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49 rows where experiment.library_selection = "RACE" and tissue_curation_coarse = "All anatomical structures"

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devstage_curation_coarse 3

devstage_curation 3

tissue_curation 2

experiment.library_strategy 2

experiment.library_layout 2

tissue_curation_coarse 1

  • All anatomical structures · 49 ✖

technology 1

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • RACE · 49 ✖
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
10141 10141 ERR4973564 ERX4792138 ERS5459722 ERP125703 PRJEB41864 three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E-MTAB-9899 Transcriptome Analysis mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced. ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10   Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina sibling 3 SAMEA7703213 Centre for Developmental Neurobiology King's College London ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703213|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 3                 NextSeq 500 sequencing; 3 prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E MTAB 9899:sibling 3 s sibling 3 s three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RACE SINGLE ILLUMINA NextSeq 500   ERP125703 NextSeq 500 sequencing; three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 70_AACCGA_70_ACTAGC_S2_R1_001.fastq.gz fastq     E MTAB 9899:sibling 3 0:76 1:0 A:385382600;C:210104151;G:238678838;T:315495923;N:5536 76 0     385382600 210104151 238678838 315495923 5536 ERX4792138 ERS5459722 ERA3194022 Centre for Developmental Neurobiology King Centre for Developmental Neurobiology King 1 0.82613   0.13111   0.77597   0.53833   76   B   usable mapping rate illumina nextseq 3prime other lexogen bulk unknown unknown   United Kingdom 2020-12-10 Multi-stage Multi-stage Whole Organism All anatomical structures
10142 10142 ERR4973563 ERX4792137 ERS5459721 ERP125703 PRJEB41864 three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E-MTAB-9899 Transcriptome Analysis mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced. ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10   Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina sibling 2 SAMEA7703212 Centre for Developmental Neurobiology King's College London ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703212|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 2                 NextSeq 500 sequencing; 3 prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E MTAB 9899:sibling 2 s sibling 2 s three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RACE SINGLE ILLUMINA NextSeq 500   ERP125703 NextSeq 500 sequencing; three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 69_AGTTGA_69_CTTACA_S7_R1_001.fastq.gz fastq     E MTAB 9899:sibling 2 0:76 1:0 A:405337161;C:226099266;G:255734601;T:341120121;N:5955 76 0     405337161 226099266 255734601 341120121 5955 ERX4792137 ERS5459721 ERA3194022 Centre for Developmental Neurobiology King Centre for Developmental Neurobiology King 1 0.84066   0.12241   0.77755   0.56472   76   B   usable mapping rate illumina nextseq 3prime other lexogen bulk unknown unknown   United Kingdom 2020-12-10 Multi-stage Multi-stage Whole Organism All anatomical structures
10143 10143 ERR4973562 ERX4792136 ERS5459720 ERP125703 PRJEB41864 three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E-MTAB-9899 Transcriptome Analysis mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced. ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10   Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina sibling 1 SAMEA7703211 Centre for Developmental Neurobiology King's College London ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703211|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 1                 NextSeq 500 sequencing; 3 prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E MTAB 9899:sibling 1 s sibling 1 s three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RACE SINGLE ILLUMINA NextSeq 500   ERP125703 NextSeq 500 sequencing; three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 68_CCAATT_68_GTCCCG_S11_R1_001.fastq.gz fastq     E MTAB 9899:sibling 1 0:76 1:0 A:440539801;C:236835299;G:268057277;T:355636994;N:6169 76 0     440539801 236835299 268057277 355636994 6169 ERX4792136 ERS5459720 ERA3194022 Centre for Developmental Neurobiology King Centre for Developmental Neurobiology King 1 0.82002   0.12908   0.77766   0.54981   76   B   usable mapping rate illumina nextseq 3prime other lexogen bulk unknown unknown   United Kingdom 2020-12-10 Multi-stage Multi-stage Whole Organism All anatomical structures
10144 10144 ERR4973561 ERX4792135 ERS5459719 ERP125703 PRJEB41864 three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E-MTAB-9899 Transcriptome Analysis mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced. ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10   Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina sfpq 3 SAMEA7703210 Centre for Developmental Neurobiology King's College London ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703210|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 3                 NextSeq 500 sequencing; 3 prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E MTAB 9899:sfpq 3 s sfpq 3 s three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Experimental Factor: genotype:sfpq / RNA-Seq TRANSCRIPTOMIC RACE SINGLE ILLUMINA NextSeq 500   ERP125703 NextSeq 500 sequencing; three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 67_TCGTTC_67_TGCTAT_S22_R1_001.fastq.gz fastq     E MTAB 9899:sfpq 3 0:76 1:0 A:493165327;C:268347233;G:303443918;T:399152596;N:7138 76 0     493165327 268347233 303443918 399152596 7138 ERX4792135 ERS5459719 ERA3194022 Centre for Developmental Neurobiology King Centre for Developmental Neurobiology King 1 0.82521   0.12349   0.78545   0.57446   76   B   usable mapping rate illumina nextseq 3prime other lexogen bulk unknown unknown   United Kingdom 2020-12-10 Multi-stage Multi-stage Whole Organism All anatomical structures
10145 10145 ERR4973560 ERX4792134 ERS5459718 ERP125703 PRJEB41864 three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E-MTAB-9899 Transcriptome Analysis mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced. ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10   Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina sfpq 2 SAMEA7703209 Centre for Developmental Neurobiology King's College London ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703209|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 2                 NextSeq 500 sequencing; 3 prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E MTAB 9899:sfpq 2 s sfpq 2 s three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Experimental Factor: genotype:sfpq / RNA-Seq TRANSCRIPTOMIC RACE SINGLE ILLUMINA NextSeq 500   ERP125703 NextSeq 500 sequencing; three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 66_GACGAT_66_TCAGTC_S18_R1_001.fastq.gz fastq     E MTAB 9899:sfpq 2 0:76 1:0 A:426637005;C:227027693;G:257342561;T:338159540;N:5909 76 0     426637005 227027693 257342561 338159540 5909 ERX4792134 ERS5459718 ERA3194022 Centre for Developmental Neurobiology King Centre for Developmental Neurobiology King 1 0.81933   0.11571   0.78593   0.56675   76   B   usable mapping rate illumina nextseq 3prime other lexogen bulk unknown unknown   United Kingdom 2020-12-10 Multi-stage Multi-stage Whole Organism All anatomical structures
10146 10146 ERR4973559 ERX4792133 ERS5459717 ERP125703 PRJEB41864 three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E-MTAB-9899 Transcriptome Analysis mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced. ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10   Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina sfpq 1 SAMEA7703208 Centre for Developmental Neurobiology King's College London ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703208|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 1                 NextSeq 500 sequencing; 3 prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf E MTAB 9899:sfpq 1 s sfpq 1 s three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Experimental Factor: genotype:sfpq / RNA-Seq TRANSCRIPTOMIC RACE SINGLE ILLUMINA NextSeq 500   ERP125703 NextSeq 500 sequencing; three prime mRNA seq of sfpq / zebrafish embryos and siblings at 24 hpf ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10 65_AAGCTC_65_AAGAAG_S3_R1_001.fastq.gz fastq     E MTAB 9899:sfpq 1 0:76 1:0 A:425613638;C:225707961;G:254738302;T:336863560;N:5847 76 0     425613638 225707961 254738302 336863560 5847 ERX4792133 ERS5459717 ERA3194022 Centre for Developmental Neurobiology King Centre for Developmental Neurobiology King 1 0.81857   0.11342   0.78587   0.56439   76   B   usable mapping rate illumina nextseq 3prime other lexogen bulk unknown unknown   United Kingdom 2020-12-10 Multi-stage Multi-stage Whole Organism All anatomical structures
31687 31687 SRR28490625 SRX24092863 SRS20882184 SRP498456 PRJNA1093028 Effect of depletion of Sas10 in pre rRNA processing GSE262698 Transcriptome Analysis Ribosome small subunit SSU is assembled by the SSU processome which contains approximately 70 non ribosomal protein factors. The biochemical mechanism for the SSU processome in 18S rRNA processing and maturation has been extensively studied however how the SSU processome components enter to the nucleolus has not been systematically investigated. Here we checked the nucleolar localization of 50 human SSU processome components and find that UTP3 and other 24 proteins enter to the nucleolus autonomously. For the remaining 25 proteins we find that UTP3/SAS10 assists the nucleolar localization of five proteins namely MPP10 UTP25 EMG1 and two UTP B components UTP12 and UTP13 and this ferry function of UTP3 is conserved in zebrafish. We also find that knockdown of human UTP3 impairs the cleavage at A0 site while loss of function of either utp3/sas10 or utp13/tbl3 in zebrafish causes an accumulation of the processed products containing the five primeETS supporting the crucial role of UTP3 in mediating the five primeETS processing and degradation. Moreover UTP3 directly interacts with and delivers EXOSC10 into the nucleolus suggesting that UTP3 may play a direct role in recruiting the nuclear exosome to the SSU processome for degradation of the processed five primeETS. These findings lay the ground for studying the mechanism of cytoplasm to nucleolus trafficking of the SSU processome components and the multifaceted roles of UTP3 during pre rRNA processing. Overall design: To validate pre rRNA processing defect in zebrafish sas10 tbl3 mutants and human UTP3 knock down cells we performed three primeRACE seq of these samples.   pubmed:39036955   zebrafish embryo 5dpf sas10 mutant rep 2 GSM8174002   source name:embryo|tissue:embryo|genotype:sas10 mutant|geo loc name:missing|collection date:missing zebrafish embryo 5dpf sas10 mutant rep 2 Sequence reads were trimmed of adapter sequences and low quality sequences using Cutadpat. Trimmed sequences were deduplicated zebrafish five primeETS sequence searched and mapped to zebrafish pre rRNA reference sequence to analyze the three prime end of each read. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including each read's relative postion in pre rRNA corresponding sequence modification status and modification size. embryo   Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.   tissue:embryo|genotype:sas10 mutant GSM8174002 GSM8174002: zebrafish embryo 5dpf sas10 mutant rep 2; Danio rerio; RNA Seq GSM8174002 r1 GSM8174002 1 Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.   RNA-Seq TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498456     RACE_S_2_R2.fq.gz RACE_S_2_R1.fq.gz fastq fastq 2676884700.0 8922949.0 GSM8174002 r1 0:150 1:150 A:386375545;C:575923603;G:1262958328;T:451548053;N:79171 150 150     386375545 575923603 1262958328 451548053 79171 SRX24092863 SRS20882184 SRA1835384 MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University 2 0.19638 0.00802 0.19587 0.00751 0.99937 0.99941 0.67088 0.57731 150 150 B T mate2 technical by mapping diff illumina novaseq_era 3prime other unknown bulk unknown unknown   China 2024-03-28 Larval Larval Embryo Imprecise All anatomical structures
31688 31688 SRR28490626 SRX24092862 SRS20882183 SRP498456 PRJNA1093028 Effect of depletion of Sas10 in pre rRNA processing GSE262698 Transcriptome Analysis Ribosome small subunit SSU is assembled by the SSU processome which contains approximately 70 non ribosomal protein factors. The biochemical mechanism for the SSU processome in 18S rRNA processing and maturation has been extensively studied however how the SSU processome components enter to the nucleolus has not been systematically investigated. Here we checked the nucleolar localization of 50 human SSU processome components and find that UTP3 and other 24 proteins enter to the nucleolus autonomously. For the remaining 25 proteins we find that UTP3/SAS10 assists the nucleolar localization of five proteins namely MPP10 UTP25 EMG1 and two UTP B components UTP12 and UTP13 and this ferry function of UTP3 is conserved in zebrafish. We also find that knockdown of human UTP3 impairs the cleavage at A0 site while loss of function of either utp3/sas10 or utp13/tbl3 in zebrafish causes an accumulation of the processed products containing the five primeETS supporting the crucial role of UTP3 in mediating the five primeETS processing and degradation. Moreover UTP3 directly interacts with and delivers EXOSC10 into the nucleolus suggesting that UTP3 may play a direct role in recruiting the nuclear exosome to the SSU processome for degradation of the processed five primeETS. These findings lay the ground for studying the mechanism of cytoplasm to nucleolus trafficking of the SSU processome components and the multifaceted roles of UTP3 during pre rRNA processing. Overall design: To validate pre rRNA processing defect in zebrafish sas10 tbl3 mutants and human UTP3 knock down cells we performed three primeRACE seq of these samples.   pubmed:39036955   zebrafish embryo 5dpf sas10 mutant rep 1 GSM8174001   source name:embryo|tissue:embryo|genotype:sas10 mutant|geo loc name:missing|collection date:missing zebrafish embryo 5dpf sas10 mutant rep 1 Sequence reads were trimmed of adapter sequences and low quality sequences using Cutadpat. Trimmed sequences were deduplicated zebrafish five primeETS sequence searched and mapped to zebrafish pre rRNA reference sequence to analyze the three prime end of each read. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including each read's relative postion in pre rRNA corresponding sequence modification status and modification size. embryo   Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.   tissue:embryo|genotype:sas10 mutant GSM8174001 GSM8174001: zebrafish embryo 5dpf sas10 mutant rep 1; Danio rerio; RNA Seq GSM8174001 r1 GSM8174001 1 Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.   RNA-Seq TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498456     RACE_S_1_R2.fq.gz RACE_S_1_R1.fq.gz fastq fastq 4094487600.0 13648292.0 GSM8174001 r1 0:150 1:150 A:548452011;C:815932223;G:2109931363;T:620046982;N:125021 150 150     548452011 815932223 2109931363 620046982 125021 SRX24092862 SRS20882183 SRA1835384 MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University 2 0.17506 0.00958 0.17451 0.00908 0.99937 0.99933 0.66326 0.70212 150 150 B T mate2 technical by mapping diff illumina novaseq_era 3prime other unknown bulk unknown unknown   China 2024-03-28 Larval Larval Embryo Imprecise All anatomical structures
31689 31689 SRR28490627 SRX24092861 SRS20882182 SRP498456 PRJNA1093028 Effect of depletion of Sas10 in pre rRNA processing GSE262698 Transcriptome Analysis Ribosome small subunit SSU is assembled by the SSU processome which contains approximately 70 non ribosomal protein factors. The biochemical mechanism for the SSU processome in 18S rRNA processing and maturation has been extensively studied however how the SSU processome components enter to the nucleolus has not been systematically investigated. Here we checked the nucleolar localization of 50 human SSU processome components and find that UTP3 and other 24 proteins enter to the nucleolus autonomously. For the remaining 25 proteins we find that UTP3/SAS10 assists the nucleolar localization of five proteins namely MPP10 UTP25 EMG1 and two UTP B components UTP12 and UTP13 and this ferry function of UTP3 is conserved in zebrafish. We also find that knockdown of human UTP3 impairs the cleavage at A0 site while loss of function of either utp3/sas10 or utp13/tbl3 in zebrafish causes an accumulation of the processed products containing the five primeETS supporting the crucial role of UTP3 in mediating the five primeETS processing and degradation. Moreover UTP3 directly interacts with and delivers EXOSC10 into the nucleolus suggesting that UTP3 may play a direct role in recruiting the nuclear exosome to the SSU processome for degradation of the processed five primeETS. These findings lay the ground for studying the mechanism of cytoplasm to nucleolus trafficking of the SSU processome components and the multifaceted roles of UTP3 during pre rRNA processing. Overall design: To validate pre rRNA processing defect in zebrafish sas10 tbl3 mutants and human UTP3 knock down cells we performed three primeRACE seq of these samples.   pubmed:39036955   zebrafish embryo 5dpf wild type rep 2 GSM8174000   source name:embryo|tissue:embryo|genotype:wild type|geo loc name:missing|collection date:missing zebrafish embryo 5dpf wild type rep 2 Sequence reads were trimmed of adapter sequences and low quality sequences using Cutadpat. Trimmed sequences were deduplicated zebrafish five primeETS sequence searched and mapped to zebrafish pre rRNA reference sequence to analyze the three prime end of each read. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including each read's relative postion in pre rRNA corresponding sequence modification status and modification size. embryo   Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.   tissue:embryo|genotype:wild type GSM8174000 GSM8174000: zebrafish embryo 5dpf wild type rep 2; Danio rerio; RNA Seq GSM8174000 r1 GSM8174000 1 Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.   RNA-Seq TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498456     RACE_AB_2_R1.fq.gz RACE_AB_2_R2.fq.gz fastq fastq 4279654200.0 14265514.0 GSM8174000 r1 0:150 1:150 A:664011716;C:1017127170;G:1816549931;T:781834743;N:130640 150 150     664011716 1017127170 1816549931 781834743 130640 SRX24092861 SRS20882182 SRA1835384 MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University 2 0.10741 0.00626 0.10706 0.00596 0.99939 0.99943 0.65454 0.73684 150 150 B T mate2 technical by mapping diff illumina novaseq_era 3prime other unknown bulk unknown unknown   China 2024-03-28 Larval Larval Embryo Imprecise All anatomical structures
31690 31690 SRR28490628 SRX24092860 SRS20882181 SRP498456 PRJNA1093028 Effect of depletion of Sas10 in pre rRNA processing GSE262698 Transcriptome Analysis Ribosome small subunit SSU is assembled by the SSU processome which contains approximately 70 non ribosomal protein factors. The biochemical mechanism for the SSU processome in 18S rRNA processing and maturation has been extensively studied however how the SSU processome components enter to the nucleolus has not been systematically investigated. Here we checked the nucleolar localization of 50 human SSU processome components and find that UTP3 and other 24 proteins enter to the nucleolus autonomously. For the remaining 25 proteins we find that UTP3/SAS10 assists the nucleolar localization of five proteins namely MPP10 UTP25 EMG1 and two UTP B components UTP12 and UTP13 and this ferry function of UTP3 is conserved in zebrafish. We also find that knockdown of human UTP3 impairs the cleavage at A0 site while loss of function of either utp3/sas10 or utp13/tbl3 in zebrafish causes an accumulation of the processed products containing the five primeETS supporting the crucial role of UTP3 in mediating the five primeETS processing and degradation. Moreover UTP3 directly interacts with and delivers EXOSC10 into the nucleolus suggesting that UTP3 may play a direct role in recruiting the nuclear exosome to the SSU processome for degradation of the processed five primeETS. These findings lay the ground for studying the mechanism of cytoplasm to nucleolus trafficking of the SSU processome components and the multifaceted roles of UTP3 during pre rRNA processing. Overall design: To validate pre rRNA processing defect in zebrafish sas10 tbl3 mutants and human UTP3 knock down cells we performed three primeRACE seq of these samples.   pubmed:39036955   zebrafish embryo 5dpf wild type rep 1 GSM8173999   source name:embryo|tissue:embryo|genotype:wild type|geo loc name:missing|collection date:missing zebrafish embryo 5dpf wild type rep 1 Sequence reads were trimmed of adapter sequences and low quality sequences using Cutadpat. Trimmed sequences were deduplicated zebrafish five primeETS sequence searched and mapped to zebrafish pre rRNA reference sequence to analyze the three prime end of each read. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including each read's relative postion in pre rRNA corresponding sequence modification status and modification size. embryo   Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.   tissue:embryo|genotype:wild type GSM8173999 GSM8173999: zebrafish embryo 5dpf wild type rep 1; Danio rerio; RNA Seq GSM8173999 r1 GSM8173999 1 Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.   RNA-Seq TRANSCRIPTOMIC RACE PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498456     RACE_AB_1_R2.fq.gz RACE_AB_1_R1.fq.gz fastq fastq 4575871800.0 15252906.0 GSM8173999 r1 0:150 1:150 A:718107616;C:1095325729;G:1919360747;T:842938887;N:138821 150 150     718107616 1095325729 1919360747 842938887 138821 SRX24092860 SRS20882181 SRA1835384 MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University 2 0.14402 0.00584 0.14352 0.00565 0.99935 0.99955 0.60273 0.77777 150 150 B T mate2 technical by mapping diff illumina novaseq_era 3prime other unknown bulk unknown unknown   China 2024-03-28 Larval Larval Embryo Imprecise All anatomical structures
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

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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");;