644390 SRS3742460 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         TDCIPP 3hpf 4 S12   strain:5D|isolate:96|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 TDCIPP 3hpf 4 S12 TDCIPP 3hpf 4 S12 TDCIPP 3hpf 4 S12 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     TDCIPP-3hpf-4_S12_L001_R1_001.fastq.gz TDCIPP-3hpf-4_S12_L001_R2_001.fastq.gz fastq fastq 126387362.0 600422.0 TDCIPP 3hpf 4 S12 L001 R1 001.fastq.gz 0:105.21 1:105.28 A:32731869;C:30187130;G:30351165;T:32470755;N:646443 105 105     32731869 30187130 30351165 32470755 646443 SRX4644390 SRS3742460 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.97915 0.97875 0.00012 0.00011 0.99933 0.99933 0.44431 0.44577 117 117 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Blastula Embryo Embryo Imprecise All anatomical structures
48760 48760 SRR7789614 SRX4644389 SRS3742459 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DMSO 6hpf 1 S4   strain:5D|isolate:97|dev stage:6 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 6hpf 1 S4 DMSO 6hpf 1 S4 DMSO 6hpf 1 S4 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     DMSO-6hpf-1_S4_L001_R2_001.fastq.gz DMSO-6hpf-1_S4_L001_R1_001.fastq.gz fastq fastq 95806388.0 464892.0 DMSO 6hpf 1 S4 L001 R2 001.fastq.gz 0:103.02 1:103.07 A:24562000;C:23294432;G:23307788;T:24218011;N:424157 103 103     24562000 23294432 23307788 24218011 424157 SRX4644389 SRS3742459 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.95656 0.95712 0.0004 0.00039 0.99918 0.99916 0.34071 0.34145 94 151 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Gastrula Embryo Embryo Imprecise All anatomical structures
48761 48761 SRR7789615 SRX4644388 SRS3742458 SRP159670 PRJNA475635 Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis PRJNA475635 Other The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.         DMSO 6hpf 3 S5   strain:5D|isolate:98|dev stage:6 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal                 DMSO 6hpf 3 S5 DMSO 6hpf 3 S5 DMSO 6hpf 3 S5 Nextera XT DNA Library Prep kit     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiniSeq   SRP159670     DMSO-6hpf-3_S5_L001_R1_001.fastq.gz DMSO-6hpf-3_S5_L001_R2_001.fastq.gz fastq fastq 105210098.0 508250.0 DMSO 6hpf 3 S5 L001 R1 001.fastq.gz 0:103.44 1:103.57 A:26828273;C:25677269;G:25721655;T:26524232;N:458669 103 103     26828273 25677269 25721655 26524232 458669 SRX4644388 SRS3742458 SRA767209 University of California, Riverside|Environmental Sciences University of California, Riverside 2 0.95583 0.95513 0.00047 0.00045 0.99916 0.99918 0.30844 0.29023 42 42 B B biological fallback assumption illumina miseq unknown random_priming nextera bulk unknown unknown   United States 2018-09-05 Gastrula Embryo Embryo Imprecise All anatomical structures
62308 62308 SRR13190536 SRX9625062 SRS7826258 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C03 6F C03 6F   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:female|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C03 6F C03 6F DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C03_6F_E37_225_R1.fastq.gz C03_6F_E37_225_R2.fastq.gz fastq fastq 35763616.0 59408.0 C03 6F E37 225 R1.fastq.gz 0:301 1:301 A:9029678;C:8898456;G:8511578;T:9323840;N:64 301 301     9029678 8898456 8511578 9323840 64 SRX9625062 SRS7826258 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 0.0 0.0 0.0 0.0 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62309 62309 SRR13190537 SRX9625061 SRS7826257 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C03 5M C03 5M   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:male|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C03 5M C03 5M DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C03_5M_E37_230_R1.fastq.gz C03_5M_E37_230_R2.fastq.gz fastq fastq 39170334.0 65067.0 C03 5M E37 230 R1.fastq.gz 0:301 1:301 A:9414891;C:10269665;G:9759519;T:9726159;N:100 301 301     9414891 10269665 9759519 9726159 100 SRX9625061 SRS7826257 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 2e-05 0.0 1e-05 0.0 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62310 62310 SRR13190538 SRX9625060 SRS7826256 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C03 5F C03 5F   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:female|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C03 5F C03 5F DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C03_5F_E37_224_R1.fastq.gz C03_5F_E37_224_R2.fastq.gz fastq fastq 34138818.0 56709.0 C03 5F E37 224 R1.fastq.gz 0:301 1:301 A:8590923;C:8531890;G:8159072;T:8856765;N:168 301 301     8590923 8531890 8159072 8856765 168 SRX9625060 SRS7826256 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 0.0 0.0 0.0 0.0 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62311 62311 SRR13190539 SRX9625059 SRS7826255 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C03 4F C03 4F   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:female|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C03 4F C03 4F DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C03_4F_E37_223_R1.fastq.gz C03_4F_E37_223_R2.fastq.gz fastq fastq 26582514.0 44157.0 C03 4F E37 223 R1.fastq.gz 0:301 1:301 A:6082846;C:7306041;G:6930703;T:6262863;N:61 301 301     6082846 7306041 6930703 6262863 61 SRX9625059 SRS7826255 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 0.0 0.0 0.0 0.0 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62312 62312 SRR13190540 SRX9625058 SRS7826254 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C03 3M C03 3M   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:male|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C03 3M C03 3M DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C03_3M_E37_228_R1.fastq.gz C03_3M_E37_228_R2.fastq.gz fastq fastq 32995620.0 54810.0 C03 3M E37 228 R1.fastq.gz 0:301 1:301 A:7367616;C:9186385;G:8768695;T:7672916;N:8 301 301     7367616 9186385 8768695 7672916 8 SRX9625058 SRS7826254 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 2e-05 3e-05 1e-05 2e-05 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62313 62313 SRR13190541 SRX9625057 SRS7826253 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C03 3F C03 3F   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:female|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C03 3F C03 3F DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C03_3F_E37_222_R1.fastq.gz C03_3F_E37_222_R2.fastq.gz fastq fastq 31568278.0 52439.0 C03 3F E37 222 R1.fastq.gz 0:301 1:301 A:7933526;C:7897232;G:7546800;T:8190713;N:7 301 301     7933526 7897232 7546800 8190713 7 SRX9625057 SRS7826253 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 0.0 0.0 0.0 0.0 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62314 62314 SRR13190542 SRX9625056 SRS7826252 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C03 2M C03 2M   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:male|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C03 2M C03 2M DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C03_2M_E37_227_R1.fastq.gz C03_2M_E37_227_R2.fastq.gz fastq fastq 42783538.0 71069.0 C03 2M E37 227 R1.fastq.gz 0:301 1:301 A:9765039;C:11749187;G:11137288;T:10131989;N:35 301 301     9765039 11749187 11137288 10131989 35 SRX9625056 SRS7826252 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 2e-05 0.0 0.0 0.0 0.99997 1.0 0.0   301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62315 62315 SRR13190543 SRX9625055 SRS7826251 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C03 2F C03 2F   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:female|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C03 2F C03 2F DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C03_2F_E37_221_R1.fastq.gz C03_2F_E37_221_R2.fastq.gz fastq fastq 28485436.0 47318.0 C03 2F E37 221 R1.fastq.gz 0:301 1:301 A:6426581;C:7909072;G:7491919;T:6657804;N:60 301 301     6426581 7909072 7491919 6657804 60 SRX9625055 SRS7826251 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 7e-05 8e-05 4e-05 7e-05 0.99997 1.0 0.0   301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62316 62316 SRR13190544 SRX9625054 SRS7826250 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C03 1M C03 1M   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:male|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C03 1M C03 1M DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C03_1M_E37_226_R1.fastq.gz C03_1M_E37_226_R2.fastq.gz fastq fastq 23402148.0 38874.0 C03 1M E37 226 R1.fastq.gz 0:301 1:301 A:5618166;C:6125695;G:5821344;T:5836756;N:187 301 301     5618166 6125695 5821344 5836756 187 SRX9625054 SRS7826250 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 0.0 0.0 0.0 0.0 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62317 62317 SRR13190545 SRX9625053 SRS7826249 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C03 1F C03 1F   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:female|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C03 1F C03 1F DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C03_1F_E37_220_R1.fastq.gz C03_1F_E37_220_R2.fastq.gz fastq fastq 31665200.0 52600.0 C03 1F E37 220 R1.fastq.gz 0:301 1:301 A:7448421;C:8449694;G:8003786;T:7762994;N:305 301 301     7448421 8449694 8003786 7762994 305 SRX9625053 SRS7826249 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 0.0 0.0 0.0 0.0 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62318 62318 SRR13190546 SRX9625052 SRS7826248 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       mi dmso 3c mi dmso 3c   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:120 dpf|dev stage:120 dpf|sex:male|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish mi dmso 3c mi dmso 3c DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     mi-DMSO-3c_S169_L001_R1_001.fastq.gz mi-DMSO-3c_S169_L001_R2_001.fastq.gz fastq fastq 36793460.0 61216.0 mi DMSO 3c S169 L001 R1 001.fastq.gz 0:300.50 1:300.55 A:8657651;C:9730592;G:9252832;T:9148483;N:3902 300 300     8657651 9730592 9252832 9148483 3902 SRX9625052 SRS7826248 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 0.0 0.0 0.0 0.0 1.0 1.0     298 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62319 62319 SRR13190547 SRX9625051 SRS7826247 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C003 6M C003 6M   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:male|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C003 6M C003 6M DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C003_6M_E37_219_R1.fastq.gz C003_6M_E37_219_R2.fastq.gz fastq fastq 34348916.0 57058.0 C003 6M E37 219 R1.fastq.gz 0:301 1:301 A:7854162;C:9466965;G:8942055;T:8085380;N:354 301 301     7854162 9466965 8942055 8085380 354 SRX9625051 SRS7826247 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 0.0 0.0 0.0 0.0 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62320 62320 SRR13190548 SRX9625050 SRS7826245 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C003 6F C003 6F   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:female|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C003 6F C003 6F DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C003_6F_E37_213_R1.fastq.gz C003_6F_E37_213_R2.fastq.gz fastq fastq 33217156.0 55178.0 C003 6F E37 213 R1.fastq.gz 0:301 1:301 A:7984190;C:8678795;G:8293257;T:8260864;N:50 301 301     7984190 8678795 8293257 8260864 50 SRX9625050 SRS7826245 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 0.0 0.0 0.0 0.0 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62321 62321 SRR13190549 SRX9625049 SRS7826246 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C003 5F C003 5F   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:female|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C003 5F C003 5F DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C003_5F_E37_212_R1.fastq.gz C003_5F_E37_212_R2.fastq.gz fastq fastq 32279842.0 53621.0 C003 5F E37 212 R1.fastq.gz 0:301 1:301 A:7391913;C:8803622;G:8385323;T:7698885;N:99 301 301     7391913 8803622 8385323 7698885 99 SRX9625049 SRS7826246 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 0.0 0.0 0.0 0.0 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62322 62322 SRR13190550 SRX9625048 SRS7826244 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C003 4M C003 4M   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:male|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C003 4M C003 4M DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C003_4M_E37_217_R1.fastq.gz C003_4M_E37_217_R2.fastq.gz fastq fastq 29091650.0 48325.0 C003 4M E37 217 R1.fastq.gz 0:301 1:301 A:6414899;C:8113691;G:7810357;T:6752548;N:155 301 301     6414899 8113691 7810357 6752548 155 SRX9625048 SRS7826244 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 0.0 0.0 0.0 0.0 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62323 62323 SRR13190551 SRX9625047 SRS7826243 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C003 4F C003 4F   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:female|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C003 4F C003 4F DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C003_4F_E37_211_R1.fastq.gz C003_4F_E37_211_R2.fastq.gz fastq fastq 36166956.0 60078.0 C003 4F E37 211 R1.fastq.gz 0:301 1:301 A:9364951;C:8583771;G:8096060;T:10122030;N:144 301 301     9364951 8583771 8096060 10122030 144 SRX9625047 SRS7826243 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 2e-05 2e-05 1e-05 1e-05 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62324 62324 SRR13190552 SRX9625046 SRS7826242 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C003 3M C003 3M   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:male|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C003 3M C003 3M DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C003_3M_E37_216_R1.fastq.gz C003_3M_E37_216_R2.fastq.gz fastq fastq 32724720.0 54360.0 C003 3M E37 216 R1.fastq.gz 0:301 1:301 A:7368104;C:9093247;G:8586364;T:7676943;N:62 301 301     7368104 9093247 8586364 7676943 62 SRX9625046 SRS7826242 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 6e-05 7e-05 5e-05 6e-05 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62325 62325 SRR13190553 SRX9625045 SRS7826241 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C003 3F C003 3F   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:female|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C003 3F C003 3F DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C003_3F_E37_210_R1.fastq.gz C003_3F_E37_210_R2.fastq.gz fastq fastq 41061216.0 68208.0 C003 3F E37 210 R1.fastq.gz 0:301 1:301 A:9828974;C:10742677;G:10268095;T:10221288;N:182 301 301     9828974 10742677 10268095 10221288 182 SRX9625045 SRS7826241 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 2e-05 2e-05 1e-05 1e-05 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System
62326 62326 SRR13190554 SRX9625044 SRS7826240 SRP295652 PRJNA682251 microbiota in gastrointestinal tract of zebrafish PRJNA682251 Other Effects of TCS on microbiota of gastrointestinal tract in zebrafish       C003 2M C003 2M   strain:wild type strain AB|isolate:gastrointestinal tract|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4 month|dev stage:4 month|sex:male|tissue:gastrointestinal tract|BioSampleModel:Model organism or animal                 16SrRNA Seq of zebrafish C003 2M C003 2M DNA bacorde     AMPLICON TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP295652     C003_2M_E37_215_R1.fastq.gz C003_2M_E37_215_R2.fastq.gz fastq fastq 31199854.0 51827.0 C003 2M E37 215 R1.fastq.gz 0:301 1:301 A:7022763;C:8640470;G:8225321;T:7311300;N:0 301 301     7022763 8640470 8225321 7311300 0 SRX9625044 SRS7826240 SRA1166526 Xinhua Hospital, Shanghai Jiao Tong university school of medicine|Ministry of Education and Shanghai Key Laboratory Xinhua Hospital, Shanghai Jiao Tong university school of medicine 2 0.0 0.0 0.0 0.0 1.0 1.0     301 301 T T mates < 9% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   China 2020-12-03 Adult Adult Gut Digestive System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;