run_metadata
11,656 rows where experiment.library_layout = "SINGLE" and technology = "unknown"
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| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 14 | 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. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 28 degrees rep 3 | SAMD00422597 | sample name:rRNA mock community 28 degrees rep 3|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:28|treatment:rRNA | NextSeq 2000 sequencing of SAMD00422597 | DRX323973 | t28 3 tRNA.fastq | 1 | NEBNext Kit for Illumina | 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 SAMD00422597 | 3791170746.0 | 37701921.0 | DRR334977 | 0:100.56 1:0 | A:967477491;C:926887571;G:898697642;T:998107868;N:174 | 100 | 0 | 967477491 | 926887571 | 898697642 | 998107868 | 174 | DRX323973 | DRS217313 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.31527 | 0.06446 | 0.88844 | 0.62118 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 15 | 15 | DRR334976 | DRX323972 | DRS217312 | 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. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 28 degrees rep 2 | SAMD00422596 | 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 | NextSeq 2000 sequencing of SAMD00422596 | DRX323972 | t28 2 tRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 2801693695.0 | 27860658.0 | DRR334976 | 0:100.56 1:0 | A:700189496;C:702936549;G:679920984;T:718646067;N:599 | 100 | 0 | 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 | 0.08819 | 0.85859 | 0.69447 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 16 | 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. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 28 degrees rep 1 | SAMD00422595 | 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 | NextSeq 2000 sequencing of SAMD00422595 | DRX323971 | t28 1 tRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 3148691934.0 | 31307464.0 | DRR334975 | 0:100.57 1:0 | A:785000734;C:791315678;G:766594599;T:805780465;N:458 | 100 | 0 | 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 | 0.09061 | 0.94065 | 0.74047 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 17 | 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. 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. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 19 degrees rep 3 | SAMD00422594 | 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 | NextSeq 2000 sequencing of SAMD00422594 | DRX323970 | t19 3 tRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 2856186273.0 | 28400524.0 | DRR334974 | 0:100.57 1:0 | A:695685787;C:733754277;G:715270279;T:711475544;N:386 | 100 | 0 | 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 | 0.10933 | 0.87105 | 0.7287 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 18 | 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. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 19 degrees rep 2 | SAMD00422593 | 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 | NextSeq 2000 sequencing of SAMD00422593 | DRX323969 | t19 2 tRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 3199929804.0 | 31816971.0 | DRR334973 | 0:100.57 1:0 | A:777149590;C:825478743;G:804835148;T:792466124;N:199 | 100 | 0 | 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 | 0.10282 | 0.89706 | 0.74667 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 19 | 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. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 19 degrees rep 1 | SAMD00422592 | 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 | NextSeq 2000 sequencing of SAMD00422592 | DRX323968 | t19 1 tRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 3658675391.0 | 36374718.0 | DRR334972 | 0:100.58 1:0 | A:879342063;C:954687406;G:929537615;T:895107890;N:417 | 100 | 0 | 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 | 0.11691 | 0.88239 | 0.73925 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 20 | 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. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 10 degrees rep 3 | SAMD00422591 | 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 | NextSeq 2000 sequencing of SAMD00422591 | DRX323967 | t10 3 tRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 3017524690.0 | 30006334.0 | DRR334971 | 0:100.56 1:0 | A:771967717;C:738814269;G:712866126;T:793876235;N:343 | 100 | 0 | 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 | 0.07363 | 0.9093 | 0.73422 | 100 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 21 | 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. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 10 degrees rep 2 | SAMD00422590 | 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 | NextSeq 2000 sequencing of SAMD00422590 | DRX323966 | t10 2 tRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 3115915184.0 | 30982336.0 | DRR334970 | 0:100.57 1:0 | A:765727966;C:794741415;G:771082024;T:784363609;N:170 | 100 | 0 | 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 | 0.10504 | 0.89357 | 0.749 | 100 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 22 | 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. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 10 degrees rep 1 | SAMD00422589 | 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 | NextSeq 2000 sequencing of SAMD00422589 | DRX323965 | t10 1 tRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 3206657309.0 | 31883532.0 | DRR334969 | 0:100.57 1:0 | A:792874386;C:814578518;G:787469614;T:811734581;N:210 | 100 | 0 | 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 | 0.09664 | 0.92898 | 0.74114 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 23 | 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. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 28 degrees rep 3 | SAMD00422588 | 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 | NextSeq 2000 sequencing of SAMD00422588 | DRX323964 | m28 3 mRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 3157078356.0 | 31416275.0 | DRR334968 | 0:100.49 1:0 | A:816263259;C:752748024;G:759884392;T:828182261;N:420 | 100 | 0 | 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 | 0.01832 | 0.73996 | 0.46811 | 99 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 24 | 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. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 28 degrees rep 2 | SAMD00422587 | 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 | NextSeq 2000 sequencing of SAMD00422587 | DRX323963 | m28 2 mRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 3155807651.0 | 31404635.0 | DRR334967 | 0:100.49 1:0 | A:819014350;C:749873295;G:756284406;T:830635394;N:206 | 100 | 0 | 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 | 0.02238 | 0.72427 | 0.47376 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 25 | 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. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 28 degrees rep 1 | SAMD00422586 | 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 | NextSeq 2000 sequencing of SAMD00422586 | DRX323962 | m28 1 mRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 2589772286.0 | 25765782.0 | DRR334966 | 0:100.51 1:0 | A:679223577;C:610675892;G:617869465;T:682003195;N:157 | 100 | 0 | 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 | 0.03367 | 0.73555 | 0.49223 | 100 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 26 | 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. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 19 degrees rep 3 | SAMD00422602 | 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 | NextSeq 2000 sequencing of SAMD00422602 | DRX323961 | m19 3 mRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 3124746628.0 | 31095367.0 | DRR334965 | 0:100.49 1:0 | A:821891547;C:734660854;G:739230475;T:828963220;N:532 | 100 | 0 | 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 | 0.03264 | 0.69449 | 0.47416 | 99 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 27 | 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. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 19 degrees rep 2 | SAMD00422601 | 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 | NextSeq 2000 sequencing of SAMD00422601 | DRX323960 | m19 2 mRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 3171661466.0 | 31561473.0 | DRR334964 | 0:100.49 1:0 | A:836793307;C:742872021;G:750053514;T:841942389;N:235 | 100 | 0 | 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 | 0.03639 | 0.69027 | 0.48494 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 28 | 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. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 19 degrees rep 1 | SAMD00422600 | 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 | NextSeq 2000 sequencing of SAMD00422600 | DRX323959 | m19 1 mRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 2916453082.0 | 29023768.0 | DRR334963 | 0:100.48 1:0 | A:761416880;C:692014182;G:696272089;T:766749729;N:202 | 100 | 0 | 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 | 0.03406 | 0.68696 | 0.47496 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 29 | 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. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 10 degrees rep 3 | SAMD00422599 | 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 | NextSeq 2000 sequencing of SAMD00422599 | DRX323958 | m10 3 mRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 2600103192.0 | 25872833.0 | DRR334962 | 0:100.50 1:0 | A:668944597;C:625686885;G:631010166;T:674461210;N:334 | 100 | 0 | 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 | 0.02949 | 0.71918 | 0.47633 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 30 | 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. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 10 degrees rep 2 | SAMD00422598 | 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 | NextSeq 2000 sequencing of SAMD00422598 | DRX323957 | m10 2 mRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 2608660833.0 | 25958804.0 | DRR334961 | 0:100.49 1:0 | A:683370128;C:615324906;G:621209484;T:688756167;N:148 | 100 | 0 | 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 | 0.04316 | 0.69656 | 0.48579 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 31 | 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. | mRNA metatranscriptomic sequences from mock communities consist of five model species | mRNA mock community at 10 degrees rep 1 | SAMD00422585 | 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 | NextSeq 2000 sequencing of SAMD00422585 | DRX323956 | m10 1 mRNA.fastq | 1 | NEBNext Kit for Illumina | 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 | 2879915507.0 | 28651533.0 | DRR334960 | 0:100.52 1:0 | A:761972464;C:675761096;G:678969165;T:763212637;N:145 | 100 | 0 | 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 | 0.05671 | 0.72622 | 0.49269 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | poly_a | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 32 | 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. | zebrafish wild type AB adult gut replicate 3 | zebrafish adult gut replicate 3 | SAMD00529462 | sample name:zebrafish adult gut replicate 3|biological replicate:adult 3|strain:AB | Illumina HiSeq 1500 sequencing of SAMD00529462 | DRX393848 | AR019 gut 6 adult | 1 | 1 | 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 | 3546347364.0 | 28145614.0 | DRR408242 | 0:126 1:0 | A:919466631;C:829424335;G:818581155;T:978810217;N:65026 | 126 | 0 | 919466631 | 829424335 | 818581155 | 978810217 | 65026 | DRX393848 | DRS407006 | DRA014885 | NIBB|NIBB core research facilities, National Institute for Basic Biology | University of Hyogo | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | trueseq | bulk | unknown | unknown | Japan | 2024-09-20 | Adult | Adult | Gut | Digestive System | ||||||||||||||||||||||||||||||
| 33 | 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. | zebrafish wild type AB adult gut replicate 2 | zebrafish adult gut replicate 2 | SAMD00529461 | sample name:zebrafish adult gut replicate 2|biological replicate:adult 2|strain:AB | Illumina HiSeq 1500 sequencing of SAMD00529461 | DRX393847 | AR006 gut 4 adult | 1 | 1 | 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 | 3671973648.0 | 29142648.0 | DRR408241 | 0:126 1:0 | A:942167543;C:859431290;G:852661772;T:1017643011;N:70032 | 126 | 0 | 942167543 | 859431290 | 852661772 | 1017643011 | 70032 | DRX393847 | DRS407005 | DRA014885 | NIBB|NIBB core research facilities, National Institute for Basic Biology | University of Hyogo | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | trueseq | bulk | unknown | unknown | Japan | 2024-09-20 | Adult | Adult | Gut | Digestive System | ||||||||||||||||||||||||||||||
| 34 | 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. | zebrafish wild type AB adult gut replicate 1 | zebrafish adult gut replicate 1 | SAMD00529460 | sample name:zebrafish adult gut replicate 1|biological replicate:adult 1|strain:AB | Illumina HiSeq 1500 sequencing of SAMD00529460 | DRX393846 | AR004 gut 2 adult | 1 | 1 | 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 | 3480523704.0 | 27623204.0 | DRR408240 | 0:126 1:0 | A:898051986;C:827557593;G:816541244;T:938307607;N:65274 | 126 | 0 | 898051986 | 827557593 | 816541244 | 938307607 | 65274 | DRX393846 | DRS407004 | DRA014885 | NIBB|NIBB core research facilities, National Institute for Basic Biology | University of Hyogo | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | trueseq | bulk | unknown | unknown | Japan | 2024-09-20 | Adult | Adult | Gut | Digestive System | ||||||||||||||||||||||||||||||
| 35 | 35 | DRR408239 | DRX393845 | DRS407003 | 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. | zebrafish wild type AB larval gut replicate 3 | zebrafish larval gut replicate 3 | SAMD00529459 | sample name:zebrafish larval gut replicate 3|biological replicate:larval 3|strain:AB | Illumina HiSeq 1500 sequencing of SAMD00529459 | DRX393845 | AR012 gut 5 5 dpf 6 dpf larvae | 1 | 1 | 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 SAMD00529459 | 3463982046.0 | 27491921.0 | DRR408239 | 0:126 1:0 | A:842552557;C:849757648;G:837664725;T:933942026;N:65090 | 126 | 0 | 842552557 | 849757648 | 837664725 | 933942026 | 65090 | DRX393845 | DRS407003 | DRA014885 | NIBB|NIBB core research facilities, National Institute for Basic Biology | University of Hyogo | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | trueseq | bulk | unknown | unknown | Japan | 2024-09-20 | Larval | Larval | Gut | Digestive System | ||||||||||||||||||||||||||||||
| 36 | 36 | DRR408238 | DRX393844 | DRS407002 | 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. | zebrafish wild type AB larval gut replicate 2 | zebrafish larval gut replicate 2 | SAMD00529458 | sample name:zebrafish larval gut replicate 2|biological replicate:larval 2|strain:AB | Illumina HiSeq 1500 sequencing of SAMD00529458 | DRX393844 | AR005 gut 3 5 dpf 6 dpf larvae | 1 | 1 | 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 SAMD00529458 | 3782320416.0 | 30018416.0 | DRR408238 | 0:126 1:0 | A:930337206;C:920645770;G:906559955;T:1024704277;N:73208 | 126 | 0 | 930337206 | 920645770 | 906559955 | 1024704277 | 73208 | DRX393844 | DRS407002 | DRA014885 | NIBB|NIBB core research facilities, National Institute for Basic Biology | University of Hyogo | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | trueseq | bulk | unknown | unknown | Japan | 2024-09-20 | Larval | Larval | Gut | Digestive System | ||||||||||||||||||||||||||||||
| 37 | 37 | DRR408237 | DRX393843 | DRS407001 | 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. | zebrafish wild type AB larval gut replicate 1 | zebrafish larval gut replicate 1 | SAMD00529457 | sample name:zebrafish larval gut replicate 1|biological replicate:larval 1|strain:AB | Illumina HiSeq 1500 sequencing of SAMD00529457 | DRX393843 | AR002 gut 1 5 dpf 6 dpf larvae | 1 | 1 | 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 SAMD00529457 | 3606885828.0 | 28626078.0 | DRR408237 | 0:126 1:0 | A:879148446;C:885673723;G:870330963;T:971663212;N:69484 | 126 | 0 | 879148446 | 885673723 | 870330963 | 971663212 | 69484 | DRX393843 | DRS407001 | DRA014885 | NIBB|NIBB core research facilities, National Institute for Basic Biology | University of Hyogo | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | trueseq | bulk | unknown | unknown | Japan | 2024-09-20 | Larval | Larval | Gut | Digestive System | ||||||||||||||||||||||||||||||
| 50 | 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. | ovulation duirng natural paring | zebrafish ovary isolated from adult fish at ovulation duirng natural paring. [RNAseq] | SAMD00025434 | sample name:6 Ovu|strain:roy|tissue type:ovary|dev stage:adult | Illumina HiSeq 2500 sequencing of SAMD00025434 | DRX026962 | 6 Ovu | 1 | 1 | 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 | 351766656.0 | 9771296.0 | DRR029944 | 0:36 | A:79811727;C:85391142;G:90185809;T:96371771;N:6207 | 36 | 79811727 | 85391142 | 90185809 | 96371771 | 6207 | DRX026962 | DRS086502 | DRA003031 | SHIZUOKA|Shizuoka University | Shizuoka University | 1 | 0.91956 | 0.01686 | 0.76637 | 0.45997 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2019-01-23 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||||||
| 51 | 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. | oocyte maturation duirng natural paring | zebrafish ovary isolated from adult fish at oocyte maturation duirng natural paring. [RNAseq] | SAMD00025433 | sample name:5 OM|strain:roy|tissue type:ovary|dev stage:adult | Illumina HiSeq 2500 sequencing of SAMD00025433 | DRX026961 | 5 OM | 1 | 1 | 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 | 573617016.0 | 15933806.0 | DRR029943 | 0:36 | A:130606804;C:141376330;G:145891720;T:155734276;N:7886 | 36 | 130606804 | 141376330 | 145891720 | 155734276 | 7886 | DRX026961 | DRS086501 | DRA003031 | SHIZUOKA|Shizuoka University | Shizuoka University | 1 | 0.91108 | 0.0173 | 0.76205 | 0.46319 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2019-01-23 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 52 | 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. | in vivo testosterone treatment | zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq replicate] | SAMD00025432 | sample name:4 Tes rep|strain:roy|tissue type:ovary|dev stage:adult | Illumina HiSeq 2500 sequencing of SAMD00025432 | DRX026960 | 4 Tes rep | 1 | 1 | 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 | 366042528.0 | 10167848.0 | DRR029942 | 0:36 | A:84988522;C:88640326;G:93559022;T:98847003;N:7655 | 36 | 84988522 | 88640326 | 93559022 | 98847003 | 7655 | DRX026960 | DRS086500 | DRA003031 | SHIZUOKA|Shizuoka University | Shizuoka University | 1 | 0.91602 | 0.01846 | 0.76015 | 0.46475 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2019-01-23 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||||||
| 53 | 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. | in vivo testosterone treatment | zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq] | SAMD00025431 | sample name:4 Tes|strain:roy|tissue type:ovary|dev stage:adult | Illumina HiSeq 2500 sequencing of SAMD00025431 | DRX026959 | 4 Tes | 1 | 1 | 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 | 1269835992.0 | 35273222.0 | DRR029941 | 0:36 | A:275250658;C:323605136;G:316729009;T:354204170;N:47019 | 36 | 275250658 | 323605136 | 316729009 | 354204170 | 47019 | DRX026959 | DRS086499 | DRA003031 | SHIZUOKA|Shizuoka University | Shizuoka University | 1 | 0.91467 | 0.02353 | 0.75962 | 0.46861 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2019-01-23 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||||||
| 54 | 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. | in vivo diethylstilbestrol DES treatment | zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate] | SAMD00025430 | sample name:3 DES rep|strain:roy|tissue type:ovary|dev stage:adult | Illumina HiSeq 2500 sequencing of SAMD00025430 | DRX026958 | 3 DES rep | 1 | 1 | 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 | 658651536.0 | 18295876.0 | DRR029940 | DRX026958 | DRS086498 | DRA003031 | SHIZUOKA|Shizuoka University | Shizuoka University | 1 | 0.89964 | 0.01785 | 0.76451 | 0.45872 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2019-01-23 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||||||||||||||
| 55 | 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. | in vivo diethylstilbestrol DES treatment | zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq] | SAMD00025429 | sample name:3 DES|strain:roy|tissue type:ovary|dev stage:adult | Illumina HiSeq 2500 sequencing of SAMD00025429 | DRX026957 | 3 DES | 1 | 1 | 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 | 1202024016.0 | 33389556.0 | DRR029939 | 0:36 | A:263319430;C:305852921;G:298798093;T:334008544;N:45028 | 36 | 263319430 | 305852921 | 298798093 | 334008544 | 45028 | DRX026957 | DRS086497 | DRA003031 | SHIZUOKA|Shizuoka University | Shizuoka University | 1 | 0.90643 | 0.02337 | 0.75008 | 0.47587 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2019-01-23 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||||||
| 56 | 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. | in vivo maturation inducing hormone DHP treatment | zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq replicate] | SAMD00025428 | sample name:2 DHP rep|strain:roy|tissue type:ovary|dev stage:adult | Illumina HiSeq 2500 sequencing of SAMD00025428 | DRX026956 | 2 DHP rep | 1 | 1 | 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 | 434243088.0 | 12062308.0 | DRR029938 | 0:36 | A:99859342;C:105890785;G:110526688;T:117957580;N:8693 | 36 | 99859342 | 105890785 | 110526688 | 117957580 | 8693 | DRX026956 | DRS086496 | DRA003031 | SHIZUOKA|Shizuoka University | Shizuoka University | 1 | 0.91529 | 0.02061 | 0.7595 | 0.45809 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2019-01-23 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||||||
| 57 | 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. | in vivo maturation inducing hormone DHP treatment | zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq] | SAMD00025427 | sample name:2 DHP|strain:roy|tissue type:ovary|dev stage:adult | Illumina HiSeq 2500 sequencing of SAMD00025427 | DRX026955 | 2 DHP | 1 | 1 | 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 | 1463868972.0 | 40663027.0 | DRR029937 | 0:36 | A:316060780;C:369221844;G:372845502;T:405685804;N:55042 | 36 | 316060780 | 369221844 | 372845502 | 405685804 | 55042 | DRX026955 | DRS086495 | DRA003031 | SHIZUOKA|Shizuoka University | Shizuoka University | 1 | 0.91556 | 0.01967 | 0.76621 | 0.46541 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2019-01-23 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||||||
| 58 | 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. | in vivo ethanol treatment | zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate] | SAMD00025426 | sample name:1 EtOH rep|strain:roy|tissue type:ovary|dev stage:adult | Illumina HiSeq 2500 sequencing of SAMD00025426 | DRX026954 | 1 EtOH rep | 1 | 1 | 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 | 438020208.0 | 12167228.0 | DRR029936 | 0:36 | A:101672612;C:105602774;G:110120652;T:120615069;N:9101 | 36 | 101672612 | 105602774 | 110120652 | 120615069 | 9101 | DRX026954 | DRS086494 | DRA003031 | SHIZUOKA|Shizuoka University | Shizuoka University | 1 | 0.90777 | 0.01929 | 0.7652 | 0.45988 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2019-01-23 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||||||
| 59 | 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. | in vivo ethanol treatment | zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq] | SAMD00025425 | sample name:1 EtOH|strain:roy|tissue type:ovary|dev stage:adult | Illumina HiSeq 2500 sequencing of SAMD00025425 | DRX026953 | 1 EtOH | 1 | 1 | 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 SAMD00025425 | 1365603372.0 | 37933427.0 | DRR029935 | 0:36 | A:299786286;C:345487829;G:342408447;T:377870789;N:50021 | 36 | 299786286 | 345487829 | 342408447 | 377870789 | 50021 | DRX026953 | DRS086493 | DRA003031 | SHIZUOKA|Shizuoka University | Shizuoka University | 1 | 0.91103 | 0.02142 | 0.75402 | 0.46574 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2019-01-23 | Adult | Adult | Gonad | Reproductive System | |||||||||||||||||||||||||
| 60 | 60 | DRR032764 | DRX029570 | DRS049969 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 100 individuals | Dr shield 2 | SAMD00028161 | sample name:Dr shield 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:shield|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028161 | DRX029570 | Dr shield 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028161 | 3644397900.0 | 36443979.0 | DRR032764 | 0:100 1:0 | A:986071173;C:842367218;G:837686080;T:978236607;N:36822 | 100 | 0 | 986071173 | 842367218 | 837686080 | 978236607 | 36822 | DRX029570 | DRS049969 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92419 | 0.08269 | 0.75558 | 0.47863 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Gastrula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 61 | 61 | DRR032763 | DRX029569 | DRS049968 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 100 individuals | Dr shield 1 | SAMD00028160 | sample name:Dr shield 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:shield|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028160 | DRX029569 | Dr shield 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028160 | 3834622000.0 | 38346220.0 | DRR032763 | 0:100 1:0 | A:1043352851;C:880011834;G:876775415;T:1034444253;N:37647 | 100 | 0 | 1043352851 | 880011834 | 876775415 | 1034444253 | 37647 | DRX029569 | DRS049968 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92305 | 0.09126 | 0.75481 | 0.47587 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Gastrula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 62 | 62 | DRR032762 | DRX029568 | DRS049967 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr prime5 6 3 | SAMD00028159 | sample name:Dr prime5 6 3|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime5 6|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028159 | DRX029568 | Dr prime5 6 3 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028159 | 3903332800.0 | 39033328.0 | DRR032762 | 0:100 1:0 | A:1050045822;C:908538410;G:900588661;T:1044116537;N:43370 | 100 | 0 | 1050045822 | 908538410 | 900588661 | 1044116537 | 43370 | DRX029568 | DRS049967 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92761 | 0.07976 | 0.69126 | 0.46568 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 63 | 63 | DRR032761 | DRX029567 | DRS049966 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr prime5 6 2 | SAMD00028158 | sample name:Dr prime5 6 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime5 6|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028158 | DRX029567 | Dr prime5 6 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028158 | 3678549700.0 | 36785497.0 | DRR032761 | 0:100 1:0 | A:986526644;C:857762765;G:853417738;T:980801764;N:40789 | 100 | 0 | 986526644 | 857762765 | 853417738 | 980801764 | 40789 | DRX029567 | DRS049966 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92689 | 0.07872 | 0.6928 | 0.46577 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 64 | 64 | DRR032760 | DRX029566 | DRS049965 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr prime5 6 1 | SAMD00028157 | sample name:Dr prime5 6 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime5 6|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028157 | DRX029566 | Dr prime5 6 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028157 | 3863129500.0 | 38631295.0 | DRR032760 | 0:100 1:0 | A:1035240477;C:901625010;G:895370149;T:1030851937;N:41927 | 100 | 0 | 1035240477 | 901625010 | 895370149 | 1030851937 | 41927 | DRX029566 | DRS049965 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92337 | 0.07522 | 0.69315 | 0.46516 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 65 | 65 | DRR032759 | DRX029565 | DRS049964 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr prime25 2 | SAMD00028156 | sample name:Dr prime25 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime25|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028156 | DRX029565 | Dr prime25 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028156 | 3750136100.0 | 37501361.0 | DRR032759 | 0:100 1:0 | A:1013528040;C:866734984;G:862431819;T:1007403208;N:38049 | 100 | 0 | 1013528040 | 866734984 | 862431819 | 1007403208 | 38049 | DRX029565 | DRS049964 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92019 | 0.09079 | 0.68304 | 0.47083 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 66 | 66 | DRR032758 | DRX029564 | DRS049963 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr prime25 1 | SAMD00028155 | sample name:Dr prime25 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime25|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028155 | DRX029564 | Dr prime25 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028155 | 3544862700.0 | 35448627.0 | DRR032758 | 0:100 1:0 | A:952135895;C:825841753;G:821757889;T:945087927;N:39236 | 100 | 0 | 952135895 | 825841753 | 821757889 | 945087927 | 39236 | DRX029564 | DRS049963 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92229 | 0.08344 | 0.68525 | 0.466 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 67 | 67 | DRR032757 | DRX029563 | DRS049962 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 97 individuals | Dr bud 2 | SAMD00028154 | sample name:Dr bud 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:bud|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028154 | DRX029563 | Dr bud 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028154 | 4104778200.0 | 41047782.0 | DRR032757 | 0:100 1:0 | A:1116316188;C:944738800;G:936257056;T:1107423486;N:42670 | 100 | 0 | 1116316188 | 944738800 | 936257056 | 1107423486 | 42670 | DRX029563 | DRS049962 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92945 | 0.10493 | 0.73407 | 0.47824 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 68 | 68 | DRR032756 | DRX029562 | DRS049961 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 100 individuals | Dr bud 1 | SAMD00028153 | sample name:Dr bud 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:bud|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028153 | DRX029562 | Dr bud 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028153 | 4540291000.0 | 45402910.0 | DRR032756 | 0:100 1:0 | A:1237914068;C:1042346110;G:1033172731;T:1226799791;N:58300 | 100 | 0 | 1237914068 | 1042346110 | 1033172731 | 1226799791 | 58300 | DRX029562 | DRS049961 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92628 | 0.10478 | 0.7391 | 0.46461 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Undetermined | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 69 | 69 | DRR032755 | DRX029561 | DRS049960 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 100 individuals | Dr 90epiboly 2 | SAMD00028152 | sample name:Dr 90epiboly 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:90epiboly|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028152 | DRX029561 | Dr 90epiboly 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028152 | 3572358600.0 | 35723586.0 | DRR032755 | 0:100 1:0 | A:971653450;C:821326559;G:816855636;T:962477457;N:45498 | 100 | 0 | 971653450 | 821326559 | 816855636 | 962477457 | 45498 | DRX029561 | DRS049960 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92485 | 0.10642 | 0.74213 | 0.47012 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Gastrula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 70 | 70 | DRR032754 | DRX029560 | DRS049959 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 100 individuals | Dr 90epiboly 1 | SAMD00028151 | sample name:Dr 90epiboly 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:90epiboly|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028151 | DRX029560 | Dr 90epiboly 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028151 | 3423980500.0 | 34239805.0 | DRR032754 | 0:100 1:0 | A:933088185;C:785251613;G:780911148;T:924686406;N:43148 | 100 | 0 | 933088185 | 785251613 | 780911148 | 924686406 | 43148 | DRX029560 | DRS049959 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92436 | 0.10881 | 0.74255 | 0.47068 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Gastrula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 71 | 71 | DRR032753 | DRX029559 | DRS049958 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 114 individuals | Dr 8cell 2 | SAMD00028150 | sample name:Dr 8cell 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:8cell|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028150 | DRX029559 | Dr 8cell 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028150 | 3708921900.0 | 37089219.0 | DRR032753 | 0:100 1:0 | A:985502141;C:874161613;G:869551685;T:979663686;N:42775 | 100 | 0 | 985502141 | 874161613 | 869551685 | 979663686 | 42775 | DRX029559 | DRS049958 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.93329 | 0.02366 | 0.78896 | 0.47447 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Cleavage | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 72 | 72 | DRR032752 | DRX029558 | DRS049957 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 96 individuals | Dr 8cell 1 | SAMD00028149 | sample name:Dr 8cell 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:8cell|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028149 | DRX029558 | Dr 8cell 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028149 | 3666991200.0 | 36669912.0 | DRR032752 | 0:100 1:0 | A:976118513;C:862559696;G:858017821;T:970254302;N:40868 | 100 | 0 | 976118513 | 862559696 | 858017821 | 970254302 | 40868 | DRX029558 | DRS049957 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.934 | 0.02403 | 0.78877 | 0.46902 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Cleavage | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 73 | 73 | DRR032751 | DRX029557 | DRS049956 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 100 individuals | Dr 75epiboly 2 | SAMD00028148 | sample name:Dr 75epiboly 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:75epiboly|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028148 | DRX029557 | Dr 75epiboly 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028148 | 3252021500.0 | 32520215.0 | DRR032751 | 0:100 1:0 | A:885527595;C:746750899;G:742907892;T:876794123;N:40991 | 100 | 0 | 885527595 | 746750899 | 742907892 | 876794123 | 40991 | DRX029557 | DRS049956 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92594 | 0.10181 | 0.74862 | 0.47789 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Gastrula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 74 | 74 | DRR032750 | DRX029556 | DRS049955 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 100 individuals | Dr 75epiboly 1 | SAMD00028147 | sample name:Dr 75epiboly 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:75epiboly|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028147 | DRX029556 | Dr 75epiboly 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028147 | 3785053700.0 | 37850537.0 | DRR032750 | 0:100 1:0 | A:1029014798;C:870946157;G:867537069;T:1017508684;N:46992 | 100 | 0 | 1029014798 | 870946157 | 867537069 | 1017508684 | 46992 | DRX029556 | DRS049955 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92346 | 0.10046 | 0.74921 | 0.47295 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Gastrula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 75 | 75 | DRR032749 | DRX029555 | DRS049954 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr 72h 2 | SAMD00028146 | sample name:Dr 72h 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:72h Protruding mouth|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028146 | DRX029555 | Dr 72h 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028146 | 3429795800.0 | 34297958.0 | DRR032749 | 0:100 1:0 | A:928062015;C:792470305;G:786930881;T:922296289;N:36310 | 100 | 0 | 928062015 | 792470305 | 786930881 | 922296289 | 36310 | DRX029555 | DRS049954 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.91821 | 0.09774 | 0.65437 | 0.46443 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Larval | Larval | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 76 | 76 | DRR032748 | DRX029554 | DRS049953 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr 72h 1 | SAMD00028145 | sample name:Dr 72h 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:72h Protruding mouth|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028145 | DRX029554 | Dr 72h 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028145 | 3897194500.0 | 38971945.0 | DRR032748 | 0:100 1:0 | A:1050989414;C:903225496;G:895783177;T:1047153493;N:42920 | 100 | 0 | 1050989414 | 903225496 | 895783177 | 1047153493 | 42920 | DRX029554 | DRS049953 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92211 | 0.09393 | 0.65486 | 0.45971 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Larval | Larval | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 77 | 77 | DRR032747 | DRX029553 | DRS049952 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr 6somite 2 | SAMD00028144 | sample name:Dr 6somite 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:6somite|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028144 | DRX029553 | Dr 6somite 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028144 | 3704431000.0 | 37044310.0 | DRR032747 | 0:100 1:0 | A:1001844161;C:856702913;G:850695568;T:995148798;N:39560 | 100 | 0 | 1001844161 | 856702913 | 850695568 | 995148798 | 39560 | DRX029553 | DRS049952 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92633 | 0.09211 | 0.72107 | 0.47195 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Segmentation | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 78 | 78 | DRR032746 | DRX029552 | DRS049951 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr 6somite 1 | SAMD00028143 | sample name:Dr 6somite 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:6somite|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028143 | DRX029552 | Dr 6somite 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028143 | 3529311900.0 | 35293119.0 | DRR032746 | 0:100 1:0 | A:953957996;C:816824469;G:811403696;T:947089530;N:36209 | 100 | 0 | 953957996 | 816824469 | 811403696 | 947089530 | 36209 | DRX029552 | DRS049951 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92437 | 0.09257 | 0.72113 | 0.47004 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Segmentation | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 79 | 79 | DRR032745 | DRX029551 | DRS049950 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr 60h 2 | SAMD00028142 | sample name:Dr 60h 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:60h Pec fin|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028142 | DRX029551 | Dr 60h 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028142 | 3875337000.0 | 38753370.0 | DRR032745 | 0:100 1:0 | A:1042558903;C:899892111;G:896867583;T:1035981420;N:36983 | 100 | 0 | 1042558903 | 899892111 | 896867583 | 1035981420 | 36983 | DRX029551 | DRS049950 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.91891 | 0.09445 | 0.66156 | 0.45564 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Hatching | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 80 | 80 | DRR032744 | DRX029550 | DRS049949 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr 60h 1 | SAMD00028141 | sample name:Dr 60h 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:60h Pec fin|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028141 | DRX029550 | Dr 60h 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028141 | 3538468200.0 | 35384682.0 | DRR032744 | 0:100 1:0 | A:960664313;C:812459988;G:809014008;T:956295205;N:34686 | 100 | 0 | 960664313 | 812459988 | 809014008 | 956295205 | 34686 | DRX029550 | DRS049949 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.91388 | 0.10346 | 0.66076 | 0.45203 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Hatching | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 81 | 81 | DRR032743 | DRX029549 | DRS049948 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr 5day 3 | SAMD00028140 | sample name:Dr 5day 3|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:5day|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028140 | DRX029549 | Dr 5day 3 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028140 | 3884716000.0 | 38847160.0 | DRR032743 | 0:100 1:0 | A:1040550584;C:905663425;G:904247323;T:1034215019;N:39649 | 100 | 0 | 1040550584 | 905663425 | 904247323 | 1034215019 | 39649 | DRX029549 | DRS049948 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92219 | 0.08287 | 0.65863 | 0.47377 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Larval | Larval | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 82 | 82 | DRR032742 | DRX029548 | DRS049947 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr 5day 2 | SAMD00028139 | sample name:Dr 5day 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:5day|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028139 | DRX029548 | Dr 5day 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028139 | 3893708700.0 | 38937087.0 | DRR032742 | 0:100 1:0 | A:1050850168;C:899863467;G:897224776;T:1045729184;N:41105 | 100 | 0 | 1050850168 | 899863467 | 897224776 | 1045729184 | 41105 | DRX029548 | DRS049947 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.91671 | 0.0991 | 0.65161 | 0.47454 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Larval | Larval | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 83 | 83 | DRR032741 | DRX029547 | DRS049946 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr 5day 1 | SAMD00028138 | sample name:Dr 5day 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:5day|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028138 | DRX029547 | Dr 5day 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028138 | 3807570600.0 | 38075706.0 | DRR032741 | 0:100 1:0 | A:1022590228;C:884655401;G:882546091;T:1017737883;N:40997 | 100 | 0 | 1022590228 | 884655401 | 882546091 | 1017737883 | 40997 | DRX029547 | DRS049946 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.9182 | 0.09442 | 0.65525 | 0.46661 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Larval | Larval | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 84 | 84 | DRR032740 | DRX029546 | DRS049945 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr 48h 2 | SAMD00028137 | sample name:Dr 48h 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:48h Long pec|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028137 | DRX029546 | Dr 48h 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028137 | 3702804700.0 | 37028047.0 | DRR032740 | 0:100 1:0 | A:993931475;C:862403562;G:857808891;T:988623734;N:37038 | 100 | 0 | 993931475 | 862403562 | 857808891 | 988623734 | 37038 | DRX029546 | DRS049945 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92508 | 0.08526 | 0.68349 | 0.45769 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Hatching | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 85 | 85 | DRR032739 | DRX029545 | DRS049944 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 50 individuals | Dr 48h 1 | SAMD00028136 | sample name:Dr 48h 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:48h Long pec|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028136 | DRX029545 | Dr 48h 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028136 | 3980240400.0 | 39802404.0 | DRR032739 | 0:100 1:0 | A:1070497788;C:925240883;G:920038728;T:1064422474;N:40527 | 100 | 0 | 1070497788 | 925240883 | 920038728 | 1064422474 | 40527 | DRX029545 | DRS049944 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92349 | 0.08681 | 0.67874 | 0.46565 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Hatching | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 86 | 86 | DRR032738 | DRX029544 | DRS049943 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 100 individuals | Dr 32cell 2 | SAMD00028135 | sample name:Dr 32cell 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:32cell|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028135 | DRX029544 | Dr 32cell 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028135 | 3678713000.0 | 36787130.0 | DRR032738 | 0:100 1:0 | A:981005900;C:863203049;G:859660640;T:974807835;N:35576 | 100 | 0 | 981005900 | 863203049 | 859660640 | 974807835 | 35576 | DRX029544 | DRS049943 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.93302 | 0.02468 | 0.77441 | 0.47485 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Cleavage | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 87 | 87 | DRR032737 | DRX029543 | DRS049942 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 95 individuals | Dr 32cell 1 | SAMD00028134 | sample name:Dr 32cell 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:32cell|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028134 | DRX029543 | Dr 32cell 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028134 | 3870906500.0 | 38709065.0 | DRR032737 | 0:100 1:0 | A:1030407751;C:909948718;G:905608620;T:1024897443;N:43968 | 100 | 0 | 1030407751 | 909948718 | 905608620 | 1024897443 | 43968 | DRX029543 | DRS049942 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.93364 | 0.02484 | 0.77307 | 0.47588 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Cleavage | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 88 | 88 | DRR032736 | DRX029542 | DRS049941 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 100 individuals | Dr zfs:0000015 2 | SAMD00028133 | sample name:Dr zfs:0000015 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:zfs:0000015|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028133 | DRX029542 | Dr zfs:0000015 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028133 | 3129028500.0 | 31290285.0 | DRR032736 | 0:100 1:0 | A:849515903;C:721550282;G:717777586;T:840154982;N:29747 | 100 | 0 | 849515903 | 721550282 | 717777586 | 840154982 | 29747 | DRX029542 | DRS049941 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92724 | 0.07971 | 0.74657 | 0.47796 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Blastula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 89 | 89 | DRR032735 | DRX029541 | DRS049940 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 100 individuals | Dr zfs:0000015 1 | SAMD00028132 | sample name:Dr zfs:0000015 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:zfs:0000015|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028132 | DRX029541 | Dr zfs:0000015 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028132 | 4310219700.0 | 43102197.0 | DRR032735 | 0:100 1:0 | A:1169701983;C:993241399;G:986263558;T:1160969083;N:43677 | 100 | 0 | 1169701983 | 993241399 | 986263558 | 1160969083 | 43677 | DRX029541 | DRS049940 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92609 | 0.07773 | 0.74349 | 0.47849 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Blastula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 90 | 90 | DRR032734 | DRX029540 | DRS049939 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 107 individuals | Dr 2cell 2 | SAMD00028131 | sample name:Dr 2cell 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:2cell|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028131 | DRX029540 | Dr 2cell 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028131 | 3687517000.0 | 36875170.0 | DRR032734 | 0:100 1:0 | A:975272080;C:873518282;G:869743434;T:968941851;N:41353 | 100 | 0 | 975272080 | 873518282 | 869743434 | 968941851 | 41353 | DRX029540 | DRS049939 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.93204 | 0.02088 | 0.81639 | 0.47553 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Cleavage | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 91 | 91 | DRR032733 | DRX029539 | DRS049938 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 108 individuals | Dr 2cell 1 | SAMD00028130 | sample name:Dr 2cell 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:2cell|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028130 | DRX029539 | Dr 2cell 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028130 | 4156651100.0 | 41566511.0 | DRR032733 | 0:100 1:0 | A:1099943617;C:985498415;G:978884426;T:1092278665;N:45977 | 100 | 0 | 1099943617 | 985498415 | 978884426 | 1092278665 | 45977 | DRX029539 | DRS049938 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.93452 | 0.02198 | 0.81197 | 0.47342 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Cleavage | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 92 | 92 | DRR032732 | DRX029538 | DRS049937 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 80 individuals | Dr 14somite 3 | SAMD00028129 | sample name:Dr 14somite 3|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:14somite|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028129 | DRX029538 | Dr 14somite 3 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028129 | 3734610500.0 | 37346105.0 | DRR032732 | 0:100 1:0 | A:1009418541;C:863710067;G:858061383;T:1003378800;N:41709 | 100 | 0 | 1009418541 | 863710067 | 858061383 | 1003378800 | 41709 | DRX029538 | DRS049937 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92401 | 0.08815 | 0.70816 | 0.46602 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Segmentation | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 93 | 93 | DRR032731 | DRX029537 | DRS049936 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 80 individuals | Dr 14somite 2 | SAMD00028128 | sample name:Dr 14somite 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:14somite|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028128 | DRX029537 | Dr 14somite 2 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028128 | 3715174200.0 | 37151742.0 | DRR032731 | 0:100 1:0 | A:1000703508;C:862290629;G:858173468;T:993968396;N:38199 | 100 | 0 | 1000703508 | 862290629 | 858173468 | 993968396 | 38199 | DRX029537 | DRS049936 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92491 | 0.0819 | 0.71068 | 0.46957 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Segmentation | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 94 | 94 | DRR032730 | DRX029536 | DRS049935 | DRP003810 | PRJDB3785 | EXPANDE project | DRP003810 | Other | EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates. | mRNA extracted from pooled embryos of 80 individuals | Dr 14somite 1 | SAMD00028127 | sample name:Dr 14somite 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:14somite|genotype:wild type|phenotype:wild type|sex:male female and mixed | Illumina HiSeq 2000 sequencing of SAMD00028127 | DRX029536 | Dr 14somite 1 | 1 | Total RNA QIAGEN RNeasy followed by TruSeq | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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> | DRP003810 | Illumina HiSeq 2000 sequencing of SAMD00028127 | 3744386000.0 | 37443860.0 | DRR032730 | 0:100 1:0 | A:1014537326;C:864070910;G:859190201;T:1006549502;N:38061 | 100 | 0 | 1014537326 | 864070910 | 859190201 | 1006549502 | 38061 | DRX029536 | DRS049935 | DRA003460 | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo | 1 | 0.92378 | 0.08957 | 0.7068 | 0.47493 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | other | trueseq | bulk | unknown | unknown | Japan | 2017-09-20 | Segmentation | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 95 | 95 | DRR050167 | DRX045209 | DRS025834 | DRP003043 | PRJDB4416 | Transcriptome analysis in ES1 expressing rods of zebrafish | DRP003043 | Transcriptome Analysis | Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used. | Zebrafish rods expressing ES1 and EGFP | ES1 3 | SAMD00044057 | sample name:ES1 EGFP rod 003|strain:Tubingen long fin|cell type:rod | Ion Torrent PGM sequencing of SAMD00044057 | DRX045209 | 1 | 1 | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent PGM | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>105</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> | DRP003043 | Ion Torrent PGM sequencing of SAMD00044057 | 371748120.0 | 3469843.0 | DRR050167 | 0:107.14 | A:107190409;C:79475572;G:83520360;T:101561779;N:0 | 107 | 107190409 | 79475572 | 83520360 | 101561779 | 0 | DRX045209 | DRS025834 | DRA004229 | OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. | Osaka university | 1 | 0.81026 | 0.26715 | 0.86953 | 0.52321 | 51 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2016-03-09 | Undetermined | Undetermined | Fin | Surface Structure | |||||||||||||||||||||||||
| 96 | 96 | DRR050166 | DRX045208 | DRS025833 | DRP003043 | PRJDB4416 | Transcriptome analysis in ES1 expressing rods of zebrafish | DRP003043 | Transcriptome Analysis | Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used. | Zebrafish rods expressing ES1 and EGFP | ES1 2 | SAMD00044056 | sample name:ES1 EGFP rod 002|strain:Tubingen long fin|cell type:rod | Ion Torrent PGM sequencing of SAMD00044056 | DRX045208 | 1 | 1 | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent PGM | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>128</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> | DRP003043 | Ion Torrent PGM sequencing of SAMD00044056 | 425549011.0 | 3275261.0 | DRR050166 | 0:129.93 | A:126640704;C:86415371;G:90822163;T:121670773;N:0 | 129 | 126640704 | 86415371 | 90822163 | 121670773 | 0 | DRX045208 | DRS025833 | DRA004229 | OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. | Osaka university | 1 | 0.80223 | 0.31429 | 0.85861 | 0.5272 | 57 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2016-03-09 | Undetermined | Undetermined | Fin | Surface Structure | |||||||||||||||||||||||||
| 97 | 97 | DRR050165 | DRX045207 | DRS025832 | DRP003043 | PRJDB4416 | Transcriptome analysis in ES1 expressing rods of zebrafish | DRP003043 | Transcriptome Analysis | Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used. | Zebrafish rods expressing ES1 and EGFP | ES1 1 | SAMD00044055 | sample name:ES1 EGFP rod 001|strain:Tubingen long fin|cell type:rod | Ion Torrent PGM sequencing of SAMD00044055 | DRX045207 | 1 | 1 | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent PGM | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>147</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> | DRP003043 | Ion Torrent PGM sequencing of SAMD00044055 | 584599765.0 | 3941083.0 | DRR050165 | 0:148.33 | A:164329030;C:129885620;G:136727379;T:153657736;N:0 | 148 | 164329030 | 129885620 | 136727379 | 153657736 | 0 | DRX045207 | DRS025832 | DRA004229 | OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. | Osaka university | 1 | 0.83769 | 0.25395 | 0.83116 | 0.52784 | 185 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2016-03-09 | Undetermined | Undetermined | Fin | Surface Structure | |||||||||||||||||||||||||
| 98 | 98 | DRR050164 | DRX045206 | DRS025831 | DRP003043 | PRJDB4416 | Transcriptome analysis in ES1 expressing rods of zebrafish | DRP003043 | Transcriptome Analysis | Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used. | Zebrafish rods expressing EGFP | EGFP 3 | SAMD00044054 | sample name:EGFP rod 003|strain:Tubingen long fin|cell type:rod | Ion Torrent PGM sequencing of SAMD00044054 | DRX045206 | 1 | 1 | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent PGM | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>88</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> | DRP003043 | Ion Torrent PGM sequencing of SAMD00044054 | 343014114.0 | 3827762.0 | DRR050164 | 0:89.61 | A:99421434;C:73070267;G:77738821;T:92783592;N:0 | 89 | 99421434 | 73070267 | 77738821 | 92783592 | 0 | DRX045206 | DRS025831 | DRA004229 | OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. | Osaka university | 1 | 0.78953 | 0.25529 | 0.87367 | 0.52148 | 24 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2016-03-09 | Undetermined | Undetermined | Fin | Surface Structure | |||||||||||||||||||||||||
| 99 | 99 | DRR050163 | DRX045205 | DRS025830 | DRP003043 | PRJDB4416 | Transcriptome analysis in ES1 expressing rods of zebrafish | DRP003043 | Transcriptome Analysis | Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used. | Zebrafish rods expressing EGFP | EGFP 2 | SAMD00044053 | sample name:EGFP rod 002|strain:Tubingen long fin|cell type:rod | Ion Torrent PGM sequencing of SAMD00044053 | DRX045205 | 1 | 1 | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent PGM | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>137</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> | DRP003043 | Ion Torrent PGM sequencing of SAMD00044053 | 533069427.0 | 3824140.0 | DRR050163 | 0:139.40 | A:152608173;C:113928273;G:120051739;T:146481242;N:0 | 139 | 152608173 | 113928273 | 120051739 | 146481242 | 0 | DRX045205 | DRS025830 | DRA004229 | OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. | Osaka university | 1 | 0.80412 | 0.26768 | 0.85338 | 0.52255 | 245 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2016-03-09 | Undetermined | Undetermined | Fin | Surface Structure | |||||||||||||||||||||||||
| 100 | 100 | DRR050162 | DRX045204 | DRS025829 | DRP003043 | PRJDB4416 | Transcriptome analysis in ES1 expressing rods of zebrafish | DRP003043 | Transcriptome Analysis | Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used. | Zebrafish rods expressing EGFP | EGFP 1 | SAMD00044052 | sample name:EGFP rod 001|strain:Tubingen long fin|cell type:rod | Ion Torrent PGM sequencing of SAMD00044052 | DRX045204 | 1 | 1 | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent PGM | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>113</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> | DRP003043 | Ion Torrent PGM sequencing of SAMD00044052 | 478262965.0 | 4224064.0 | DRR050162 | 0:113.22 | A:136348264;C:104872341;G:113114502;T:123927858;N:0 | 113 | 136348264 | 104872341 | 113114502 | 123927858 | 0 | DRX045204 | DRS025829 | DRA004229 | OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. | Osaka university | 1 | 0.86947 | 0.29839 | 0.83317 | 0.51453 | 80 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2016-03-09 | Undetermined | Undetermined | Fin | Surface Structure | |||||||||||||||||||||||||
| 101 | 101 | DRR189403 | DRX179868 | DRS200418 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 30 min post test session of 2 weeks memory test in non trace 2 Way Active Avoidance coditioning 3 | SAMD00182246 | sample name:CSUS Tel 30 2w memory 3|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182246 | DRX179868 | CSUS Tel 30 2w memory 3 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182246 | 2791119960.0 | 77531110.0 | DRR189403 | 0:36 | A:685050951;C:641519684;G:664655385;T:799677669;N:216271 | 36 | 685050951 | 641519684 | 664655385 | 799677669 | 216271 | DRX179868 | DRS200418 | DRA008865 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.89653 | 0.1773 | 0.70725 | 0.49873 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 102 | 102 | DRR189402 | DRX179867 | DRS200417 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 30 min post test session of 2 weeks memory test in non trace 2 Way Active Avoidance coditioning 2 | SAMD00182245 | sample name:CSUS Tel 30 2w memory 2|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182245 | DRX179867 | CSUS Tel 30 2w memory 2 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182245 | 1505449224.0 | 41818034.0 | DRR189402 | 0:36 | A:369895057;C:346914787;G:358624651;T:429897489;N:117240 | 36 | 369895057 | 346914787 | 358624651 | 429897489 | 117240 | DRX179867 | DRS200417 | DRA008865 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.89514 | 0.17677 | 0.7025 | 0.49571 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 103 | 103 | DRR189401 | DRX179866 | DRS200416 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 30 min post test session of 2 weeks memory test in non trace 2 Way Active Avoidance coditioning 1 | SAMD00182244 | sample name:CSUS Tel 30 2w memory 1|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182244 | DRX179866 | CSUS Tel 30 2w memory 1 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182244 | 2088507024.0 | 58014084.0 | DRR189401 | 0:36 | A:516255405;C:478036869;G:496415722;T:597637091;N:161937 | 36 | 516255405 | 478036869 | 496415722 | 597637091 | 161937 | DRX179866 | DRS200416 | DRA008865 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.89533 | 0.18553 | 0.70981 | 0.49554 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 104 | 104 | DRR189400 | DRX179865 | DRS200401 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 30 min post test session of 1 day memory test in non trace 2 Way Active Avoidance coditioning 3 | SAMD00182243 | sample name:CSUS Tel 30 1d memory 3|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182243 | DRX179865 | CSUS Tel 30 1d memory 3 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182243 | 1340808120.0 | 37244670.0 | DRR189400 | 0:36 | A:330513975;C:306935584;G:320089399;T:383165274;N:103888 | 36 | 330513975 | 306935584 | 320089399 | 383165274 | 103888 | DRX179865 | DRS200401 | DRA008864 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.89272 | 0.19494 | 0.70335 | 0.49456 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 105 | 105 | DRR189399 | DRX179864 | DRS200400 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 30 min post test session of 1 day memory test in non trace 2 Way Active Avoidance coditioning 2 | SAMD00182242 | sample name:CSUS Tel 30 1d memory 2|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182242 | DRX179864 | CSUS Tel 30 1d memory 2 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182242 | 1279740096.0 | 35548336.0 | DRR189399 | 0:36 | A:314850837;C:294188093;G:304654881;T:365946483;N:99802 | 36 | 314850837 | 294188093 | 304654881 | 365946483 | 99802 | DRX179864 | DRS200400 | DRA008864 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.89485 | 0.18205 | 0.70593 | 0.49333 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 106 | 106 | DRR189398 | DRX179863 | DRS200399 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 30 min post test session of 1 day memory test in non trace 2 Way Active Avoidance coditioning 1 | SAMD00182241 | sample name:CSUS Tel 30 1d memory 1|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182241 | DRX179863 | CSUS Tel 30 1d memory 1 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182241 | 3012353100.0 | 83676475.0 | DRR189398 | 0:36 | A:740795057;C:693120664;G:717419185;T:860784745;N:233449 | 36 | 740795057 | 693120664 | 717419185 | 860784745 | 233449 | DRX179863 | DRS200399 | DRA008864 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.89676 | 0.1791 | 0.70569 | 0.49835 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 107 | 107 | DRR189397 | DRX179862 | DRS200428 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 60 min post exposure to the conditioning tank 3 | SAMD00182240 | sample name:Cont Tel 60 3|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182240 | DRX179862 | Cont Tel 60 3 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182240 | 5590147750.0 | 111802955.0 | DRR189397 | 0:50 | A:1365131560;C:1269631295;G:1366791321;T:1588422020;N:171554 | 50 | 1365131560 | 1269631295 | 1366791321 | 1588422020 | 171554 | DRX179862 | DRS200428 | DRA008863 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.89334 | 0.16354 | 0.7011 | 0.49383 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 108 | 108 | DRR189396 | DRX179861 | DRS200427 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 60 min post exposure to the conditioning tank 2 | SAMD00182239 | sample name:Cont Tel 60 2|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182239 | DRX179861 | Cont Tel 60 2 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182239 | 6429019650.0 | 128580393.0 | DRR189396 | 0:50 | A:1570141412;C:1457539089;G:1572785681;T:1828358007;N:195461 | 50 | 1570141412 | 1457539089 | 1572785681 | 1828358007 | 195461 | DRX179861 | DRS200427 | DRA008863 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.89595 | 0.16204 | 0.70743 | 0.49805 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 109 | 109 | DRR189395 | DRX179860 | DRS200426 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 60 min post exposure to the conditioning tank 1 | SAMD00182238 | sample name:Cont Tel 60 1|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182238 | DRX179860 | Cont Tel 60 1 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182238 | 6644185850.0 | 132883717.0 | DRR189395 | 0:50 | A:1637322491;C:1498943556;G:1616212676;T:1891505597;N:201530 | 50 | 1637322491 | 1498943556 | 1616212676 | 1891505597 | 201530 | DRX179860 | DRS200426 | DRA008863 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.89573 | 0.16421 | 0.7037 | 0.49805 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 110 | 110 | DRR189394 | DRX179859 | DRS200407 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 60 min post light stimulation in the conditioning tank 3 | SAMD00182237 | sample name:CS Tel 60 3|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182237 | DRX179859 | CS Tel 60 3 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182237 | 1387078956.0 | 38529971.0 | DRR189394 | 0:36 | A:333990578;C:315361737;G:337599372;T:400057968;N:69301 | 36 | 333990578 | 315361737 | 337599372 | 400057968 | 69301 | DRX179859 | DRS200407 | DRA008862 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.88133 | 0.18418 | 0.70747 | 0.4971 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 111 | 111 | DRR189393 | DRX179858 | DRS200406 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 60 min post light stimulation in the conditioning tank 2 | SAMD00182236 | sample name:CS Tel 60 2|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182236 | DRX179858 | CS Tel 60 2 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182236 | 537029424.0 | 14917484.0 | DRR189393 | 0:36 | A:127421487;C:122494467;G:132164579;T:154921150;N:27741 | 36 | 127421487 | 122494467 | 132164579 | 154921150 | 27741 | DRX179858 | DRS200406 | DRA008862 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.88264 | 0.17793 | 0.7083 | 0.49123 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 112 | 112 | DRR189392 | DRX179857 | DRS200405 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 60 min post light stimulation in the conditioning tank 1 | SAMD00182235 | sample name:CS Tel 60 1|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182235 | DRX179857 | CS Tel 60 1 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182235 | 3163663656.0 | 87879546.0 | DRR189392 | 0:36 | A:766146692;C:714108562;G:771785405;T:911468887;N:154110 | 36 | 766146692 | 714108562 | 771785405 | 911468887 | 154110 | DRX179857 | DRS200405 | DRA008862 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.88114 | 0.1803 | 0.7052 | 0.4917 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 113 | 113 | DRR189391 | DRX179856 | DRS200404 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 60 min post electrical shock delivery in the conditioning tank 3 | SAMD00182234 | sample name:US Tel 60 3|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182234 | DRX179856 | US Tel 60 3 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182234 | 1535884704.0 | 42663464.0 | DRR189391 | 0:36 | A:367444721;C:350978310;G:375524359;T:441859454;N:77860 | 36 | 367444721 | 350978310 | 375524359 | 441859454 | 77860 | DRX179856 | DRS200404 | DRA008861 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.88103 | 0.1788 | 0.7082 | 0.49462 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 114 | 114 | DRR189390 | DRX179855 | DRS200403 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 60 min post electrical shock delivery in the conditioning tank 2 | SAMD00182233 | sample name:US Tel 60 2|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182233 | DRX179855 | US Tel 60 2 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182233 | 737309916.0 | 20480831.0 | DRR189390 | 0:36 | A:176982713;C:168284406;G:179343270;T:212662841;N:36686 | 36 | 176982713 | 168284406 | 179343270 | 212662841 | 36686 | DRX179855 | DRS200403 | DRA008861 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.87995 | 0.18515 | 0.70816 | 0.49393 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 115 | 115 | DRR189389 | DRX179854 | DRS200402 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 60 min post electrical shock delivery in the conditioning tank 1 | SAMD00182232 | sample name:US Tel 60 1|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182232 | DRX179854 | US Tel 60 1 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182232 | 595837404.0 | 16551039.0 | DRR189389 | 0:36 | A:143956004;C:134783754;G:145443580;T:171624939;N:29127 | 36 | 143956004 | 134783754 | 145443580 | 171624939 | 29127 | DRX179854 | DRS200402 | DRA008861 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.87682 | 0.18328 | 0.70309 | 0.49081 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 116 | 116 | DRR189388 | DRX179853 | DRS200452 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 60 min post light and electrical shock association in non trace 2 Way Active Avoidance coditioning 3 | SAMD00182231 | sample name:CSUS Tel 60 3|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182231 | DRX179853 | CSUS Tel 60 3 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182231 | 608050044.0 | 16890279.0 | DRR189388 | 0:36 | A:145025778;C:137906052;G:149542672;T:175545338;N:30204 | 36 | 145025778 | 137906052 | 149542672 | 175545338 | 30204 | DRX179853 | DRS200452 | DRA008860 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.87983 | 0.18602 | 0.70445 | 0.49195 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 117 | 117 | DRR189387 | DRX179852 | DRS200451 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 60 min post light and electrical shock association in non trace 2 Way Active Avoidance coditioning 2 | SAMD00182230 | sample name:CSUS Tel 60 2|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182230 | DRX179852 | CSUS Tel 60 2 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182230 | 777589452.0 | 21599707.0 | DRR189387 | 0:36 | A:185463269;C:177742981;G:190443063;T:223900096;N:40043 | 36 | 185463269 | 177742981 | 190443063 | 223900096 | 40043 | DRX179852 | DRS200451 | DRA008860 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.88331 | 0.17918 | 0.70516 | 0.48956 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 118 | 118 | DRR189386 | DRX179851 | DRS200450 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of adult zebrafrish 60 min post light and electrical shock association in non trace 2 Way Active Avoidance coditioning 1 | SAMD00182229 | sample name:CSUS Tel 60 1|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182229 | DRX179851 | CSUS Tel 60 1 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182229 | 2738622348.0 | 76072843.0 | DRR189386 | 0:36 | A:662989485;C:622023190;G:663013857;T:790459930;N:135886 | 36 | 662989485 | 622023190 | 663013857 | 790459930 | 135886 | DRX179851 | DRS200450 | DRA008860 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.87743 | 0.19164 | 0.70025 | 0.49073 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 119 | 119 | DRR189385 | DRX179850 | DRS200435 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of EMX3 / adult zebrafish 3 | SAMD00182228 | sample name:Emx3 Adult Tel 3|genotype:Emx3 / |tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182228 | DRX179850 | Emx3 / Adult Tel 3 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182228 | 1323636552.0 | 36767682.0 | DRR189385 | 0:36 | A:309582925;C:310206951;G:325673647;T:378136039;N:36990 | 36 | 309582925 | 310206951 | 325673647 | 378136039 | 36990 | DRX179850 | DRS200435 | DRA008859 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.8932 | 0.19244 | 0.71334 | 0.50591 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 120 | 120 | DRR189384 | DRX179849 | DRS200434 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of EMX3 / adult zebrafish 2 | SAMD00182227 | sample name:Emx3 Adult Tel 2|genotype:Emx3 / |tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182227 | DRX179849 | Emx3 / Adult Tel 2 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182227 | 2994105168.0 | 83169588.0 | DRR189384 | 0:36 | A:709730692;C:691531995;G:727245229;T:865514929;N:82323 | 36 | 709730692 | 691531995 | 727245229 | 865514929 | 82323 | DRX179849 | DRS200434 | DRA008859 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.90382 | 0.1826 | 0.70197 | 0.49719 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 121 | 121 | DRR189383 | DRX179848 | DRS200433 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of EMX3 / adult zebrafish 1 | SAMD00182226 | sample name:Emx3 Adult Tel 1|genotype:Emx3 / |tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182226 | DRX179848 | Emx3 / Adult Tel 1 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182226 | 1151464896.0 | 31985136.0 | DRR189383 | 0:36 | A:272427216;C:266708394;G:280781178;T:331515997;N:32111 | 36 | 272427216 | 266708394 | 280781178 | 331515997 | 32111 | DRX179848 | DRS200433 | DRA008859 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.89942 | 0.17402 | 0.70364 | 0.49438 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 122 | 122 | DRR189382 | DRX179847 | DRS200421 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of wild type adult zebrafish 3 | SAMD00182225 | sample name:WT Adult Tel 3|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182225 | DRX179847 | WT Adult Tel 3 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182225 | 2837488824.0 | 78819134.0 | DRR189382 | 0:36 | A:678395895;C:655098137;G:687520693;T:816395518;N:78581 | 36 | 678395895 | 655098137 | 687520693 | 816395518 | 78581 | DRX179847 | DRS200421 | DRA008858 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.89483 | 0.18623 | 0.70544 | 0.49839 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 123 | 123 | DRR189381 | DRX179846 | DRS200420 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of wild type adult zebrafish 2 | SAMD00182224 | sample name:WT Adult Tel 2|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182224 | DRX179846 | WT Adult Tel 2 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182224 | 1456800264.0 | 40466674.0 | DRR189381 | 0:36 | A:345320431;C:336838149;G:356264798;T:418336552;N:40334 | 36 | 345320431 | 336838149 | 356264798 | 418336552 | 40334 | DRX179846 | DRS200420 | DRA008858 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.89496 | 0.18691 | 0.70802 | 0.49721 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 124 | 124 | DRR189380 | DRX179845 | DRS200419 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Telencephalon of wild type adult zebrafish 1 | SAMD00182223 | sample name:WT Adult Tel 1|genotype:wild type|tissue:brain | Illumina HiSeq 3000 sequencing of SAMD00182223 | DRX179845 | WT Adult Tel 1 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182223 | 2533282452.0 | 70368957.0 | DRR189380 | 0:36 | A:602595083;C:585466052;G:616064286;T:729086926;N:70105 | 36 | 602595083 | 585466052 | 616064286 | 729086926 | 70105 | DRX179845 | DRS200419 | DRA008858 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.89412 | 0.19005 | 0.70816 | 0.49843 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||||||||
| 125 | 125 | DRR189379 | DRX179844 | DRS200410 | DRP003977 | PRJDB4470 | Gene expression analysis of the zebrafish brain | DRP003977 | Other | Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors. | Whole body of EMX3 / larval zebrafish 5dpf 3 | SAMD00182222 | sample name:Emx3 Larva body 3|genotype:Emx3 / |tissue:whole body | Illumina HiSeq 3000 sequencing of SAMD00182222 | DRX179844 | Emx3 / Larva body 3 | 1 | SureSelect Strand Specific RNA Library Prep Kit | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | <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> | DRP003977 | Illumina HiSeq 3000 sequencing of SAMD00182222 | 1759409208.0 | 48872478.0 | DRR189379 | 0:36 | A:401147348;C:424523813;G:426350919;T:507310828;N:76300 | 36 | 401147348 | 424523813 | 426350919 | 507310828 | 76300 | DRX179844 | DRS200410 | DRA008857 | NIG|National Institute of Genetics (Japan) | National Institute of Genetics (Japan) | 1 | 0.90975 | 0.11439 | 0.66076 | 0.47775 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Japan | 2021-08-08 | Larval | Larval | Trunk | Surface Structure |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;