{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Undetermined\" and tissue_curation = \"Whole Organism\"", "rows": [[33296, "SRR29925297", "SRX25419305", "SRS22079478", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  usp39  4", "GSM8413284", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO|geo loc name:missing|collection date:missing", "Zebrafish  usp39  4", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO", "GSM8413284", "GSM8413284: Zebrafish  usp39  4; Danio rerio; RNA Seq", "GSM8413284 r1", "GSM8413284", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "usp39_4_S8_R1_001.fastq.gz", "fastq", 6295309328.0, 56208119.0, "GSM8413284 r1", "0:112", "A:1916741141;C:1289239611;G:1409536874;T:1678402242;N:1389460", 112, null, null, null, 1916741141, 1289239611, 1409536874, 1678402242, 1389460, "SRX25419305", "SRS22079478", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.612, null, 0.25838, null, 0.70928, null, 0.47251, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [33297, "SRR29925294", "SRX25419304", "SRS22079477", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  usp39  3", "GSM8413283", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO|geo loc name:missing|collection date:missing", "Zebrafish  usp39  3", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO", "GSM8413283", "GSM8413283: Zebrafish  usp39  3; Danio rerio; RNA Seq", "GSM8413283 r1", "GSM8413283", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "usp39_3_S7_R1_001.fastq.gz", "fastq", 4746730912.0, 42381526.0, "GSM8413283 r1", "0:112", "A:1404624435;C:989965185;G:1138331976;T:1212764925;N:1044391", 112, null, null, null, 1404624435, 989965185, 1138331976, 1212764925, 1044391, "SRX25419304", "SRS22079477", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.58824, null, 0.22238, null, 0.71181, null, 0.46377, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [33298, "SRR29925295", "SRX25419303", "SRS22079474", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  usp39  2", "GSM8413282", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO|geo loc name:missing|collection date:missing", "Zebrafish  usp39  2", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO", "GSM8413282", "GSM8413282: Zebrafish  usp39  2; Danio rerio; RNA Seq", "GSM8413282 r1", "GSM8413282", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "usp39_2_S6_R1_001.fastq.gz", "fastq", 5258831648.0, 46953854.0, "GSM8413282 r1", "0:112", "A:1574548331;C:1105202446;G:1259800817;T:1318114513;N:1165541", 112, null, null, null, 1574548331, 1105202446, 1259800817, 1318114513, 1165541, "SRX25419303", "SRS22079474", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.57786, null, 0.22723, null, 0.71502, null, 0.46758, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [33299, "SRR29925296", "SRX25419302", "SRS22079472", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  usp39  1", "GSM8413281", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO|geo loc name:missing|collection date:missing", "Zebrafish  usp39  1", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO", "GSM8413281", "GSM8413281: Zebrafish  usp39  1; Danio rerio; RNA Seq", "GSM8413281 r1", "GSM8413281", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "usp39_1_S5_R1_001.fastq.gz", "fastq", 6219261664.0, 55529122.0, "GSM8413281 r1", "0:112", "A:1884475909;C:1283923393;G:1434823696;T:1614670192;N:1368474", 112, null, null, null, 1884475909, 1283923393, 1434823696, 1614670192, 1368474, "SRX25419302", "SRS22079472", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.55692, null, 0.23871, null, 0.72368, null, 0.47061, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [33300, "SRR29925298", "SRX25419301", "SRS22079473", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  gfp  4", "GSM8413280", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:WT|geo loc name:missing|collection date:missing", "Zebrafish  gfp  4", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:WT", "GSM8413280", "GSM8413280: Zebrafish  gfp  4; Danio rerio; RNA Seq", "GSM8413280 r1", "GSM8413280", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "gfp_4_S4_R1_001.fastq.gz", "fastq", 5026290192.0, 44877591.0, "GSM8413280 r1", "0:112", "A:1507589049;C:1029477633;G:1172973804;T:1315148479;N:1101227", 112, null, null, null, 1507589049, 1029477633, 1172973804, 1315148479, 1101227, "SRX25419301", "SRS22079473", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.62232, null, 0.2749, null, 0.70907, null, 0.45946, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [33301, "SRR29925299", "SRX25419300", "SRS22079475", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  gfp  3", "GSM8413279", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:WT|geo loc name:missing|collection date:missing", "Zebrafish  gfp  3", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:WT", "GSM8413279", "GSM8413279: Zebrafish  gfp  3; Danio rerio; RNA Seq", "GSM8413279 r1", "GSM8413279", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "gfp_3_S3_R1_001.fastq.gz", "fastq", 6191810800.0, 55284025.0, "GSM8413279 r1", "0:112", "A:1881286910;C:1233644529;G:1388707003;T:1686807249;N:1365109", 112, null, null, null, 1881286910, 1233644529, 1388707003, 1686807249, 1365109, "SRX25419300", "SRS22079475", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.64098, null, 0.2934, null, 0.71151, null, 0.46325, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [33302, "SRR29925300", "SRX25419299", "SRS22079476", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  gfp  2", "GSM8413278", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:WT|geo loc name:missing|collection date:missing", "Zebrafish  gfp  2", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:WT", "GSM8413278", "GSM8413278: Zebrafish  gfp  2; Danio rerio; RNA Seq", "GSM8413278 r1", "GSM8413278", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "gfp_2_S2_R1_001.fastq.gz", "fastq", 6342165088.0, 56626474.0, "GSM8413278 r1", "0:112", "A:1934945429;C:1301674304;G:1435430621;T:1668715260;N:1399474", 112, null, null, null, 1934945429, 1301674304, 1435430621, 1668715260, 1399474, "SRX25419299", "SRS22079476", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.61901, null, 0.26573, null, 0.70666, null, 0.47037, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [33303, "SRR29925301", "SRX25419298", "SRS22079471", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  gfp  1", "GSM8413277", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:WT|geo loc name:missing|collection date:missing", "Zebrafish  gfp  1", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:WT", "GSM8413277", "GSM8413277: Zebrafish  gfp  1; Danio rerio; RNA Seq", "GSM8413277 r1", "GSM8413277", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "gfp_1_S1_R1_001.fastq.gz", "fastq", 5995698912.0, 53533026.0, "GSM8413277 r1", "0:112", "A:1785573790;C:1251424786;G:1355613253;T:1601762911;N:1324172", 112, null, null, null, 1785573790, 1251424786, 1355613253, 1601762911, 1324172, "SRX25419298", "SRS22079471", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.64323, null, 0.28918, null, 0.70857, null, 0.46537, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRA library 28d Calm4", null, "breed:AB|chain:alpha|index:26|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRA library 28d Calm2", null, "breed:AB|chain:alpha|index:25|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRA library 28d KLH6", null, "breed:AB|chain:alpha|index:21|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRA library 28d PHA6", null, "breed:AB|chain:alpha|index:32|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2016-02-14", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRA library 7d KLH2", null, "breed:AB|chain:alpha|index:34|sex:male|time point:7d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2016-02-14", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRA library 21d KLH6", null, "breed:AB|chain:alpha|index:24|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRA library 7d Calm6", null, "breed:AB|chain:alpha|index:33|sex:male|time point:7d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2016-02-14", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRA library 7d PHA7", null, "breed:AB|chain:alpha|index:36|sex:male|time point:7d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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", null, null, null, null, null, null, null, null, null, null, null, "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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRA library 7d PHA3", null, "breed:AB|chain:alpha|index:35|sex:male|time point:7d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 28d Calm7", null, "breed:AB|chain:beta|index:56|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 28d Calm5", null, "breed:AB|chain:beta|index:55|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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, null, 0.07692, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Israel", "2016-03-02", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 28d Calm3", null, "breed:AB|chain:beta|index:54|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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, null, 0.01511, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 28d KLH6", null, "breed:AB|chain:beta|index:27|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 28d KLH2", null, "breed:AB|chain:beta|index:23|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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, null, 0.01388, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Israel", "2016-03-02", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 28d KLH1", null, "breed:AB|chain:beta|index:22|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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, null, 0.00767, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 28d PHA7", null, "breed:AB|chain:beta|index:30|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2016-03-02", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 28d PHA5", null, "breed:AB|chain:beta|index:29|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 28d PHA2", null, "breed:AB|chain:beta|index:28|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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, null, 0.15819, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 28d IFA 5", null, "breed:AB|chain:beta|index:11|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 28d IFA 2", null, "breed:AB|chain:beta|index:10|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 28d IFA 1", null, "breed:AB|chain:beta|index:28|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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, null, 0.15591, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 21d Calm6", null, "breed:AB|chain:beta|index:44|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2016-03-02", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 21d Calm5", null, "breed:AB|chain:beta|index:43|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 21d Calm1", null, "breed:AB|chain:beta|index:42|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2016-03-02", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 21d KLH6", null, "breed:AB|chain:beta|index:50|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 21d KLH5", null, "breed:AB|chain:beta|index:49|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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, null, 0.00123, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 21d KLH1", null, "breed:AB|chain:beta|index:48|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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, null, 0.0303, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 21d PHA6", null, "breed:AB|chain:beta|index:53|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 21d PHA4", null, "breed:AB|chain:beta|index:52|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 21d PHA1", null, "breed:AB|chain:beta|index:51|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 21d IFA 8", null, "breed:AB|chain:beta|index:47|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 21d IFA 4", null, "breed:AB|chain:beta|index:46|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 21d IFA 2", null, "breed:AB|chain:beta|index:45|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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, null, 0.10802, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Israel", "2016-03-02", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 14d Calm6", null, "breed:AB|chain:beta|index:37|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2016-03-02", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library Naive6", null, "breed:AB|chain:beta|index:31|sex:male|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library Naive6", "126 Naive6 beta", "126 Naive6 beta", "five prime RACE amplification of TCRb transcript", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 14d IFA1", null, "breed:AB|chain:beta|index:38|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 14d PHA7", null, "breed:AB|chain:beta|index:41|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2017-02-12", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 14d PHA6", null, "breed:AB|chain:beta|index:40|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2016-03-02", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "TCRB library 14d PHA5", null, "breed:AB|chain:beta|index:39|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "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", null, null, "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, null, null, 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", null, "Israel", "2016-03-02", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [48115, "SRR7252252", "SRX4156979", "SRS3369496", "SRP149646", "PRJNA453111", "Danio rerio Transcriptome or Gene expression", "PRJNA453111", "Other", "The effect of oligosaccharides on zebrafish genes", null, null, null, "Model organism or animal sample from Danio rerio 02", "zebrafish 2", null, "breed:zebrafish|dev stage:sexual maturity|sex:not determined|tissue:the whole fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "T02", "T02", "Liver of FOS exposure", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP149646", null, null, "Zebrafish_G017-T02_good_2.fq Zebrafish_G017-T02_good_1.fq", "fastq fastq", 14376728630.0, 48016590.0, "Zebrafish G017 T02 good 2.fq", "0:149.71 1:149.71", "A:3691193836;C:3492856068;G:3505759208;T:3686065491;N:854027", 149, 149, null, null, 3691193836, 3492856068, 3505759208, 3686065491, 854027, "SRX4156979", "SRS3369496", "SRA714653", "Henan University of Scientific and Technology|College of Animal Science and Technology", "Henan University of Scientific and Technology", 2, 0.91739, 0.92142, 0.02484, 0.02505, 0.6873, 0.69402, 0.47704, 0.47922, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-06-04", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [48116, "SRR7252253", "SRX4156978", "SRS3369495", "SRP149646", "PRJNA453111", "Danio rerio Transcriptome or Gene expression", "PRJNA453111", "Other", "The effect of oligosaccharides on zebrafish genes", null, null, null, "Model organism or animal sample from Danio rerio", "zebrafish", null, "breed:zebrafish|dev stage:sexual maturity|sex:not determined|tissue:the whole fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "T01", "T01", "Liver of control", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP149646", null, null, "Zebrafish_G017-T01_good_1.fq Zebrafish_G017-T01_good_2.fq", "fastq fastq", 14807578386.0, 49468651.0, "Zebrafish G017 T01 good 2.fq", "0:149.67 1:149.67", "A:3802207986;C:3595045362;G:3614407174;T:3795034464;N:883400", 149, 149, null, null, 3802207986, 3595045362, 3614407174, 3795034464, 883400, "SRX4156978", "SRS3369495", "SRA714653", "Henan University of Scientific and Technology|College of Animal Science and Technology", "Henan University of Scientific and Technology", 2, 0.92048, 0.92419, 0.03167, 0.03195, 0.67105, 0.67489, 0.43695, 0.44187, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-06-04", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [56353, "SRR10951081", "SRX7618052", "SRS6050656", "SRP243909", "PRJNA602675", "Identification of mecciRNAs and their roles in the mitochondrial entry of proteins", "GSE144063", "Other", "To identify mitochondrial RNAs  we isolated mitochondria and performed RNA sequencing. Differential expression of mRNAs and circRNAs were then analyzed. Overall design: RNA seq of Mitochondria", null, "pubmed:32048164", null, "Mitochondria of fish", "GSM4278970", null, "source name:whole fish|tissue:whole fish", "Mitochondria of fish", "For circular RNA circRNA prediction  we identified the candidates with find circ Memczak et al.  2013 and the junction reads were calculated as Transcripts Per Kilobase Million TPM. Genome build: hg19  mm9  danRer11 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "whole fish", null, "The isolated mitochondria were homogenized in TRizol reagent Life Technologies by homogenizer. Total RNA was extracted by using TRizol reagent according to the manufacturer\u2019s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:whole fish", "GSM4278970", "GSM4278970: Mitochondria of fish; Danio rerio; RNA Seq", "GSM4278970", null, "1", "The isolated mitochondria were homogenized in TRizol reagent Life Technologies by homogenizer. Total RNA was extracted by using TRizol reagent according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4278970", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP243909", null, null, "zb-mito_1.clean.fq.gz zb-mito_2.clean.fq.gz", "fastq fastq", 10952542200.0, 36508474.0, "GSM4278970 r1", "0:150 1:150", "A:2318277579;C:3207781428;G:3157469050;T:2269014143;N:0", 150, 150, null, null, 2318277579, 3207781428, 3157469050, 2269014143, 0, "SRX7618052", "SRS6050656", "SRA1029966", "GEO", "School of Life Sciences, University of Science and Technology of China", 2, 0.98468, 0.98448, 0.12861, 0.13005, 0.99555, 0.99577, 0.83968, 0.8042, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-01-22", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [68109, "SRR17600926", "SRX13769748", "SRS11649751", "SRP354867", "PRJNA796827", "Transcriptome sequencing of LGG fed zebrafish", "PRJNA796827", "Other", "We aimed to reveal the relationship between biofilm and intestinal immunity.", null, null, "WT+E.coli1", "WT+E.coli1", "GF WT E1", null, "strain:not applicable|isolate:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:Danio rerio|collection date:2020 06 20|treatment:WT+E.coli1|ID:10|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio", "GF WT E1", "GF WT E1", "WT+E.coli", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP354867", null, null, "GF_WT_E1_Clean_Data1.fq.gz GF_WT_E1_Clean_Data2.fq.gz", "fastq fastq", 5722208611.0, 20607920.0, "GF WT E1 Clean Data1.fq.gz", "0:138.84 1:138.83", "A:1540223471;C:1318102846;G:1330098519;T:1533783551;N:224", 138, 138, null, null, 1540223471, 1318102846, 1330098519, 1533783551, 224, "SRX13769748", "SRS11649751", "SRA1356218", "zhejiang university|School of Animal Sciences", "zhejiang university", 2, 0.94934, 0.95004, 0.10193, 0.10143, 0.67375, 0.67298, 0.47471, 0.47424, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-01-13", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [68110, "SRR17600927", "SRX13769747", "SRS11649750", "SRP354867", "PRJNA796827", "Transcriptome sequencing of LGG fed zebrafish", "PRJNA796827", "Other", "We aimed to reveal the relationship between biofilm and intestinal immunity.", null, null, "luxS+E.coli3", "luxS+E.coli3", "GF KO E3", null, "strain:not applicable|isolate:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:Danio rerio|collection date:2020 06 20|treatment:luxS+E.coli3|ID:9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio", "GF KO E3", "GF KO E3", "KO+E.coli", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP354867", null, null, "GF_KO_E3_Clean_Data1.fq.gz GF_KO_E3_Clean_Data2.fq.gz", "fastq fastq", 5889250016.0, 21144775.0, "GF KO E3 Clean Data1.fq.gz", "0:139.26 1:139.26", "A:1620329671;C:1324010520;G:1330595847;T:1614313735;N:243", 139, 139, null, null, 1620329671, 1324010520, 1330595847, 1614313735, 243, "SRX13769747", "SRS11649750", "SRA1356218", "zhejiang university|School of Animal Sciences", "zhejiang university", 2, 0.94698, 0.94852, 0.11876, 0.11831, 0.67495, 0.67517, 0.47639, 0.48061, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-01-13", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [68111, "SRR17600928", "SRX13769746", "SRS11649749", "SRP354867", "PRJNA796827", "Transcriptome sequencing of LGG fed zebrafish", "PRJNA796827", "Other", "We aimed to reveal the relationship between biofilm and intestinal immunity.", null, null, "luxS+E.coli2", "luxS+E.coli2", "GF KO E2", null, "strain:not applicable|isolate:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:Danio rerio|collection date:2020 06 20|treatment:luxS+E.coli2|ID:8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio", "GF KO E2", "GF KO E2", "KO+E.coli", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP354867", null, null, "GF_KO_E2_Clean_Data1.fq.gz GF_KO_E2_Clean_Data2.fq.gz", "fastq fastq", 6504274425.0, 23249789.0, "GF KO E2 Clean Data1.fq.gz", "0:139.88 1:139.87", "A:1766001900;C:1480404718;G:1494298349;T:1763569217;N:241", 139, 139, null, null, 1766001900, 1480404718, 1494298349, 1763569217, 241, "SRX13769746", "SRS11649749", "SRA1356218", "zhejiang university|School of Animal Sciences", "zhejiang university", 2, 0.94738, 0.94849, 0.10481, 0.10434, 0.67022, 0.66918, 0.46937, 0.46181, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-01-13", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [68112, "SRR17600929", "SRX13769745", "SRS11649748", "SRP354867", "PRJNA796827", "Transcriptome sequencing of LGG fed zebrafish", "PRJNA796827", "Other", "We aimed to reveal the relationship between biofilm and intestinal immunity.", null, null, "luxS+E.coli1", "luxS+E.coli1", "GF KO E1", null, "strain:not applicable|isolate:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:Danio rerio|collection date:2020 06 20|treatment:luxS+E.coli1|ID:7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio", "GF KO E1", "GF KO E1", "KO+E.coli", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP354867", null, null, "GF_KO_E1_Clean_Data1.fq.gz GF_KO_E1_Clean_Data2.fq.gz", "fastq fastq", 6723052797.0, 24155410.0, "GF KO E1 Clean Data1.fq.gz", "0:139.16 1:139.16", "A:1841129365;C:1517886618;G:1529873607;T:1834162936;N:271", 139, 139, null, null, 1841129365, 1517886618, 1529873607, 1834162936, 271, "SRX13769745", "SRS11649748", "SRA1356218", "zhejiang university|School of Animal Sciences", "zhejiang university", 2, 0.94667, 0.94708, 0.11716, 0.11601, 0.67521, 0.67414, 0.47792, 0.47067, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-01-13", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [68113, "SRR17600930", "SRX13769744", "SRS11649747", "SRP354867", "PRJNA796827", "Transcriptome sequencing of LGG fed zebrafish", "PRJNA796827", "Other", "We aimed to reveal the relationship between biofilm and intestinal immunity.", null, null, "E.coli3", "E.coli3", "GF E3", null, "strain:not applicable|isolate:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:Danio rerio|collection date:2020 06 20|treatment:E.coli3|ID:6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio", "GF E3", "GF E3", "E.coli", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP354867", null, null, "GF_E3_Clean_Data1.fq.gz GF_E3_Clean_Data2.fq.gz", "fastq fastq", 4907699666.0, 17532965.0, "GF E3 Clean Data1.fq.gz", "0:139.96 1:139.95", "A:1313371994;C:1137331297;G:1142894993;T:1314101187;N:195", 139, 139, null, null, 1313371994, 1137331297, 1142894993, 1314101187, 195, "SRX13769744", "SRS11649747", "SRA1356218", "zhejiang university|School of Animal Sciences", "zhejiang university", 2, 0.95257, 0.95317, 0.08924, 0.08818, 0.65906, 0.65782, 0.49004, 0.49077, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-01-13", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [68114, "SRR17600931", "SRX13769743", "SRS11649746", "SRP354867", "PRJNA796827", "Transcriptome sequencing of LGG fed zebrafish", "PRJNA796827", "Other", "We aimed to reveal the relationship between biofilm and intestinal immunity.", null, null, "E.coli2", "E.coli2", "GF E2", null, "strain:not applicable|isolate:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:Danio rerio|collection date:2020 06 20|treatment:E.coli2|ID:5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio", "GF E2", "GF E2", "E.coli", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP354867", null, null, "GF_E2_Clean_Data1.fq.gz GF_E2_Clean_Data2.fq.gz", "fastq fastq", 5297962158.0, 18917352.0, "GF E2 Clean Data1.fq.gz", "0:140.03 1:140.03", "A:1418683575;C:1225022840;G:1234832199;T:1419423335;N:209", 140, 140, null, null, 1418683575, 1225022840, 1234832199, 1419423335, 209, "SRX13769743", "SRS11649746", "SRA1356218", "zhejiang university|School of Animal Sciences", "zhejiang university", 2, 0.9504, 0.95145, 0.08893, 0.08853, 0.65884, 0.65758, 0.47798, 0.48072, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-01-13", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [68115, "SRR17600932", "SRX13769742", "SRS11649745", "SRP354867", "PRJNA796827", "Transcriptome sequencing of LGG fed zebrafish", "PRJNA796827", "Other", "We aimed to reveal the relationship between biofilm and intestinal immunity.", null, null, "E.coli1", "E.coli1", "GF E1", null, "strain:not applicable|isolate:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:Danio rerio|collection date:2020 06 20|treatment:E.coli1|ID:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio", "GF E1", "GF E1", "E.coli", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP354867", null, null, "GF_E1_Clean_Data1.fq.gz GF_E1_Clean_Data2.fq.gz", "fastq fastq", 5071249140.0, 18130619.0, "GF E1 Clean Data1.fq.gz", "0:139.86 1:139.85", "A:1349570050;C:1179084754;G:1191487646;T:1351106481;N:209", 139, 139, null, null, 1349570050, 1179084754, 1191487646, 1351106481, 209, "SRX13769742", "SRS11649745", "SRA1356218", "zhejiang university|School of Animal Sciences", "zhejiang university", 2, 0.94788, 0.95007, 0.08632, 0.08584, 0.66312, 0.66186, 0.48354, 0.47951, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-01-13", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [68116, "SRR17600933", "SRX13769741", "SRS11649744", "SRP354867", "PRJNA796827", "Transcriptome sequencing of LGG fed zebrafish", "PRJNA796827", "Other", "We aimed to reveal the relationship between biofilm and intestinal immunity.", null, null, "CON3", "CON3", "GF3", null, "strain:not applicable|isolate:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:Danio rerio|collection date:2020 06 20|treatment:germ free|ID:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio", "GF3", "GF3", "con", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP354867", null, null, "GF3_Clean_Data1.fq.gz GF3_Clean_Data2.fq.gz", "fastq fastq", 6819708063.0, 24463230.0, "GF3 Clean Data1.fq.gz", "0:139.39 1:139.39", 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rerio|collection date:2020 06 20|treatment:WT+E.coli3|ID:12|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio", "GF WT E3", "GF WT E3", "WT+E.coli", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP354867", null, null, "GF_WT_E3_Clean_Data1.fq.gz GF_WT_E3_Clean_Data2.fq.gz", "fastq fastq", 6793678785.0, 24320155.0, "GF WT E3 Clean Data1.fq.gz", "0:139.67 1:139.67", "A:1830160129;C:1563893212;G:1574235384;T:1825389791;N:269", 139, 139, null, null, 1830160129, 1563893212, 1574235384, 1825389791, 269, "SRX13769740", "SRS11649743", "SRA1356218", "zhejiang university|School of Animal Sciences", "zhejiang university", 2, 0.95157, 0.95265, 0.10564, 0.10461, 0.67233, 0.67205, 0.48987, 0.48557, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-01-13", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [68118, "SRR17600935", "SRX13769739", "SRS11649742", "SRP354867", "PRJNA796827", "Transcriptome sequencing of LGG fed zebrafish", "PRJNA796827", "Other", "We aimed to reveal the relationship between biofilm and intestinal immunity.", null, null, "WT+E.coli2", "WT+E.coli2", "GF WT E2", null, "strain:not applicable|isolate:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:Danio rerio|collection date:2020 06 20|treatment:WT+E.coli2|ID:11|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio", "GF WT E2", "GF WT E2", "WT+E.coli", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP354867", null, null, "GF_WT_E2_Clean_Data1.fq.gz GF_WT_E2_Clean_Data2.fq.gz", "fastq fastq", 6659933953.0, 23885221.0, "GF WT E2 Clean Data1.fq.gz", "0:139.42 1:139.41", 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