{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Adult\" and experiment.library_layout = \"SINGLE\"", "rows": [[14, "DRR334977", "DRX323973", "DRS217313", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. 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Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "totalRNA metatranscriptomic sequences from mock communities consist of five model species", "rRNA mock community at 28 degrees rep 2", "SAMD00422596", null, "sample name:rRNA mock community 28 degrees rep 2|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:28|treatment:rRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422596", "DRX323972", "t28 2 tRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422596", null, null, null, 2801693695.0, 27860658.0, "DRR334976", "0:100.56 1:0", "A:700189496;C:702936549;G:679920984;T:718646067;N:599", 100, 0, null, null, 700189496, 702936549, 679920984, 718646067, 599, "DRX323972", "DRS217312", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.43508, null, 0.08819, null, 0.85859, null, 0.69447, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [16, "DRR334975", "DRX323971", "DRS217311", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "totalRNA metatranscriptomic sequences from mock communities consist of five model species", "rRNA mock community at 28 degrees rep 1", "SAMD00422595", null, "sample name:rRNA mock community 28 degrees rep 1|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:28|treatment:rRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422595", "DRX323971", "t28 1 tRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422595", null, null, null, 3148691934.0, 31307464.0, "DRR334975", "0:100.57 1:0", "A:785000734;C:791315678;G:766594599;T:805780465;N:458", 100, 0, null, null, 785000734, 791315678, 766594599, 805780465, 458, "DRX323971", "DRS217311", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.37139, null, 0.09061, null, 0.94065, null, 0.74047, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [17, "DRR334974", "DRX323970", "DRS217310", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. 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Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "totalRNA metatranscriptomic sequences from mock communities consist of five model species", "rRNA mock community at 19 degrees rep 3", "SAMD00422594", null, "sample name:rRNA mock community 19 degrees rep 3|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:19|treatment:rRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422594", "DRX323970", "t19 3 tRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422594", null, null, null, 2856186273.0, 28400524.0, "DRR334974", "0:100.57 1:0", "A:695685787;C:733754277;G:715270279;T:711475544;N:386", 100, 0, null, null, 695685787, 733754277, 715270279, 711475544, 386, "DRX323970", "DRS217310", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.48152, null, 0.10933, null, 0.87105, null, 0.7287, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [18, "DRR334973", "DRX323969", "DRS217309", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "totalRNA metatranscriptomic sequences from mock communities consist of five model species", "rRNA mock community at 19 degrees rep 2", "SAMD00422593", null, "sample name:rRNA mock community 19 degrees rep 2|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:19|treatment:rRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422593", "DRX323969", "t19 2 tRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422593", null, null, null, 3199929804.0, 31816971.0, "DRR334973", "0:100.57 1:0", "A:777149590;C:825478743;G:804835148;T:792466124;N:199", 100, 0, null, null, 777149590, 825478743, 804835148, 792466124, 199, "DRX323969", "DRS217309", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.4418, null, 0.10282, null, 0.89706, null, 0.74667, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [19, "DRR334972", "DRX323968", "DRS217308", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "totalRNA metatranscriptomic sequences from mock communities consist of five model species", "rRNA mock community at 19 degrees rep 1", "SAMD00422592", null, "sample name:rRNA mock community 19 degrees rep 1|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:19|treatment:rRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422592", "DRX323968", "t19 1 tRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422592", null, null, null, 3658675391.0, 36374718.0, "DRR334972", "0:100.58 1:0", "A:879342063;C:954687406;G:929537615;T:895107890;N:417", 100, 0, null, null, 879342063, 954687406, 929537615, 895107890, 417, "DRX323968", "DRS217308", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.49439, null, 0.11691, null, 0.88239, null, 0.73925, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [20, "DRR334971", "DRX323967", "DRS217307", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "totalRNA metatranscriptomic sequences from mock communities consist of five model species", "rRNA mock community at 10 degrees rep 3", "SAMD00422591", null, "sample name:rRNA mock community 10 degrees rep 3|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:10|treatment:rRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422591", "DRX323967", "t10 3 tRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422591", null, null, null, 3017524690.0, 30006334.0, "DRR334971", "0:100.56 1:0", "A:771967717;C:738814269;G:712866126;T:793876235;N:343", 100, 0, null, null, 771967717, 738814269, 712866126, 793876235, 343, "DRX323967", "DRS217307", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.33157, null, 0.07363, null, 0.9093, null, 0.73422, null, 100, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [21, "DRR334970", "DRX323966", "DRS217306", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "totalRNA metatranscriptomic sequences from mock communities consist of five model species", "rRNA mock community at 10 degrees rep 2", "SAMD00422590", null, "sample name:rRNA mock community 10 degrees rep 2|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:10|treatment:rRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422590", "DRX323966", "t10 2 tRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422590", null, null, null, 3115915184.0, 30982336.0, "DRR334970", "0:100.57 1:0", "A:765727966;C:794741415;G:771082024;T:784363609;N:170", 100, 0, null, null, 765727966, 794741415, 771082024, 784363609, 170, "DRX323966", "DRS217306", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.45458, null, 0.10504, null, 0.89357, null, 0.749, null, 100, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [22, "DRR334969", "DRX323965", "DRS217305", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "totalRNA metatranscriptomic sequences from mock communities consist of five model species", "rRNA mock community at 10 degrees rep 1", "SAMD00422589", null, "sample name:rRNA mock community 10 degrees rep 1|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:10|treatment:rRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422589", "DRX323965", "t10 1 tRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422589", null, null, null, 3206657309.0, 31883532.0, "DRR334969", "0:100.57 1:0", "A:792874386;C:814578518;G:787469614;T:811734581;N:210", 100, 0, null, null, 792874386, 814578518, 787469614, 811734581, 210, "DRX323965", "DRS217305", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.40156, null, 0.09664, null, 0.92898, null, 0.74114, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [23, "DRR334968", "DRX323964", "DRS217304", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "mRNA metatranscriptomic sequences from mock communities consist of five model species", "mRNA mock community at 28 degrees rep 3", "SAMD00422588", null, "sample name:mRNA mock community 28 degrees rep 3|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:28|treatment:mRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422588", "DRX323964", "m28 3 mRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422588", null, null, null, 3157078356.0, 31416275.0, "DRR334968", "0:100.49 1:0", "A:816263259;C:752748024;G:759884392;T:828182261;N:420", 100, 0, null, null, 816263259, 752748024, 759884392, 828182261, 420, "DRX323964", "DRS217304", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.64888, null, 0.01832, null, 0.73996, null, 0.46811, null, 99, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [24, "DRR334967", "DRX323963", "DRS217303", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "mRNA metatranscriptomic sequences from mock communities consist of five model species", "mRNA mock community at 28 degrees rep 2", "SAMD00422587", null, "sample name:mRNA mock community 28 degrees rep 2|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:28|treatment:mRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422587", "DRX323963", "m28 2 mRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422587", null, null, null, 3155807651.0, 31404635.0, "DRR334967", "0:100.49 1:0", "A:819014350;C:749873295;G:756284406;T:830635394;N:206", 100, 0, null, null, 819014350, 749873295, 756284406, 830635394, 206, "DRX323963", "DRS217303", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.76742, null, 0.02238, null, 0.72427, null, 0.47376, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [25, "DRR334966", "DRX323962", "DRS217302", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "mRNA metatranscriptomic sequences from mock communities consist of five model species", "mRNA mock community at 28 degrees rep 1", "SAMD00422586", null, "sample name:mRNA mock community 28 degrees rep 1|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:28|treatment:mRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422586", "DRX323962", "m28 1 mRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422586", null, null, null, 2589772286.0, 25765782.0, "DRR334966", "0:100.51 1:0", "A:679223577;C:610675892;G:617869465;T:682003195;N:157", 100, 0, null, null, 679223577, 610675892, 617869465, 682003195, 157, "DRX323962", "DRS217302", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.42984, null, 0.03367, null, 0.73555, null, 0.49223, null, 100, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [26, "DRR334965", "DRX323961", "DRS217318", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "mRNA metatranscriptomic sequences from mock communities consist of five model species", "mRNA mock community at 19 degrees rep 3", "SAMD00422602", null, "sample name:mRNA mock community 19 degrees rep 3|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:19|treatment:mRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422602", "DRX323961", "m19 3 mRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422602", null, null, null, 3124746628.0, 31095367.0, "DRR334965", "0:100.49 1:0", "A:821891547;C:734660854;G:739230475;T:828963220;N:532", 100, 0, null, null, 821891547, 734660854, 739230475, 828963220, 532, "DRX323961", "DRS217318", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.72881, null, 0.03264, null, 0.69449, null, 0.47416, null, 99, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [27, "DRR334964", "DRX323960", "DRS217317", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "mRNA metatranscriptomic sequences from mock communities consist of five model species", "mRNA mock community at 19 degrees rep 2", "SAMD00422601", null, "sample name:mRNA mock community 19 degrees rep 2|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:19|treatment:mRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422601", "DRX323960", "m19 2 mRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422601", null, null, null, 3171661466.0, 31561473.0, "DRR334964", "0:100.49 1:0", "A:836793307;C:742872021;G:750053514;T:841942389;N:235", 100, 0, null, null, 836793307, 742872021, 750053514, 841942389, 235, "DRX323960", "DRS217317", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.63153, null, 0.03639, null, 0.69027, null, 0.48494, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [28, "DRR334963", "DRX323959", "DRS217316", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "mRNA metatranscriptomic sequences from mock communities consist of five model species", "mRNA mock community at 19 degrees rep 1", "SAMD00422600", null, "sample name:mRNA mock community 19 degrees rep 1|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:19|treatment:mRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422600", "DRX323959", "m19 1 mRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422600", null, null, null, 2916453082.0, 29023768.0, "DRR334963", "0:100.48 1:0", "A:761416880;C:692014182;G:696272089;T:766749729;N:202", 100, 0, null, null, 761416880, 692014182, 696272089, 766749729, 202, "DRX323959", "DRS217316", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.71651, null, 0.03406, null, 0.68696, null, 0.47496, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [29, "DRR334962", "DRX323958", "DRS217315", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "mRNA metatranscriptomic sequences from mock communities consist of five model species", "mRNA mock community at 10 degrees rep 3", "SAMD00422599", null, "sample name:mRNA mock community 10 degrees rep 3|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:10|treatment:mRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422599", "DRX323958", "m10 3 mRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422599", null, null, null, 2600103192.0, 25872833.0, "DRR334962", "0:100.50 1:0", "A:668944597;C:625686885;G:631010166;T:674461210;N:334", 100, 0, null, null, 668944597, 625686885, 631010166, 674461210, 334, "DRX323958", "DRS217315", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.57077, null, 0.02949, null, 0.71918, null, 0.47633, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [30, "DRR334961", "DRX323957", "DRS217314", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "mRNA metatranscriptomic sequences from mock communities consist of five model species", "mRNA mock community at 10 degrees rep 2", "SAMD00422598", null, "sample name:mRNA mock community 10 degrees rep 2|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:10|treatment:mRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422598", "DRX323957", "m10 2 mRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422598", null, null, null, 2608660833.0, 25958804.0, "DRR334961", "0:100.49 1:0", "A:683370128;C:615324906;G:621209484;T:688756167;N:148", 100, 0, null, null, 683370128, 615324906, 621209484, 688756167, 148, "DRX323957", "DRS217314", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.63764, null, 0.04316, null, 0.69656, null, 0.48579, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [31, "DRR334960", "DRX323956", "DRS217301", "DRP008001", "PRJDB12578", "Allometric scaling of RNA abundance from genes to communities", "DRP008001", "Other", "The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.", null, null, "mRNA metatranscriptomic sequences from mock communities consist of five model species", "mRNA mock community at 10 degrees rep 1", "SAMD00422585", null, "sample name:mRNA mock community 10 degrees rep 1|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:10|treatment:mRNA", null, null, null, null, null, null, null, null, "NextSeq 2000 sequencing of SAMD00422585", "DRX323956", "m10 1 mRNA.fastq", "1", "NEBNext Kit for Illumina", null, "RNA-Seq", "METATRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008001", "NextSeq 2000 sequencing of SAMD00422585", null, null, null, 2879915507.0, 28651533.0, "DRR334960", "0:100.52 1:0", "A:761972464;C:675761096;G:678969165;T:763212637;N:145", 100, 0, null, null, 761972464, 675761096, 678969165, 763212637, 145, "DRX323956", "DRS217301", "DRA013226", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", "SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica", 1, 0.47851, null, 0.05671, null, 0.72622, null, 0.49269, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2021-12-23", "Adult", "Adult", "Undetermined", "Undetermined"], [32, "DRR408242", "DRX393848", "DRS407006", "DRP012035", "PRJDB14274", "Zebrafish Gut RNA seq.", "DRP012035", "Transcriptome Analysis", "A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.", null, null, "zebrafish wild type AB adult gut replicate 3", "zebrafish adult gut replicate 3", "SAMD00529462", null, "sample name:zebrafish adult gut replicate 3|biological replicate:adult 3|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 1500 sequencing of SAMD00529462", "DRX393848", "AR019 gut 6  adult", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012035", "Illumina HiSeq 1500 sequencing of SAMD00529462", null, null, null, 3546347364.0, 28145614.0, "DRR408242", "0:126 1:0", "A:919466631;C:829424335;G:818581155;T:978810217;N:65026", 126, 0, null, null, 919466631, 829424335, 818581155, 978810217, 65026, "DRX393848", "DRS407006", "DRA014885", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2024-09-20", "Adult", "Adult", "Gut", "Digestive System"], [33, "DRR408241", "DRX393847", "DRS407005", "DRP012035", "PRJDB14274", "Zebrafish Gut RNA seq.", "DRP012035", "Transcriptome Analysis", "A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.", null, null, "zebrafish wild type AB adult gut replicate 2", "zebrafish adult gut replicate 2", "SAMD00529461", null, "sample name:zebrafish adult gut replicate 2|biological replicate:adult 2|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 1500 sequencing of SAMD00529461", "DRX393847", "AR006 gut 4  adult", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012035", "Illumina HiSeq 1500 sequencing of SAMD00529461", null, null, null, 3671973648.0, 29142648.0, "DRR408241", "0:126 1:0", "A:942167543;C:859431290;G:852661772;T:1017643011;N:70032", 126, 0, null, null, 942167543, 859431290, 852661772, 1017643011, 70032, "DRX393847", "DRS407005", "DRA014885", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2024-09-20", "Adult", "Adult", "Gut", "Digestive System"], [34, "DRR408240", "DRX393846", "DRS407004", "DRP012035", "PRJDB14274", "Zebrafish Gut RNA seq.", "DRP012035", "Transcriptome Analysis", "A project to find differential expressed genes between larval and adult zebrafish gut. We dissected guts of wild type AB line  and prepared three duplicates for each of larval and adult gut. Libraries for NGS are prepared using illumina TruSeq standard mRNA sample prep kit.", null, null, "zebrafish wild type AB adult gut replicate 1", "zebrafish adult gut replicate 1", "SAMD00529460", null, "sample name:zebrafish adult gut replicate 1|biological replicate:adult 1|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 1500 sequencing of SAMD00529460", "DRX393846", "AR004 gut 2  adult", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>126</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012035", "Illumina HiSeq 1500 sequencing of SAMD00529460", null, null, null, 3480523704.0, 27623204.0, "DRR408240", "0:126 1:0", "A:898051986;C:827557593;G:816541244;T:938307607;N:65274", 126, 0, null, null, 898051986, 827557593, 816541244, 938307607, 65274, "DRX393846", "DRS407004", "DRA014885", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2024-09-20", "Adult", "Adult", "Gut", "Digestive System"], [50, "DRR029944", "DRX026962", "DRS086502", "DRP004756", "PRJDB3475", "Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004756", "Other", "To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.", null, null, "ovulation duirng natural paring", "zebrafish ovary isolated from adult fish at ovulation duirng natural paring. [RNAseq]", "SAMD00025434", null, "sample name:6 Ovu|strain:roy|tissue type:ovary|dev stage:adult", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00025434", "DRX026962", "6 Ovu", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004756", "Illumina HiSeq 2500 sequencing of SAMD00025434", null, null, null, 351766656.0, 9771296.0, "DRR029944", "0:36", "A:79811727;C:85391142;G:90185809;T:96371771;N:6207", 36, null, null, null, 79811727, 85391142, 90185809, 96371771, 6207, "DRX026962", "DRS086502", "DRA003031", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.91956, null, 0.01686, null, 0.76637, null, 0.45997, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [51, "DRR029943", "DRX026961", "DRS086501", "DRP004756", "PRJDB3475", "Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004756", "Other", "To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.", null, null, "oocyte maturation duirng natural paring", "zebrafish ovary isolated from adult fish at oocyte maturation duirng natural paring. [RNAseq]", "SAMD00025433", null, "sample name:5 OM|strain:roy|tissue type:ovary|dev stage:adult", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00025433", "DRX026961", "5 OM", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004756", "Illumina HiSeq 2500 sequencing of SAMD00025433", null, null, null, 573617016.0, 15933806.0, "DRR029943", "0:36", "A:130606804;C:141376330;G:145891720;T:155734276;N:7886", 36, null, null, null, 130606804, 141376330, 145891720, 155734276, 7886, "DRX026961", "DRS086501", "DRA003031", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.91108, null, 0.0173, null, 0.76205, null, 0.46319, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Multi-tissue", "Multi-system"], [52, "DRR029942", "DRX026960", "DRS086500", "DRP004756", "PRJDB3475", "Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004756", "Other", "To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.", null, null, "in vivo testosterone treatment", "zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq  replicate]", "SAMD00025432", null, "sample name:4 Tes rep|strain:roy|tissue type:ovary|dev stage:adult", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00025432", "DRX026960", "4 Tes rep", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004756", "Illumina HiSeq 2500 sequencing of SAMD00025432", null, null, null, 366042528.0, 10167848.0, "DRR029942", "0:36", "A:84988522;C:88640326;G:93559022;T:98847003;N:7655", 36, null, null, null, 84988522, 88640326, 93559022, 98847003, 7655, "DRX026960", "DRS086500", "DRA003031", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.91602, null, 0.01846, null, 0.76015, null, 0.46475, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [53, "DRR029941", "DRX026959", "DRS086499", "DRP004756", "PRJDB3475", "Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004756", "Other", "To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.", null, null, "in vivo testosterone treatment", "zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq]", "SAMD00025431", null, "sample name:4 Tes|strain:roy|tissue type:ovary|dev stage:adult", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00025431", "DRX026959", "4 Tes", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004756", "Illumina HiSeq 2500 sequencing of SAMD00025431", null, null, null, 1269835992.0, 35273222.0, "DRR029941", "0:36", "A:275250658;C:323605136;G:316729009;T:354204170;N:47019", 36, null, null, null, 275250658, 323605136, 316729009, 354204170, 47019, "DRX026959", "DRS086499", "DRA003031", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.91467, null, 0.02353, null, 0.75962, null, 0.46861, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [54, "DRR029940", "DRX026958", "DRS086498", "DRP004756", "PRJDB3475", "Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004756", "Other", "To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.", null, null, "in vivo diethylstilbestrol DES treatment", "zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate]", "SAMD00025430", null, "sample name:3 DES rep|strain:roy|tissue type:ovary|dev stage:adult", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00025430", "DRX026958", "3 DES rep", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004756", "Illumina HiSeq 2500 sequencing of SAMD00025430", null, null, null, 658651536.0, 18295876.0, "DRR029940", null, null, null, null, null, null, null, null, null, null, null, "DRX026958", "DRS086498", "DRA003031", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.89964, null, 0.01785, null, 0.76451, null, 0.45872, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [55, "DRR029939", "DRX026957", "DRS086497", "DRP004756", "PRJDB3475", "Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004756", "Other", "To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.", null, null, "in vivo diethylstilbestrol DES treatment", "zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq]", "SAMD00025429", null, "sample name:3 DES|strain:roy|tissue type:ovary|dev stage:adult", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00025429", "DRX026957", "3 DES", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004756", "Illumina HiSeq 2500 sequencing of SAMD00025429", null, null, null, 1202024016.0, 33389556.0, "DRR029939", "0:36", "A:263319430;C:305852921;G:298798093;T:334008544;N:45028", 36, null, null, null, 263319430, 305852921, 298798093, 334008544, 45028, "DRX026957", "DRS086497", "DRA003031", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.90643, null, 0.02337, null, 0.75008, null, 0.47587, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [56, "DRR029938", "DRX026956", "DRS086496", "DRP004756", "PRJDB3475", "Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004756", "Other", "To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.", null, null, "in vivo maturation inducing hormone DHP treatment", "zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq  replicate]", "SAMD00025428", null, "sample name:2 DHP rep|strain:roy|tissue type:ovary|dev stage:adult", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00025428", "DRX026956", "2 DHP rep", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004756", "Illumina HiSeq 2500 sequencing of SAMD00025428", null, null, null, 434243088.0, 12062308.0, "DRR029938", "0:36", "A:99859342;C:105890785;G:110526688;T:117957580;N:8693", 36, null, null, null, 99859342, 105890785, 110526688, 117957580, 8693, "DRX026956", "DRS086496", "DRA003031", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.91529, null, 0.02061, null, 0.7595, null, 0.45809, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [57, "DRR029937", "DRX026955", "DRS086495", "DRP004756", "PRJDB3475", "Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004756", "Other", "To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.", null, null, "in vivo maturation inducing hormone DHP treatment", "zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq]", "SAMD00025427", null, "sample name:2 DHP|strain:roy|tissue type:ovary|dev stage:adult", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00025427", "DRX026955", "2 DHP", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004756", "Illumina HiSeq 2500 sequencing of SAMD00025427", null, null, null, 1463868972.0, 40663027.0, "DRR029937", "0:36", "A:316060780;C:369221844;G:372845502;T:405685804;N:55042", 36, null, null, null, 316060780, 369221844, 372845502, 405685804, 55042, "DRX026955", "DRS086495", "DRA003031", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.91556, null, 0.01967, null, 0.76621, null, 0.46541, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [58, "DRR029936", "DRX026954", "DRS086494", "DRP004756", "PRJDB3475", "Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004756", "Other", "To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.", null, null, "in vivo ethanol treatment", "zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate]", "SAMD00025426", null, "sample name:1 EtOH rep|strain:roy|tissue type:ovary|dev stage:adult", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00025426", "DRX026954", "1 EtOH rep", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004756", "Illumina HiSeq 2500 sequencing of SAMD00025426", null, null, null, 438020208.0, 12167228.0, "DRR029936", "0:36", "A:101672612;C:105602774;G:110120652;T:120615069;N:9101", 36, null, null, null, 101672612, 105602774, 110120652, 120615069, 9101, "DRX026954", "DRS086494", "DRA003031", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.90777, null, 0.01929, null, 0.7652, null, 0.45988, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [59, "DRR029935", "DRX026953", "DRS086493", "DRP004756", "PRJDB3475", "Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004756", "Other", "To identify ovulation inducing genes  RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.", null, null, "in vivo ethanol treatment", "zebrafish ovary isolated from adult fish in vivo ethanol treatment. 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Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "natural paring late sample", "zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate2]", "SAMD00073602", null, "sample name:O 4th|replicate:biological replicate 2", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073602", "DRX078026", "zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate2]", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004758", "Illumina HiSeq 2500 sequencing of SAMD00073602", null, null, null, 1627945092.0, 45220697.0, "DRR084195", "0:36", "A:381205209;C:392853175;G:410714269;T:439790560;N:3381879", 36, null, null, null, 381205209, 392853175, 410714269, 439790560, 3381879, "DRX078026", "DRS086520", "DRA005484", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.89419, null, 0.02159, null, 0.76848, null, 0.46407, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [178, "DRR084194", "DRX078025", "DRS086519", "DRP004758", "PRJDB5490", "Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004758", "Other", "Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "in vivo maturation inducing hormone DHP treatment", "zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq  replicate2]", "SAMD00073601", null, "sample name:DHP 4th|replicate:biological replicate 2", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073601", "DRX078025", "zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. [RNAseq  replicate2]", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004758", "Illumina HiSeq 2500 sequencing of SAMD00073601", null, null, null, 969680196.0, 26935561.0, "DRR084194", "0:36", "A:223558856;C:233793515;G:244712298;T:265549055;N:2066472", 36, null, null, null, 223558856, 233793515, 244712298, 265549055, 2066472, "DRX078025", "DRS086519", "DRA005484", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.90178, null, 0.02203, null, 0.76579, null, 0.46491, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [179, "DRR084193", "DRX078024", "DRS086518", "DRP004758", "PRJDB5490", "Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004758", "Other", "Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "in vivo diethylstilbestrol DES treatment", "zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate2]", "SAMD00073600", null, "sample name:DES 4th|replicate:biological replicate 2", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073600", "DRX078024", "zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate2]", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004758", "Illumina HiSeq 2500 sequencing of SAMD00073600", null, null, null, 825301296.0, 22925036.0, "DRR084193", "0:36", "A:189771874;C:198593952;G:209666041;T:225480165;N:1789264", 36, null, null, null, 189771874, 198593952, 209666041, 225480165, 1789264, "DRX078024", "DRS086518", "DRA005484", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.90036, null, 0.0197, null, 0.7721, null, 0.45773, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [180, "DRR084192", "DRX078023", "DRS086517", "DRP004758", "PRJDB5490", "Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004758", "Other", "Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "natural paring late sample", "zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate1]", "SAMD00073599", null, "sample name:O|replicate:biological replicate 1", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073599", "DRX078023", "zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate1]", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004758", "Illumina HiSeq 2500 sequencing of SAMD00073599", null, null, null, 1474870356.0, 40968621.0, "DRR084192", "0:36", "A:334130826;C:361572335;G:369758908;T:409173431;N:234856", 36, null, null, null, 334130826, 361572335, 369758908, 409173431, 234856, "DRX078023", "DRS086517", "DRA005484", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.91516, null, 0.02086, null, 0.76792, null, 0.47914, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [182, "DRR084190", "DRX078021", "DRS086515", "DRP004758", "PRJDB5490", "Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004758", "Other", "Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "in vivo maturation inducing hormone DHP treatment", "zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq  replicate1]", "SAMD00073597", null, "sample name:DHP|replicate:biological replicate 1", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073597", "DRX078021", "zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. [RNAseq  replicate1]", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004758", "Illumina HiSeq 2500 sequencing of SAMD00073597", null, null, null, 1527194556.0, 42422071.0, "DRR084190", "0:36", "A:352068936;C:371030475;G:383086948;T:420761508;N:246689", 36, null, null, null, 352068936, 371030475, 383086948, 420761508, 246689, "DRX078021", "DRS086515", "DRA005484", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.91815, null, 0.02248, null, 0.76209, null, 0.46867, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [183, "DRR084189", "DRX078020", "DRS086514", "DRP004758", "PRJDB5490", "Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004758", "Other", "Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "in vivo testosterone treatment", "zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq  replicate1]", "SAMD00073596", null, "sample name:TES|replicate:biological replicate 1", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073596", "DRX078020", "zebrafish ovary isolated from adult fish in vivo testosterone treatment. [RNAseq  replicate1]", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004758", "Illumina HiSeq 2500 sequencing of SAMD00073596", null, null, null, 1403618796.0, 38989411.0, "DRR084189", "0:36", "A:321063874;C:342718133;G:352434647;T:387171455;N:230687", 36, null, null, null, 321063874, 342718133, 352434647, 387171455, 230687, "DRX078020", "DRS086514", "DRA005484", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.91583, null, 0.02212, null, 0.76073, null, 0.47596, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [184, "DRR084188", "DRX078019", "DRS086513", "DRP004758", "PRJDB5490", "Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004758", "Other", "Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "in vivo diethylstilbestrol DES treatment", "zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate1]", "SAMD00073595", null, "sample name:DES|replicate:biological replicate 1", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073595", "DRX078019", "zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate1]", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004758", "Illumina HiSeq 2500 sequencing of SAMD00073595", null, null, null, 1532053512.0, 42557042.0, "DRR084188", "0:36", "A:342701220;C:372650449;G:392432461;T:424025702;N:243680", 36, null, null, null, 342701220, 372650449, 392432461, 424025702, 243680, "DRX078019", "DRS086513", "DRA005484", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.91276, null, 0.01965, null, 0.77358, null, 0.46461, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [185, "DRR084187", "DRX078018", "DRS086512", "DRP004758", "PRJDB5490", "Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004758", "Other", "Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "in vivo ethanol treatment", "zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate1]", "SAMD00073594", null, "sample name:EtOH|replicate:biological replicate 1", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073594", "DRX078018", "zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate1]", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004758", "Illumina HiSeq 2500 sequencing of SAMD00073594", null, null, null, 1152032724.0, 32000909.0, "DRR084187", "0:36", "A:265166034;C:279617628;G:285136940;T:321928656;N:183466", 36, null, null, null, 265166034, 279617628, 285136940, 321928656, 183466, "DRX078018", "DRS086512", "DRA005484", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.90791, null, 0.02405, null, 0.75972, null, 0.48931, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [282, "DRR179616", "DRX170142", "DRS185505", "DRP007318", "PRJDB8340", "Gene expression analysis of zebrafish fin melanophores and xanthophores.", "DRP007318", "Other", "Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.", null, null, "Biological replicate 2", "Fin xanthophore 03", "SAMD00172019", null, "sample name:Zebrafish pigment cell 06|cell type:Xanthophore|collection date:2015 11 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172019", "DRX170142", "Zebrafish fin xanthophore 01", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>232</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172019", null, null, null, 376558775.0, 1624500.0, "DRR179616", "0:231.80", "A:107837072;C:79508449;G:79372899;T:109840355;N:0", 231, null, null, null, 107837072, 79508449, 79372899, 109840355, 0, "DRX170142", "DRS185505", "DRA008445", "OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", "Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", 1, 0.86944, null, 0.10951, null, 0.90425, null, 0.59385, null, 311, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "Japan", "2021-05-21", "Adult", "Adult", "Fin", "Surface Structure"], [283, "DRR179615", "DRX170141", "DRS185504", "DRP007318", "PRJDB8340", "Gene expression analysis of zebrafish fin melanophores and xanthophores.", "DRP007318", "Other", "Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.", null, null, "Biological replicate 1", "Fin xanthophore 02", "SAMD00172018", null, "sample name:Zebrafish pigment cell 05|cell type:Xanthophore|collection date:2015 09 10|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172018", "DRX170141", "Zebrafish fin xanthophore 01", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>243</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172018", null, null, null, 515115515.0, 2124170.0, "DRR179615", "0:242.50", "A:138421982;C:119032803;G:119412227;T:138248503;N:0", 242, null, null, null, 138421982, 119032803, 119412227, 138248503, 0, "DRX170141", "DRS185504", "DRA008445", "OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", "Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", 1, 0.88998, null, 0.05858, null, 0.88051, null, 0.50917, null, 284, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "Japan", "2021-05-21", "Adult", "Adult", "Fin", "Surface Structure"], [284, "DRR179614", "DRX170140", "DRS185503", "DRP007318", "PRJDB8340", "Gene expression analysis of zebrafish fin melanophores and xanthophores.", "DRP007318", "Other", "Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.", null, null, "Biological replicate 1", "Fin xanthophore 01", "SAMD00172017", null, "sample name:Zebrafish pigment cell 04|cell type:Xanthophore|collection date:2015 09 10|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172017", "DRX170140", "Zebrafish fin xanthophore 01", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>247</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172017", null, null, null, 371242152.0, 1504407.0, "DRR179614", "0:246.77", "A:99341086;C:86126839;G:86264882;T:99509345;N:0", 246, null, null, null, 99341086, 86126839, 86264882, 99509345, 0, "DRX170140", "DRS185503", "DRA008445", "OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", "Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", 1, 0.88672, null, 0.06422, null, 0.85679, null, 0.5066, null, 56, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "Japan", "2021-05-21", "Adult", "Adult", "Fin", "Surface Structure"], [285, "DRR179613", "DRX170139", "DRS185502", "DRP007318", "PRJDB8340", "Gene expression analysis of zebrafish fin melanophores and xanthophores.", "DRP007318", "Other", "Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.", null, null, "Biological replicate 2", "Fin melanophore 03", "SAMD00172016", null, "sample name:Zebrafish pigment cell 03|cell type:Melanophore|collection date:2015 11 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172016", "DRX170139", "Zebrafish fin melanophore 03", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>248</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172016", null, null, null, 342802993.0, 1585538.0, "DRR179613", "0:216.21", "A:90833658;C:80789744;G:80463233;T:90716358;N:0", 216, null, null, null, 90833658, 80789744, 80463233, 90716358, 0, "DRX170139", "DRS185502", "DRA008445", "OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", "Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", 1, 0.8312, null, 0.03528, null, 0.88605, null, 0.47299, null, 285, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "Japan", "2021-05-21", "Adult", "Adult", "Fin", "Surface Structure"], [286, "DRR179612", "DRX170138", "DRS185501", "DRP007318", "PRJDB8340", "Gene expression analysis of zebrafish fin melanophores and xanthophores.", "DRP007318", "Other", "Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.", null, null, "Biological replicate 1", "Fin melanophore 02", "SAMD00172015", null, "sample name:Zebrafish pigment cell 02|cell type:Melanophore|collection date:2015 05 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172015", "DRX170138", "Zebrafish fin melanophore 02", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>216</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172015", null, null, null, 538412675.0, 2168231.0, "DRR179612", "0:248.32", "A:147128403;C:121854818;G:121564109;T:147865345;N:0", 248, null, null, null, 147128403, 121854818, 121564109, 147865345, 0, "DRX170138", "DRS185501", "DRA008445", "OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", "Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", 1, 0.89106, null, 0.07081, null, 0.89286, null, 0.5935, null, 283, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "Japan", "2021-05-21", "Adult", "Adult", "Fin", "Surface Structure"], [287, "DRR179611", "DRX170137", "DRS185500", "DRP007318", "PRJDB8340", "Gene expression analysis of zebrafish fin melanophores and xanthophores.", "DRP007318", "Other", "Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.", null, null, "Biological replicate 1", "Fin melanophore 01", "SAMD00172014", null, "sample name:Zebrafish pigment cell 01|cell type:Melanophore|collection date:2015 05 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin", null, null, null, null, null, null, null, null, "Ion Torrent PGM sequencing of SAMD00172014", "DRX170137", "Zebrafish fin melanophore 01", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ION_TORRENT", "Ion Torrent PGM", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>215</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP007318", "Ion Torrent PGM sequencing of SAMD00172014", null, null, null, 282446840.0, 1311431.0, "DRR179611", "0:215.37", "A:74927237;C:66575483;G:66161471;T:74782649;N:0", 215, null, null, null, 74927237, 66575483, 66161471, 74782649, 0, "DRX170137", "DRS185500", "DRA008445", "OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", "Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University", 1, 0.85938, null, 0.0335, null, 0.89248, null, 0.58813, null, 274, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "Japan", "2021-05-21", "Adult", "Adult", "Fin", "Surface Structure"], [3759, "ERR1294279", "ERX1365625", "ERS1067820", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "Mau tVBU1/tVBU1 skin transcriptome", "SAMEA3880686", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9", "vbu13", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "vbu13_GCCAAT_L008_R1_001.fastq.gz", "fastq", 2376143675.0, 23526175.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9", "0:101", "A:655940769;C:534990399;G:527934646;T:655773043;N:1504818", 101, null, null, null, 655940769, 534990399, 527934646, 655773043, 1504818, "ERX1365625", "ERS1067820", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.95443, null, 0.10666, null, 0.73176, null, 0.50978, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3760, "ERR1294278", "ERX1365624", "ERS1067820", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "Mau tVBU1/tVBU1 skin transcriptome", "SAMEA3880686", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8", "vbu12", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "vbu12_GTGAAA_L008_R1_001.fastq.gz", "fastq", 1449181835.0, 14348335.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8", "0:101", "A:399518584;C:327615685;G:323868050;T:397240465;N:939051", 101, null, null, null, 399518584, 327615685, 323868050, 397240465, 939051, "ERX1365624", "ERS1067820", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.95893, null, 0.09315, null, 0.73464, null, 0.48744, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3761, "ERR1294277", "ERX1365623", "ERS1067820", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "Mau tVBU1/tVBU1 skin transcriptome", "SAMEA3880686", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7", "vbu11", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "vbu11_GTCCGC_L008_R1_001.fastq.gz", "fastq", 1455235169.0, 14408269.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7", "0:101", "A:392100064;C:337980617;G:331091626;T:393178582;N:884280", 101, null, null, null, 392100064, 337980617, 331091626, 393178582, 884280, "ERX1365623", "ERS1067820", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.95485, null, 0.08016, null, 0.72845, null, 0.47549, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3762, "ERR1294276", "ERX1365622", "ERS1067819", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "Mau tVE1/tVE1 skin transcriptome", "SAMEA3880685", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6", "ve13", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "ve13_CCGTCC_L008_R1_001.fastq.gz", "fastq", 1029294030.0, 10191030.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6", "0:101", "A:284612731;C:231451012;G:228443320;T:284135536;N:651431", 101, null, null, null, 284612731, 231451012, 228443320, 284135536, 651431, "ERX1365622", "ERS1067819", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.93287, null, 0.10726, null, 0.72585, null, 0.4913, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3763, "ERR1294275", "ERX1365621", "ERS1067819", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "Mau tVE1/tVE1 skin transcriptome", "SAMEA3880685", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5", "ve12", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "ve12_ATGTCA_L008_R1_001.fastq.gz", "fastq", 1446322222.0, 14320022.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5", "0:101", "A:400821160;C:324210104;G:320286425;T:400078485;N:926048", 101, null, null, null, 400821160, 324210104, 320286425, 400078485, 926048, "ERX1365621", "ERS1067819", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.92778, null, 0.09489, null, 0.73093, null, 0.48493, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3764, "ERR1294274", "ERX1365620", "ERS1067819", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "Mau tVE1/tVE1 skin transcriptome", "SAMEA3880685", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4", "ve11", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "ve11_AGTTCC_L008_R1_001.fastq.gz", "fastq", 2117238861.0, 20962761.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4", "0:101", "A:591654664;C:469803769;G:462550117;T:591863795;N:1366516", 101, null, null, null, 591654664, 469803769, 462550117, 591863795, 1366516, "ERX1365620", "ERS1067819", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.93146, null, 0.09666, null, 0.73501, null, 0.48749, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3765, "ERR1294273", "ERX1365619", "ERS1067818", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "WT skin transcriptome", "SAMEA3880684", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3", "wt3", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "wt3_AGTCAA_L008_R1_001.fastq.gz", "fastq", 2631687411.0, 26056311.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3", "0:101", "A:734843629;C:584316000;G:577487406;T:733356850;N:1683526", 101, null, null, null, 734843629, 584316000, 577487406, 733356850, 1683526, "ERX1365619", "ERS1067818", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.95114, null, 0.1036, null, 0.72474, null, 0.48261, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3766, "ERR1294272", "ERX1365618", "ERS1067818", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "WT skin transcriptome", "SAMEA3880684", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 2", "wt2", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "wt2_CTTGTA_L008_R1_001.fastq.gz", "fastq", 2093443463.0, 20727163.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 2", "0:101", "A:607582034;C:442802229;G:437957089;T:603752294;N:1349817", 101, null, null, null, 607582034, 442802229, 437957089, 603752294, 1349817, "ERX1365618", "ERS1067818", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.94792, null, 0.10892, null, 0.73277, null, 0.51067, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [3767, "ERR1294271", "ERX1365617", "ERS1067818", "ERP014370", "PRJEB12848", "Danio rerio Mau mutants skin Transcriptome", "ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265", "Other", "Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25", null, null, "WT skin transcriptome", "SAMEA3880684", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", "ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1", "wt1", "1", "Illumina TruSeq RNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP014370", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16", "wt1_CAGATC_L008_R1_001.fastq.gz", "fastq", 1701561241.0, 16847141.0, "ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1", "0:101", "A:505358711;C:348893979;G:343445186;T:502880170;N:983195", 101, null, null, null, 505358711, 348893979, 343445186, 502880170, 983195, "ERX1365617", "ERS1067818", "ERA567249", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive", "MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY", 1, 0.94565, null, 0.13032, null, 0.73669, null, 0.50473, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2016-02-25", "Adult", "Adult", "Skin", "Surface Structure"], [9166, "ERR2788341", "ERX2797590", "ERS2709706", "ERP110806", "PRJEB28589", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E-MTAB-7159", "Transcriptome Analysis", "Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11", null, "Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "5149STDY7292228", "SAMEA4890710", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK", "ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890710|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7292228|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:pool 4|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7292228|scientific name:Danio rerio|sex:2 female  1 male|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E MTAB 7159:5149STDY7292228 p", "5149STDY7292228 p", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "Experimental Factor: genotype:Tglck:EGFP|Experimental Factor: infect:n1", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP110806", "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL", "5149STDY7292228.bam 5149STDY7292228.bam.bai", "bam bam", 37970494940.0, 387454030.0, "E MTAB 7159:5149STDY7292228", "0:98", "A:11476520187;C:7571635167;G:8189594199;T:10701044279;N:31701108", 98, null, null, null, 11476520187, 7571635167, 8189594199, 10701044279, 31701108, "ERX2797590", "ERS2709706", "ERA1594569", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.87568, null, 0.2122, null, 0.82582, null, 0.5259, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [9167, "ERR2788340", "ERX2797589", "ERS2709705", "ERP110806", "PRJEB28589", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E-MTAB-7159", "Transcriptome Analysis", "Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11", null, "Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "5149STDY7274848", "SAMEA4890709", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK", "ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890709|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274848|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 3|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274848|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E MTAB 7159:5149STDY7274848 p", "5149STDY7274848 p", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Vibrio Anguillarum", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP110806", "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL", "5149STDY7274848.bam 5149STDY7274848.bam.bai", "bam bam", 34517322840.0, 352217580.0, "E MTAB 7159:5149STDY7274848", "0:98", "A:10635243399;C:6658515314;G:7525079510;T:9695995344;N:2489273", 98, null, null, null, 10635243399, 6658515314, 7525079510, 9695995344, 2489273, "ERX2797589", "ERS2709705", "ERA1594569", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.86206, null, 0.18065, null, 0.83514, null, 0.53609, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [9168, "ERR2788339", "ERX2797588", "ERS2709704", "ERP110806", "PRJEB28589", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E-MTAB-7159", "Transcriptome Analysis", "Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11", null, "Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "5149STDY7274847", "SAMEA4890708", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK", "ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890708|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274847|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 2|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274847|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E MTAB 7159:5149STDY7274847 p", "5149STDY7274847 p", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Anisakis simplex", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP110806", "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL", "5149STDY7274847.bam 5149STDY7274847.bam.bai", "bam bam", 34467649678.0, 351710711.0, "E MTAB 7159:5149STDY7274847", "0:98", "A:10609988948;C:6722093635;G:7464497879;T:9667814950;N:3254266", 98, null, null, null, 10609988948, 6722093635, 7464497879, 9667814950, 3254266, "ERX2797588", "ERS2709704", "ERA1594569", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.88751, null, 0.21835, null, 0.83771, null, 0.53927, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [9169, "ERR2788338", "ERX2797587", "ERS2709703", "ERP110806", "PRJEB28589", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E-MTAB-7159", "Transcriptome Analysis", "Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11", null, "Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "5149STDY7274846", "SAMEA4890707", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK", "ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890707|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274846|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 1|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274846|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E MTAB 7159:5149STDY7274846 p", "5149STDY7274846 p", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:n1", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP110806", "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL", "5149STDY7274846.bam 5149STDY7274846.bam.bai", "bam bam", 35052538472.0, 357678964.0, "E MTAB 7159:5149STDY7274846", "0:98", "A:10698116265;C:6858102477;G:7626019661;T:9866905792;N:3394277", 98, null, null, null, 10698116265, 6858102477, 7626019661, 9866905792, 3394277, "ERX2797587", "ERS2709703", "ERA1594569", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.88916, null, 0.21537, null, 0.83802, null, 0.5336, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [9812, "ERR3931362", "ERX3938952", "ERS4329529", "ERP120057", "PRJEB36819", "Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "E-MTAB-8800", "Transcriptome Analysis", "Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.", "ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05", null, "Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7\u00d710 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.", "WKM 7 ED", "SAMEA6565186", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565186|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 7 ED|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM7|organism part:head kidney|sample name:E MTAB 8800:WKM 7 ED", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "E MTAB 8800:WKM 7 ED s", "WKM 7 ED s", "Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7\u00d710 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.", "Experimental Factor: stimulus:n1", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP120057", "NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05", "10_WKM_7_ED.fastq.gz", "fastq", 3603783627.0, 47724788.0, "E MTAB 8800:WKM 7 ED", "0:75.51 1:0", "A:730277817;C:1059558661;G:1006087781;T:807771859;N:87509", 75, 0, null, null, 730277817, 1059558661, 1006087781, 807771859, 87509, "ERX3938952", "ERS4329529", "ERA2383450", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 1, 0.96114, null, 0.20335, null, 0.83798, null, 0.76524, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-12-31", "Adult", "Adult", "Multi-tissue", "Multi-system"], [9813, "ERR3931361", "ERX3938951", "ERS4329528", "ERP120057", "PRJEB36819", "Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "E-MTAB-8800", "Transcriptome Analysis", "Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.", "ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05", null, "Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7\u00d710 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.", "WKM 7 EaD", "SAMEA6565185", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565185|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 7 EaD|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM7|organism part:head kidney|sample name:E MTAB 8800:WKM 7 EaD", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "E MTAB 8800:WKM 7 EaD s", "WKM 7 EaD s", "Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7\u00d710 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.", "Experimental Factor: stimulus:kit ligand", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP120057", "NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05", "11_WKM_7_EaD_1.fastq.gz", "fastq", 3127207407.0, 41417754.0, "E MTAB 8800:WKM 7 EaD", "0:75.50 1:0", "A:618290483;C:948661192;G:891134088;T:669046822;N:74822", 75, 0, null, null, 618290483, 948661192, 891134088, 669046822, 74822, "ERX3938951", "ERS4329528", "ERA2383450", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 1, 0.96441, null, 0.20171, null, 0.85427, null, 0.75425, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-12-31", "Adult", "Adult", "Multi-tissue", "Multi-system"], [9814, "ERR3931360", "ERX3938950", "ERS4329527", "ERP120057", "PRJEB36819", "Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "E-MTAB-8800", "Transcriptome Analysis", "Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.", "ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05", null, "Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7\u00d710 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.", "WKM 5 ED", "SAMEA6565184", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565184|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 5 ED|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM5|organism part:head kidney|sample name:E MTAB 8800:WKM 5 ED", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "E MTAB 8800:WKM 5 ED s", "WKM 5 ED s", "Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7\u00d710 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.", "Experimental Factor: stimulus:n1", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP120057", "NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05", "8_WKM_5_ED.fastq.gz", "fastq", 3762435507.0, 49825705.0, "E MTAB 8800:WKM 5 ED", "0:75.51 1:0", "A:760573477;C:1107794761;G:1060998015;T:832975681;N:93573", 75, 0, null, null, 760573477, 1107794761, 1060998015, 832975681, 93573, "ERX3938950", "ERS4329527", "ERA2383450", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 1, 0.96233, null, 0.20628, null, 0.84141, null, 0.73601, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-12-31", "Adult", "Adult", "Multi-tissue", "Multi-system"], [9815, "ERR3931359", "ERX3938949", "ERS4329526", "ERP120057", "PRJEB36819", "Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "E-MTAB-8800", "Transcriptome Analysis", "Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.", "ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05", null, "Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7\u00d710 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.", "WKM 5 EaD", "SAMEA6565183", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565183|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 5 EaD|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM5|organism part:head kidney|sample name:E MTAB 8800:WKM 5 EaD", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "E MTAB 8800:WKM 5 EaD s", "WKM 5 EaD s", "Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7\u00d710 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.", "Experimental Factor: stimulus:kit ligand", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP120057", "NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga", "ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05", "9_WKM_5_EaD.fastq.gz", "fastq", 3602342027.0, 47707938.0, "E MTAB 8800:WKM 5 EaD", "0:75.51 1:0", "A:717278291;C:1084375347;G:1027250408;T:773351695;N:86286", 75, 0, null, null, 717278291, 1084375347, 1027250408, 773351695, 86286, "ERX3938949", "ERS4329526", "ERA2383450", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 1, 0.96461, null, 0.20281, null, 0.85303, null, 0.74553, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "bulk", "bulk", null, "Czech Republic", "2021-12-31", "Adult", "Adult", "Multi-tissue", "Multi-system"], [9970, "ERR5056255", "ERX4862324", "ERS4959151", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "9 days post harvest", "Zebrafish scale RNA seq total RNA", "SAMEA7198930", "University of Bristol", "ENA first public:2021 04 20|ENA last update:2020 08 20|External Id:SAMEA7198930|INSDC center alias:BRISTOL|INSDC center name:University of Bristol|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 3|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 10", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_REG3_CTTGTA_L002_R1_001.fastq.gz", "fastq", 435534645.0, 8539895.0, "ena RUN BRISTOL 08 01 2021 15:14:53:483 10", "0:51 1:0", "A:104994334;C:102642310;G:101303422;T:126578362;N:16217", 51, 0, null, null, 104994334, 102642310, 101303422, 126578362, 16217, "ERX4862324", "ERS4959151", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.92322, null, 0.08481, null, 0.71997, null, 0.45351, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9971, "ERR5056093", "ERX4862162", "ERS4959146", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "day x", "Zebrafish scale RNA seq total RNA", "SAMEA7198925", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198925|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 13:16:55:212 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_ONT1_CGATGT_L002_R1_001.fastq.gz", "fastq", 613101549.0, 12021599.0, "ena RUN BRISTOL 08 01 2021 13:16:55:212 1", "0:51 1:0", "A:152016801;C:139221646;G:139332264;T:182506912;N:23926", 51, 0, null, null, 152016801, 139221646, 139332264, 182506912, 23926, "ERX4862162", "ERS4959146", "ERA3206646", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.90335, null, 0.1072, null, 0.71784, null, 0.48228, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9972, "ERR5056077", "ERX4862146", "ERS4959146", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "day x", "Zebrafish scale RNA seq total RNA", "SAMEA7198925", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198925|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 12:07:14:527 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_ONT1_CGATGT_L001_R1_001.fastq.gz", "fastq", 600285402.0, 11770302.0, "ena RUN BRISTOL 08 01 2021 12:07:14:527 1", "0:51 1:0", "A:148729943;C:136337224;G:136545524;T:178606078;N:66633", 51, 0, null, null, 148729943, 136337224, 136545524, 178606078, 66633, "ERX4862146", "ERS4959146", "ERA3206631", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.9026, null, 0.10732, null, 0.71683, null, 0.47346, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9973, "ERR5056254", "ERX4862323", "ERS4959151", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "9 days post harvest", "Zebrafish scale RNA seq total RNA", "SAMEA7198930", "University of Bristol", "ENA first public:2021 04 20|ENA last update:2020 08 20|External Id:SAMEA7198930|INSDC center alias:BRISTOL|INSDC center name:University of Bristol|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 3|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 9", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_REG3_CTTGTA_L001_R1_001.fastq.gz", "fastq", 426117342.0, 8355242.0, "ena RUN BRISTOL 08 01 2021 15:14:53:483 9", "0:51 1:0", "A:102630499;C:100472291;G:99193964;T:123775368;N:45220", 51, 0, null, null, 102630499, 100472291, 99193964, 123775368, 45220, "ERX4862323", "ERS4959151", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.92245, null, 0.08463, null, 0.71877, null, 0.45377, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9974, "ERR5056253", "ERX4862322", "ERS4959150", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "9 days post harvest", "Zebrafish scale RNA seq total RNA", "SAMEA7198929", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198929|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 8", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_REG2_CAGATC_L002_R1_001.fastq.gz", "fastq", 434571714.0, 8521014.0, "ena RUN BRISTOL 08 01 2021 15:14:53:483 8", "0:51 1:0", "A:106135147;C:102194661;G:100594136;T:125630448;N:17322", 51, 0, null, null, 106135147, 102194661, 100594136, 125630448, 17322, "ERX4862322", "ERS4959150", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.91779, null, 0.08112, null, 0.7161, null, 0.4437, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9975, "ERR5056252", "ERX4862321", "ERS4959150", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "9 days post harvest", "Zebrafish scale RNA seq total RNA", "SAMEA7198929", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198929|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 7", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_REG2_CAGATC_L001_R1_001.fastq.gz", "fastq", 424788384.0, 8329184.0, "ena RUN BRISTOL 08 01 2021 15:14:53:483 7", "0:51 1:0", "A:103644078;C:99946940;G:98381633;T:122768121;N:47612", 51, 0, null, null, 103644078, 99946940, 98381633, 122768121, 47612, "ERX4862321", "ERS4959150", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.91867, null, 0.08097, null, 0.71388, null, 0.44882, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9976, "ERR5056251", "ERX4862320", "ERS4959149", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. 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Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "day x", "Zebrafish scale", "SAMEA7198927", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198927|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 3|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 3", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_ONT3_ACAGTG_L001_R1_001.fastq.gz", "fastq", 460312587.0, 9025737.0, "ena RUN BRISTOL 08 01 2021 15:14:53:482 3", "0:51 1:0", "A:114396758;C:103865119;G:105005018;T:136994559;N:51133", 51, 0, null, null, 114396758, 103865119, 105005018, 136994559, 51133, "ERX4862317", "ERS4959148", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.90759, null, 0.11359, null, 0.7208, null, 0.47232, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9980, "ERR5056247", "ERX4862316", "ERS4959147", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "day x", "Zebrafish scale RNA seq total RNA", "SAMEA7198926", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198926|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_ONT2_TGACCA_L002_R1_001.fastq.gz", "fastq", 502898046.0, 9860746.0, "ena RUN BRISTOL 08 01 2021 15:14:53:482 2", "0:51 1:0", "A:123893447;C:111981365;G:116049412;T:150953220;N:20602", 51, 0, null, null, 123893447, 111981365, 116049412, 150953220, 20602, "ERX4862316", "ERS4959147", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.90777, null, 0.11921, null, 0.7137, null, 0.48182, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [9981, "ERR5056246", "ERX4862315", "ERS4959147", "ERP123551", "PRJEB39971", "RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration", "ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170", "Other", "RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.", "bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20", null, "day x", "Zebrafish scale RNA seq total RNA", "SAMEA7198926", "BRISTOL", "ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198926|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP123551", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08", "ZFG-15-01_ONT2_TGACCA_L001_R1_001.fastq.gz", "fastq", 491866134.0, 9644434.0, "ena RUN BRISTOL 08 01 2021 15:14:53:482 1", "0:51 1:0", "A:121063841;C:109534722;G:113610951;T:147602721;N:53899", 51, 0, null, null, 121063841, 109534722, 113610951, 147602721, 53899, "ERX4862315", "ERS4959147", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.907, null, 0.11935, null, 0.71364, null, 0.48543, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [10000, "ERR6806877", "ERX6430470", "ERS5060067", "ERP123913", "PRJEB40292", "Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers", "ena-STUDY-I3S-10-09-2020-08:12:35:299-4", "Other", "The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA  suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However  the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges  including lack of sequence conservation. In this work  we performed a combined analysis of ATAC seq  ChIP seq  4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements  regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas  we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences  we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis  demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall  we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements  contributing to the prediction of new disease causative enhancers and their role in human disease.", "ChIP seq  ATAC seq  HiChIP seq  4C seq  RNA seq|chromatin accessibility|cis regulatory mutations|pancreas and pancreatic diseases|transcriptional enhancers|ENA FIRST PUBLIC:2020 09 11|ENA LAST UPDATE:2021 09 22", null, "Adult zebrafish muscle RNA seq replicate2 raw reads", "Zebrafish Muscle RNA seq replicate2", "SAMEA7301508", "I3S", "ENA first public:2021 09 23|ENA last update:2021 09 23|External Id:SAMEA7301508|INSDC center alias:I3S|INSDC center name:I3S|INSDC first public:2021 09 23T20:37:00Z|INSDC last update:2021 09 23T20:37:00Z|INSDC status:public|Submitter Id:Zebrafish Muscle RNA seq replicate2|common name:zebrafish|sample name:Zebrafish Muscle RNA seq replicate2|tissue type:muscle", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT I3S 23 09 2021 16:43:09:330 8", "Muscle2", "1", "Total RNA extracted with TRIZOL from zebrafish muscle and preprared for sequencing with the TruSeq kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP123913", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2021 09 23|ENA LAST UPDATE:2021 09 23", "Muscle_Old_1.fastq.gz", "fastq", 1886870950.0, 37737419.0, "ena RUN I3S 23 09 2021 16:43:09:330 8", "0:50 1:0", "A:479832533;C:470338808;G:443061655;T:493513324;N:124630", 50, 0, null, null, 479832533, 470338808, 443061655, 493513324, 124630, "ERX6430470", "ERS5060067", "ERA6385885", "I3S|European Nucleotide Archive", "I3S", 1, 0.95119, null, 0.04224, null, 0.79251, null, 0.52332, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Portugal", "2020-09-11", "Adult", "Adult", "Muscle", "Muscular System"], [10001, "ERR6806876", "ERX6430469", "ERS5060066", "ERP123913", "PRJEB40292", "Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers", "ena-STUDY-I3S-10-09-2020-08:12:35:299-4", "Other", "The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA  suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However  the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges  including lack of sequence conservation. In this work  we performed a combined analysis of ATAC seq  ChIP seq  4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements  regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas  we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences  we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis  demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall  we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements  contributing to the prediction of new disease causative enhancers and their role in human disease.", "ChIP seq  ATAC seq  HiChIP seq  4C seq  RNA seq|chromatin accessibility|cis regulatory mutations|pancreas and pancreatic diseases|transcriptional enhancers|ENA FIRST PUBLIC:2020 09 11|ENA LAST UPDATE:2021 09 22", null, "Adult zebrafish muscle RNA seq replicate1 raw reads", "Zebrafish Muscle RNA seq replicate1", "SAMEA7301507", "I3S", "ENA first public:2021 09 23|ENA last update:2021 09 23|External Id:SAMEA7301507|INSDC center alias:I3S|INSDC center name:I3S|INSDC first public:2021 09 23T20:37:00Z|INSDC last update:2021 09 23T20:37:00Z|INSDC status:public|Submitter Id:Zebrafish Muscle RNA seq replicate1|common name:zebrafish|sample name:Zebrafish Muscle RNA seq replicate1|tissue type:muscle", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT I3S 23 09 2021 16:43:09:330 7", "Muscle1", "1", "Total RNA extracted with TRIZOL from zebrafish muscle and preprared for sequencing with the TruSeq kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP123913", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2021 09 23|ENA LAST UPDATE:2021 09 23", "Muscle_Young_1.fastq.gz", "fastq", 1795352850.0, 35907057.0, "ena RUN I3S 23 09 2021 16:43:09:330 7", "0:50 1:0", "A:451489686;C:453210606;G:425250111;T:465282474;N:119973", 50, 0, null, null, 451489686, 453210606, 425250111, 465282474, 119973, "ERX6430469", "ERS5060066", "ERA6385885", "I3S|European Nucleotide Archive", "I3S", 1, 0.95698, null, 0.02942, null, 0.82126, null, 0.56075, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Portugal", "2020-09-11", "Adult", "Adult", "Muscle", "Muscular System"], [10002, "ERR6806875", "ERX6430468", "ERS5060069", "ERP123913", "PRJEB40292", "Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers", "ena-STUDY-I3S-10-09-2020-08:12:35:299-4", "Other", "The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA  suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However  the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges  including lack of sequence conservation. In this work  we performed a combined analysis of ATAC seq  ChIP seq  4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements  regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas  we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences  we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis  demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall  we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements  contributing to the prediction of new disease causative enhancers and their role in human disease.", "ChIP seq  ATAC seq  HiChIP seq  4C seq  RNA seq|chromatin accessibility|cis regulatory mutations|pancreas and pancreatic diseases|transcriptional enhancers|ENA FIRST PUBLIC:2020 09 11|ENA LAST UPDATE:2021 09 22", null, "Adult zebrafish whole pancreas RNA seq replicate2 raw reads", "Zebrafish Whole Pancreas RNA seq replicate2", "SAMEA7301510", "I3S", "ENA first public:2021 09 23|ENA last update:2021 09 23|External Id:SAMEA7301510|INSDC center alias:I3S|INSDC center name:I3S|INSDC first public:2021 09 23T20:37:00Z|INSDC last update:2021 09 23T20:37:00Z|INSDC status:public|Submitter Id:Zebrafish Whole Pancreas RNA seq replicate2|common name:zebrafish|sample name:Zebrafish Whole Pancreas RNA seq replicate2|tissue type:whole pancreas", null, null, null, null, null, null, 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