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run_metadata

1,745 rows where tissue_curation_coarse = "Undetermined"

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experiment.library_selection 10

technology 7

experiment.platform 7

experiment.library_strategy 7

devstage_curation_coarse 5

devstage_curation 5

experiment.library_source 3

experiment.library_layout 2

tissue_curation_coarse 1

  • Undetermined · 1,745 ✖

tissue_curation 1

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
41 41 DRR408245 DRX393851 DRS407176 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day GFP positive enteric neurons replicate 3 zebrafish EN replicate 3 SAMD00529465   sample name:zebrafish EN replicate 3|biological replicate:eneteric neurons 3|strain:TgSAGFFLF219B; uas:gfp                 NextSeq 550 paired end sequencing of SAMD00529465 DRX393851 190326ENvsNC N703 5day;EntericNeuron;rep3 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529465       3729799291.0 23985772.0 DRR408245 0:77.75 1:77.75 A:978752781;C:879988139;G:903976580;T:962122970;N:4958821 77 77     978752781 879988139 903976580 962122970 4958821 DRX393851 DRS407176 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Undetermined Undetermined
42 42 DRR408244 DRX393850 DRS407175 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day GFP positive enteric neurons replicate 2 zebrafish EN replicate 2 SAMD00529464   sample name:zebrafish EN replicate 2|biological replicate:eneteric neurons 2|strain:TgSAGFFLF218B; uas:gfp                 NextSeq 550 paired end sequencing of SAMD00529464 DRX393850 190326ENvsNC N702 5day;EntericNeuron;rep2 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529464       3315994810.0 21477755.0 DRR408244 0:77.19 1:77.20 A:873970427;C:778042505;G:798459853;T:859611841;N:5910184 77 77     873970427 778042505 798459853 859611841 5910184 DRX393850 DRS407175 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Undetermined Undetermined
43 43 DRR408243 DRX393849 DRS407174 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day GFP positive enteric neurons replicate 1 zebrafish EN replicate 1 SAMD00529463   sample name:zebrafish EN replicate 1|biological replicate:eneteric neurons 1|strain:TgSAGFFLF217B; uas:gfp                 NextSeq 550 paired end sequencing of SAMD00529463 DRX393849 190326ENvsNC N701 5day;EntericNeuron;rep1 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529463       2999501518.0 19455440.0 DRR408243 0:77.08 1:77.09 A:788053541;C:705895776;G:724185148;T:775760738;N:5606315 77 77     788053541 705895776 724185148 775760738 5606315 DRX393849 DRS407174 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Undetermined Undetermined
312 312 ERR977399 ERX1054382 ERS805483 ERP011343 PRJEB10137 RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48 Other Background: In contrast to mammals the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate not as a result of mutual repression but through the opposite effects of Notch signaling maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal – non diabetic – animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals besides actors of the Notch and Wnt pathways several novel markers such as id2a. Finally we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin expressing cells. Conclusions: We have shown that in the zebrafish embryo nkx6.1+ cells are bona fide multipotent pancreatic progenitors while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse pancreatic…       Ductal cells R3 SAMEA3498334 GIGA-R, University of Liege ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498334|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:3|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:3|strain:Tgnkx6.1:GPF                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 10:18:44:269 3 unspecified 1 nextera XT   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011343 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16 NGS14-B703_nkx2_TCCTGAGC_L003_R1_001.fastq.gz NGS14-B703_nkx2_TCCTGAGC_L003_R2_001.fastq.gz fastq fastq 14253683247.0 70913847.0 ena RUN GIGA R University of Liege 05 08 2015 10:18:44:269 3 0:101 1:100 A:3767730088;C:2759135663;G:2772107550;T:3905748607;N:1048961339 101 100     3767730088 2759135663 2772107550 3905748607 1048961339 ERX1054382 ERS805483 ERA463457 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.74612 0.7459 0.10937 0.11122 0.81704 0.81913 0.54841 0.53764 101 100 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
313 313 ERR977398 ERX1054381 ERS805482 ERP011343 PRJEB10137 RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48 Other Background: In contrast to mammals the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate not as a result of mutual repression but through the opposite effects of Notch signaling maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal – non diabetic – animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals besides actors of the Notch and Wnt pathways several novel markers such as id2a. Finally we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin expressing cells. Conclusions: We have shown that in the zebrafish embryo nkx6.1+ cells are bona fide multipotent pancreatic progenitors while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse pancreatic…       Ductal cells R2 SAMEA3498333 GIGA-R, University of Liege ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498333|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:2|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:2|strain:Tgnkx6.1:GPF                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 10:18:44:269 2 unspecified 1 Truseq nano DNAsample   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011343 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16 NGS14-B424_NKX6-1_3000C_CTTGTA_L005_R2_001.fastq.gz NGS14-B424_NKX6-1_3000C_CTTGTA_L005_R1_001.fastq.gz fastq fastq 17434323262.0 86308531.0 ena RUN GIGA R University of Liege 05 08 2015 10:18:44:269 2 0:101 1:101 A:5014046305;C:3245710338;G:3382410145;T:5701198546;N:90957928 101 101     5014046305 3245710338 3382410145 5701198546 90957928 ERX1054381 ERS805482 ERA463457 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.87938 0.83068 0.30659 0.31351 0.80162 0.8438 0.50285 0.47987 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
314 314 ERR977397 ERX1054380 ERS805481 ERP011343 PRJEB10137 RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48 Other Background: In contrast to mammals the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate not as a result of mutual repression but through the opposite effects of Notch signaling maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal – non diabetic – animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals besides actors of the Notch and Wnt pathways several novel markers such as id2a. Finally we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin expressing cells. Conclusions: We have shown that in the zebrafish embryo nkx6.1+ cells are bona fide multipotent pancreatic progenitors while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse pancreatic…       Ductal cells R1 SAMEA3498332 GIGA-R, University of Liege ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498332|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:1|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:1|strain:Tgnkx6.1:GPF                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 10:18:44:269 1 unspecified 1 Truseq nano DNA sample   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011343 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16 NGS14-B423_NKX6-1_1000C_GCCAAT_L005_R1_001.fastq.gz NGS14-B423_NKX6-1_1000C_GCCAAT_L005_R2_001.fastq.gz fastq fastq 8147922500.0 40336250.0 ena RUN GIGA R University of Liege 05 08 2015 10:18:44:269 1 0:101 1:101 A:2422471356;C:1435392327;G:1491979725;T:2755195660;N:42883432 101 101     2422471356 1435392327 1491979725 2755195660 42883432 ERX1054380 ERS805481 ERA463457 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.85302 0.79849 0.41437 0.41711 0.83871 0.87012 0.48354 0.50046 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
315 315 ERR1675931 ERX1745976 ERS805781 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Acinar cells from adults purified by FACS Acinar cells R2 1 SAMEA3498632 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498632|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:37|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:37                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 06 10 2016 15:53:35:325 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 A028_tefa_acinar_GTCCGC_L006_R1_001.fastq.gz A028_tefa_acinar_GTCCGC_L006_R2_001.fastq.gz fastq fastq 10323596830.0 51106915.0 ena RUN GIGA R University of Liege 06 10 2016 15:53:35:325 1 0:101 1:101 A:2531431314;C:2448656972;G:2434247998;T:2833404838;N:75855708 101 101     2531431314 2448656972 2434247998 2833404838 75855708 ERX1745976 ERS805781 ERA727496 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.86878 0.78451 0.03164 0.02157 0.95077 0.96161 0.52068 0.26664 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
316 316 ERR977594 ERX1054577 ERS805784 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Acinar cells from adults purified by FACS Acinar cells R4 SAMEA3498635 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498635|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:40|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:40                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:490 19 Acinar R4 1 Truseq nano DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 NGS14-B702_Acinar4_GTGAAA_L008_R1_001.fastq.gz NGS14-B702_Acinar4_GTGAAA_L008_R2_001.fastq.gz fastq fastq 16935208936.0 83837668.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:490 19 0:101 1:101 A:4069193994;C:3974803883;G:4029409265;T:4779969672;N:81832122 101 101     4069193994 3974803883 4029409265 4779969672 81832122 ERX1054577 ERS805784 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.93976 0.89939 0.01468 0.01416 0.93801 0.94795 0.50718 0.50041 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
317 317 ERR977593 ERX1054576 ERS805783 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Acinar cells from adults purified by FACS Acinar cells R3 SAMEA3498634 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498634|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:39|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:39                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:490 18 Acinar R3 1 Truseq nano DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 NGS14-B701_Acinar3_ACAGTG_L008_R1_001.fastq.gz NGS14-B701_Acinar3_ACAGTG_L008_R2_001.fastq.gz fastq fastq 15710260534.0 77773567.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:490 18 0:101 1:101 A:3788172647;C:3700546898;G:3749520213;T:4395516227;N:76504549 101 101     3788172647 3700546898 3749520213 4395516227 76504549 ERX1054576 ERS805783 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.95517 0.92587 0.0153 0.01529 0.91504 0.92553 0.49096 0.48449 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
318 318 ERR977592 ERX1054575 ERS805782 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Acinar cells from adults purified by FACS Acinar cells R2 2 SAMEA3498633 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498633|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:38|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:38                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:490 17 Acinar R2 2 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 Acinar_A028_GTCCGC_L003_R1_001.fastq.gz Acinar_A028_GTCCGC_L003_R2_001.fastq.gz fastq fastq 3461595220.0 17136610.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:490 17 0:101 1:101 A:847745846;C:824702298;G:830498571;T:958264119;N:384386 101 101     847745846 824702298 830498571 958264119 384386 ERX1054575 ERS805782 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.86246 0.7781 0.03038 0.02178 0.95357 0.96327 0.56719 0.35588 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
319 319 ERR977591 ERX1054574 ERS805780 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Acinar cells from adults purified by FACS Acinar cells R1 2 SAMEA3498631 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498631|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:36|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:36                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:490 16 Acinar R1 2 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 Exocrine_GTGAAA_L005_R1_001.fastq.gz Exocrine_GTGAAA_L005_R2_001.fastq.gz fastq fastq 9528535334.0 47170967.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:490 16 0:101 1:101 A:2522050794;C:2076658898;G:2097686086;T:2672752253;N:159387303 101 101     2522050794 2076658898 2097686086 2672752253 159387303 ERX1054574 ERS805780 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.48352 0.37495 0.01258 0.01002 0.94194 0.95345 0.51746 0.51938 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
320 320 ERR977590 ERX1054573 ERS805779 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Acinar cells from adults purified by FACS Acinar cells R1 1 SAMEA3498630 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498630|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:35|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:35                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:489 15 Acinar R1 1 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 Exocrine_30000_GTGAAA_L008_R1_001.fastq.gz Exocrine_30000_GTGAAA_L008_R2_001.fastq.gz fastq fastq 2352127188.0 11644194.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:489 15 0:101 1:101 A:575791638;C:562486325;G:570096367;T:643677230;N:75628 101 101     575791638 562486325 570096367 643677230 75628 ERX1054573 ERS805779 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.96358 0.92791 0.02614 0.02577 0.91534 0.92786 0.51791 0.51855 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
322 322 ERR977588 ERX1054571 ERS805777 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Delta cells from adults purified by FACS Delta cells R2 SAMEA3498628 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498628|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:33|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:33                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:489 13 Delta R2 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 STS2_cDNA_A085_CAGATC_L003_R1_001.fastq.gz STS2_cDNA_A085_CAGATC_L003_R2_001.fastq.gz fastq fastq 9070241774.0 44902187.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:489 13 0:101 1:101 A:2535637917;C:1854694115;G:1908489704;T:2770396981;N:1023057 101 101     2535637917 1854694115 1908489704 2770396981 1023057 ERX1054571 ERS805777 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.94245 0.86716 0.11229 0.13234 0.76114 0.78171 0.38511 0.43811 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
323 323 ERR977587 ERX1054570 ERS805776 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Delta cells from adults purified by FACS Delta cells R1 2 SAMEA3498627 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498627|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:32|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:32                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:489 12 Delta R1 2 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 SST1_A027_CCGTCC_L004_R1_001.fastq.gz SST1_A027_CCGTCC_L004_R2_001.fastq.gz fastq fastq 7937290636.0 39293518.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:489 12 0:101 1:101 A:2179525147;C:1634082904;G:1676353742;T:2446333583;N:995260 101 101     2179525147 1634082904 1676353742 2446333583 995260 ERX1054570 ERS805776 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.81928 0.64028 0.09426 0.0961 0.80626 0.83763 0.33992 0.39097 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
324 324 ERR977586 ERX1054569 ERS805775 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Delta cells from adults purified by FACS Delta cells R1 1 SAMEA3498626 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498626|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:31|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:31                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:488 11 Delta R1 1 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 SST_CCGTCC_L005_R1_001.fastq.gz SST_CCGTCC_L005_R2_001.fastq.gz fastq fastq 2808424382.0 13903091.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:489 11 0:101 1:101 A:745970072;C:575317830;G:590596279;T:849527061;N:47013140 101 101     745970072 575317830 590596279 849527061 47013140 ERX1054569 ERS805775 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.80308 0.60403 0.09111 0.08841 0.80582 0.84035 0.34177 0.38788 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
325 325 ERR977585 ERX1054568 ERS805774 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Alpha cells from adults purified by FACS Alpha cells R3 SAMEA3498625 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498625|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:30|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:30                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:488 10 Alpha R3 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 NGS14-B175_AlphaCells-12122013_CTTGTA_L002_R1_001.fastq.gz NGS14-B175_AlphaCells-12122013_CTTGTA_L002_R2_001.fastq.gz fastq fastq 18205394430.0 90125715.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:488 10 0:101 1:101 A:5028541426;C:3813667922;G:3871329588;T:5386457109;N:105398385 101 101     5028541426 3813667922 3871329588 5386457109 105398385 ERX1054568 ERS805774 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.84473 0.83714 0.12924 0.13497 0.76581 0.77928 0.43397 0.42534 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
326 326 ERR977584 ERX1054567 ERS805773 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Alpha cells from adults purified by FACS Alpha cells R2 2 SAMEA3498624 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498624|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:29|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:29                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:488 9 Alpha R2 2 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 A084_Alpha2cDNA_GCCAAT_L006_R1_001.fastq.gz A084_Alpha2cDNA_GCCAAT_L006_R2_001.fastq.gz fastq fastq 8621351314.0 42679957.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:488 9 0:101 1:101 A:2420008540;C:1748459249;G:1778002039;T:2610255006;N:64626480 101 101     2420008540 1748459249 1778002039 2610255006 64626480 ERX1054567 ERS805773 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.8123 0.7894 0.13948 0.14682 0.76609 0.78624 0.43594 0.4281 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
327 327 ERR977583 ERX1054566 ERS805772 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Alpha cells from adults purified by FACS Alpha cells R2 1 SAMEA3498623 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498623|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:28|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:28                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:488 8 Alpha R2 1 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 Alpha_2_cDNA_A084_GCCAAT_L003_R1_001.fastq.gz Alpha_2_cDNA_A084_GCCAAT_L003_R2_001.fastq.gz fastq fastq 7447261462.0 36867631.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:488 8 0:101 1:101 A:2085646680;C:1521470549;G:1568678066;T:2270630726;N:835441 101 101     2085646680 1521470549 1568678066 2270630726 835441 ERX1054566 ERS805772 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.81689 0.79405 0.13796 0.14503 0.76583 0.78535 0.40729 0.42815 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
328 328 ERR977582 ERX1054565 ERS805771 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Alpha cells from adults purified by FACS Alpha cells R1 2 SAMEA3498622 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498622|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:27|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:27                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:488 7 Alpha R1 2 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 A083_Alpha1cDNA_ACAGTG_L006_R1_001.fastq.gz A083_Alpha1cDNA_ACAGTG_L006_R2_001.fastq.gz fastq fastq 8598483904.0 42566752.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:488 7 0:101 1:101 A:2424152802;C:1756999772;G:1780718036;T:2571949581;N:64663713 101 101     2424152802 1756999772 1780718036 2571949581 64663713 ERX1054565 ERS805771 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.80654 0.78693 0.13676 0.14263 0.76475 0.78173 0.4476 0.44884 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
329 329 ERR977581 ERX1054564 ERS805770 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Alpha cells from adults purified by FACS Alpha cells R1 1 SAMEA3498621 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498621|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:26|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:26|strain:Tggcga:GFP; Tgins:NTR mCherry                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:487 6 Alpha R1 1 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 Alpha1_cDNA_A083_ACAGTG_L003_R2_001.fastq.gz Alpha1_cDNA_A083_ACAGTG_L003_R1_001.fastq.gz fastq fastq 7584054852.0 37544826.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:487 6 0:101 1:101 A:2134120600;C:1561394450;G:1604139016;T:2283553056;N:847730 101 101     2134120600 1561394450 1604139016 2283553056 847730 ERX1054564 ERS805770 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.8102 0.79183 0.13509 0.1414 0.76459 0.77958 0.44897 0.42232 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
9918 9918 ERR5059480 ERX4865549 ERS5523939 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05     aAM 6h rep1 JD AD30 PRPN1970901   ENA FIRST PUBLIC:2022 07 05T12:06:33Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:33Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AD30_PRPN197090.tar.gz nanopore 3739882337.0 3148027.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 0:1188.01 A:1054501690;C:834193435;G:847423060;T:1003764152;N:0 1188       1054501690 834193435 847423060 1003764152 0 ERX4865549 ERS5523939 ERA3206712 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       B   usable mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9920 9920 ERR4330695 ERX4277529 ERS4811113 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 2h rep1 WT 2h rep1 SAMEA7050483 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7050483|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD B2 PDBN005727|common name:zebrafish|sample name:JD B2 PDBN005727                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-B2_PDBN005727.tar.gz fastq     ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1                       ERX4277529   ERA2767154 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9921 9921 ERR4327134 ERX4273968 ERS4808634 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 4h rep2 WT 4h rep2 SAMEA7048000 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7048000|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD AM39 PDBN042841|common name:zebrafish|sample name:JD AM39 PDBN042841                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AM39_PDBN042841.tar.gz nanopore 719646261.0 897768.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 0:801.59 A:210217908;C:152963718;G:157393834;T:199070801;N:0 801       210217908 152963718 157393834 199070801 0 ERX4273968 ERS4808634 ERA2764800 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9922 9922 ERR4330696 ERX4277530 ERS4811114 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 4h rep1 WT 4h rep1 JD C3 PDBN006177   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-C3_PDBN006177.tar.gz nanopore 4240799932.0 4331689.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 0:979.02 A:1229803846;C:914476674;G:943703560;T:1152815852;N:0 979       1229803846 914476674 943703560 1152815852 0 ERX4277530 ERS4811114 ERA2767154 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       B   usable mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9923 9923 ERR4327135 ERX4273969 ERS4808635 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 6h rep1 WT 6h rep1 JD AC29 PDBN024889   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AC29_PDBN024889.tar.gz nanopore 1900324756.0 2013035.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 0:944.01 A:549431032;C:411510218;G:422103800;T:517279706;N:0 944       549431032 411510218 422103800 517279706 0 ERX4273969 ERS4808635 ERA2764800 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   long read ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9924 9924 ERR4326350 ERX4273208 ERS4808398 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   430 LNA 6h rep1 430 LNA 6h rep1 SAMEA7047764 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7047764|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD H8 PDBN059569|common name:zebrafish|sample name:JD H8 PDBN059569                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-H8_PDBN059569.tar.gz nanopore 722817654.0 657296.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 0:1099.68 A:206996491;C:157022109;G:155085437;T:203713617;N:0 1099       206996491 157022109 155085437 203713617 0 ERX4273208 ERS4808398 ERA2764399 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9925 9925 ERR4335436 ERX4282181 ERS4818366 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 6h rep2 WT 6h rep2 JD W23 PRPN039928   ENA FIRST PUBLIC:2022 07 05T12:06:24Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:24Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:456 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-W23_PRPN039928.tar.gz nanopore 1268761319.0 1385621.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:457 1 0:915.66 A:366823862;C:275507684;G:284634548;T:341795225;N:0 915       366823862 275507684 284634548 341795225 0 ERX4282181 ERS4818366 ERA2769006 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9926 9926 ERR4321680 ERX4268538 ERS4808125 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 0h rep1 WT 0h rep1 JD A1 GDDN003032   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 GridION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE GridION   ERP122761 GridION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-A1_GDDN003032.tar.gz nanopore 753417826.0 698774.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 0:1078.20 A:214525685;C:165042952;G:171160615;T:202688574;N:0 1078       214525685 165042952 171160615 202688574 0 ERX4268538 ERS4808125 ERA2763718 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   long read ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9951 9951 ERR5961093 ERX5601614 ERS6490233 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae uninjected controls from the same batch. Uninjected2 Uninjected2   ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 8 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14         ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 8                       ERX5601614   ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                             illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9952 9952 ERR5961092 ERX5601613 ERS6490232 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae uninjected controls from the same batch. Uninjected1 SAMEA8805898 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 06 23|ENA last update:2021 06 23|External Id:SAMEA8805898|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 06 23T08:18:31Z|INSDC last update:2021 06 23T08:18:31Z|INSDC status:public|Submitter Id:Uninjected1|common name:zebrafish|sample name:Uninjected1                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 7 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 06 23|ENA LAST UPDATE:2021 06 23 WT1_R1_001.fastq WT1_R2_001.fastq fastq fastq 5664550800.0 18881836.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 7 0:150 1:150 A:1493322675;C:1337347146;G:1388414458;T:1444981758;N:484763 150 150     1493322675 1337347146 1388414458 1444981758 484763 ERX5601613 ERS6490232 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95769 0.95822 0.04407 0.04391 0.69934 0.69958 0.4411 0.45319 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9953 9953 ERR5961096 ERX5601617 ERS6490236 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae uninjected controls from the an additional batch. Uninjected5 SAMEA8805902 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805902|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected5|common name:zebrafish|sample name:Uninjected5                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 11 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 WT5_R1_001.fastq.gz WT5_R2_001.fastq.gz fastq fastq 9088444200.0 30294814.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 11 0:150 1:150 A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622 150 150     2404715160 2098546919 2330441921 2254532578 207622 ERX5601617 ERS6490236 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95076 0.93857 0.06296 0.06222 0.68485 0.70047 0.47429 0.48524 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9954 9954 ERR5961095 ERX5601616 ERS6490235 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae uninjected controls from the an additional batch. Uninjected4 SAMEA8805901 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805901|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected4|common name:zebrafish|sample name:Uninjected4                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 10 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 WT4_R1_001.fastq.gz WT4_R2_001.fastq.gz fastq fastq 9222083700.0 30740279.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 10 0:150 1:150 A:2328864269;C:2117919914;G:2560286870;T:2214801519;N:211128 150 150     2328864269 2117919914 2560286870 2214801519 211128 ERX5601616 ERS6490235 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95124 0.92695 0.05122 0.05036 0.69118 0.70634 0.47769 0.47806 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9955 9955 ERR5961094 ERX5601615 ERS6490234 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae uninjected controls from the an additional batch. Uninjected3 SAMEA8805900 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805900|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected3|common name:zebrafish|sample name:Uninjected3                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 9 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 WT3_R1_001.fastq.gz WT3_R2_001.fastq.gz fastq fastq 9088444200.0 30294814.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 9 0:150 1:150 A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622 150 150     2404715160 2098546919 2330441921 2254532578 207622 ERX5601615 ERS6490234 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95071 0.93855 0.06295 0.06183 0.68511 0.70065 0.47621 0.48573 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9956 9956 ERR5961091 ERX5601612 ERS6490231 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage. Cas9enzyme3 SAMEA8805897 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805897|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme3|common name:zebrafish|sample name:Cas9enzyme3                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 6 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 RNA3_R1_001.fastq RNA3_R2_001.fastq fastq fastq 5814764400.0 19382548.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 6 0:150 1:150 A:1550014255;C:1359566801;G:1419514658;T:1485169819;N:498867 150 150     1550014255 1359566801 1419514658 1485169819 498867 ERX5601612 ERS6490231 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.96166 0.96182 0.04962 0.04954 0.68172 0.68144 0.45683 0.46611 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9957 9957 ERR5961090 ERX5601611 ERS6490230 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage. Cas9enzyme2 SAMEA8805896 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805896|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme2|common name:zebrafish|sample name:Cas9enzyme2                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 5 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 RNA2_R1_001.fastq RNA2_R2_001.fastq fastq fastq 5927606100.0 19758687.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 5 0:150 1:150 A:1579767222;C:1387675810;G:1439122138;T:1520529396;N:511534 150 150     1579767222 1387675810 1439122138 1520529396 511534 ERX5601611 ERS6490230 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.96217 0.96214 0.05174 0.05176 0.67083 0.6716 0.46772 0.47128 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9958 9958 ERR5961089 ERX5601610 ERS6490229 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage. Cas9enzyme1 SAMEA8805895 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805895|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme1|common name:zebrafish|sample name:Cas9enzyme1                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 RNA1_R1_001.fastq RNA1_R2_001.fastq fastq fastq 5738133000.0 19127110.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 4 0:150 1:150 A:1530616107;C:1342298453;G:1401357126;T:1463360623;N:500691 150 150     1530616107 1342298453 1401357126 1463360623 500691 ERX5601610 ERS6490229 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95709 0.9569 0.05132 0.05149 0.68771 0.68846 0.45988 0.47329 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9959 9959 ERR5961088 ERX5601609 ERS6490228 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage. Cas9mRNA3 SAMEA8805894 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805894|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA3|common name:zebrafish|sample name:Cas9mRNA3                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 PRO3_R1_001.fastq PRO3_R2_001.fastq fastq fastq 9635841900.0 32119473.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 3 0:150 1:150 A:2562857735;C:2253487693;G:2325345541;T:2493627020;N:523911 150 150     2562857735 2253487693 2325345541 2493627020 523911 ERX5601609 ERS6490228 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95769 0.95696 0.05441 0.05397 0.67424 0.67407 0.46338 0.46444 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9960 9960 ERR5961087 ERX5601608 ERS6490227 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage. Cas9mRNA2 SAMEA8805893 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805893|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA2|common name:zebrafish|sample name:Cas9mRNA2                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 10 21 PRO2_R1_001.fastq PRO2_R2_001.fastq fastq fastq 8990649900.0 29968833.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 2 0:150 1:150 A:2370044440;C:2140400380;G:2185347925;T:2294361536;N:495619 150 150     2370044440 2140400380 2185347925 2294361536 495619 ERX5601608 ERS6490227 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95444 0.95397 0.05839 0.05842 0.67377 0.67207 0.48505 0.48043 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9961 9961 ERR5961086 ERX5601607 ERS6490226 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage. Cas9mRNA1 SAMEA8805892 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805892|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA1|common name:zebrafish|sample name:Cas9mRNA1                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 PRO1_R1_001.fastq PRO1_R2_001.fastq fastq fastq 8803789500.0 29345965.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 1 0:150 1:150 A:2318913314;C:2090675347;G:2149054140;T:2244296747;N:849952 150 150     2318913314 2090675347 2149054140 2244296747 849952 ERX5601607 ERS6490226 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.954 0.9549 0.04652 0.04639 0.70806 0.71386 0.45393 0.44921 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9962 9962 ERR4902960 ERX4769932 ERS5427208 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNAseq data from 5dpf NHGRI 1 zebrafish larvae uninjected. CRISPR RNAseq SAMEA7670216 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670216|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:12Z|INSDC status:public|Submitter Id:CRISPR RNAseq8|common name:zebrafish|sample name:CRISPR RNAseq8                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 8 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   ERP123184 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 WT2_R1_001.fastq.gz WT2_R2_001.fastq.gz fastq fastq 7020700500.0 23402335.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 8 0:150 1:150 A:1879937256;C:1626166066;G:1693802223;T:1820178560;N:616395 150 150     1879937256 1626166066 1693802223 1820178560 616395 ERX4769932 ERS5427208 ERA3183786 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.92352 0.92388 0.04778 0.04768 0.6924 0.69205 0.45557 0.45865 150 150 B B biological fallback assumption illumina miseq unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9963 9963 ERR4902959 ERX4769931 ERS5427206 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNAseq data from 5dpf NHGRI 1 zebrafish larvae uninjected. CRISPR RNAseq SAMEA7670214 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670214|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq7|common name:zebrafish|sample name:CRISPR RNAseq7                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 7 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   ERP123184 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 WT1_R1_001.fastq.gz WT1_R2_001.fastq.gz fastq fastq 5664550800.0 18881836.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 7 0:150 1:150 A:1493322675;C:1337347146;G:1388414458;T:1444981758;N:484763 150 150     1493322675 1337347146 1388414458 1444981758 484763 ERX4769931 ERS5427206 ERA3183786 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95767 0.95821 0.04411 0.04384 0.69944 0.69944 0.44168 0.45263 150 150 B B biological fallback assumption illumina miseq unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9964 9964 ERR4902958 ERX4769930 ERS5427204 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA. CRISPR RNAseq SAMEA7670212 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670212|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq6|common name:zebrafish|sample name:CRISPR RNAseq6                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 6 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   ERP123184 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 RNA3_R1_001.fastq.gz RNA3_R2_001.fastq.gz fastq fastq 5814764400.0 19382548.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 6 0:150 1:150 A:1550014255;C:1359566801;G:1419514658;T:1485169819;N:498867 150 150     1550014255 1359566801 1419514658 1485169819 498867 ERX4769930 ERS5427204 ERA3183786 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.96165 0.96177 0.04961 0.04952 0.68183 0.68142 0.45636 0.46565 150 150 B B biological fallback assumption illumina miseq unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9965 9965 ERR4902957 ERX4769929 ERS5427203 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA. CRISPR RNAseq SAMEA7670211 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670211|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq5|common name:zebrafish|sample name:CRISPR RNAseq5                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 5 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   ERP123184 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 RNA2_R1_001.fastq.gz RNA2_R2_001.fastq.gz fastq fastq 5927606100.0 19758687.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 5 0:150 1:150 A:1579767222;C:1387675810;G:1439122138;T:1520529396;N:511534 150 150     1579767222 1387675810 1439122138 1520529396 511534 ERX4769929 ERS5427203 ERA3183786 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.96212 0.96213 0.0519 0.05167 0.67099 0.6715 0.46875 0.47089 150 150 B B biological fallback assumption illumina miseq unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9966 9966 ERR4902956 ERX4769928 ERS5427201 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA. CRISPR RNAseq SAMEA7670209 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670209|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq4|common name:zebrafish|sample name:CRISPR RNAseq4                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   ERP123184 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 RNA1_R1_001.fastq.gz RNA1_R2_001.fastq.gz fastq fastq 5738133000.0 19127110.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 4 0:150 1:150 A:1530616107;C:1342298453;G:1401357126;T:1463360623;N:500691 150 150     1530616107 1342298453 1401357126 1463360623 500691 ERX4769928 ERS5427201 ERA3183786 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95706 0.9569 0.05122 0.05151 0.68757 0.68822 0.46039 0.4732 150 150 B B biological fallback assumption illumina miseq unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9967 9967 ERR4902955 ERX4769927 ERS5427199 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme. CRISPR RNAseq SAMEA7670207 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670207|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq3|common name:zebrafish|sample name:CRISPR RNAseq3                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   ERP123184 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 PRO3_R1_001.fastq.gz PRO3_R2_001.fastq.gz fastq fastq 9635841900.0 32119473.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 3 0:150 1:150 A:2562857735;C:2253487693;G:2325345541;T:2493627020;N:523911 150 150     2562857735 2253487693 2325345541 2493627020 523911 ERX4769927 ERS5427199 ERA3183786 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95766 0.95695 0.05445 0.05404 0.67432 0.67403 0.46385 0.46442 150 150 B B biological fallback assumption illumina miseq unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9968 9968 ERR4902954 ERX4769926 ERS5427197 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme. CRISPR RNAseq SAMEA7670205 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670205|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq2|common name:zebrafish|sample name:CRISPR RNAseq2                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:138 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   ERP123184 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 PRO2_R1_001.fastq.gz PRO2_R2_001.fastq.gz fastq fastq 8990649900.0 29968833.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:138 2 0:150 1:150 A:2370044440;C:2140400380;G:2185347925;T:2294361536;N:495619 150 150     2370044440 2140400380 2185347925 2294361536 495619 ERX4769926 ERS5427197 ERA3183786 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95444 0.95393 0.05848 0.05894 0.67438 0.67255 0.4825 0.48028 150 150 B B biological fallback assumption illumina miseq unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9969 9969 ERR4902953 ERX4769925 ERS5427195 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme. CRISPR RNAseq SAMEA7670203 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670203|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq1|common name:zebrafish|sample name:CRISPR RNAseq1                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:138 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   ERP123184 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 PRO1_R1_001.fastq.gz PRO1_R2_001.fastq.gz fastq fastq 8803789500.0 29345965.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:138 1 0:150 1:150 A:2318913314;C:2090675347;G:2149054140;T:2244296747;N:849952 150 150     2318913314 2090675347 2149054140 2244296747 849952 ERX4769925 ERS5427195 ERA3183786 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95403 0.95489 0.04655 0.0464 0.70816 0.71403 0.45357 0.44874 150 150 B B biological fallback assumption illumina miseq unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
10383 10383 ERR8517249 ERX8083723 ERS10517669 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Modifier control hnRNPK 003 SAMEA12918519 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918519|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:hnRNPK 003|common name:zebrafish|sample name:hnRNPK 003                 NextSeq 500 paired end sequencing; Raw reads: hnRNPK 003 webin reads hnRNPK 003   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: hnRNPK 003 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 hnRNPK_003_R1.fastq.gz hnRNPK_003_R2.fastq.gz fastq fastq 2931486932.0 19421721.0 webin reads hnRNPK 003 0:75.51 1:75.43 A:759548162;C:700272829;G:700149526;T:770783019;N:733396 75 75     759548162 700272829 700149526 770783019 733396 ERX8083723 ERS10517669 ERA8937191 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.9621 0.96378 0.06994 0.06876 0.68757 0.68998 0.46746 0.47041 76 75 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10384 10384 ERR8517226 ERX8083700 ERS10517665 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Modifier control hnRNPK 001 SAMEA12918515 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918515|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:hnRNPK 001|common name:zebrafish|sample name:hnRNPK 001                 NextSeq 500 paired end sequencing; Raw reads: hnRNPK 001 webin reads hnRNPK 001   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: hnRNPK 001 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 hnRNPK_001_R1.fastq.gz hnRNPK_001_R2.fastq.gz fastq fastq 2728299749.0 18074835.0 webin reads hnRNPK 001 0:75.51 1:75.43 A:710869412;C:649804308;G:644363972;T:722599378;N:662679 75 75     710869412 649804308 644363972 722599378 662679 ERX8083700 ERS10517665 ERA8936710 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96092 0.96336 0.07296 0.07144 0.68862 0.69209 0.47036 0.47104 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10385 10385 ERR8517194 ERX8083668 ERS10517668 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 RNA control GFP 003 SAMEA12918518 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918518|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:GFP 003|common name:zebrafish|sample name:GFP 003                 NextSeq 500 paired end sequencing; Raw reads: GFP 003 webin reads GFP 003   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: GFP 003 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 GFP_003_R1.fastq.gz GFP_003_R2.fastq.gz fastq fastq 2845571506.0 18850866.0 webin reads GFP 003 0:75.52 1:75.43 A:737412560;C:678774596;G:684567775;T:744108157;N:708418 75 75     737412560 678774596 684567775 744108157 708418 ERX8083668 ERS10517668 ERA8936242 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96279 0.96355 0.06774 0.06607 0.68864 0.69183 0.469 0.46906 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10386 10386 ERR8517159 ERX8083633 ERS10517664 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 RNA control GFP 001 SAMEA12918514 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918514|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:GFP 001|common name:zebrafish|sample name:GFP 001                 NextSeq 500 paired end sequencing; Raw reads: GFP 001 webin reads GFP 001   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: GFP 001 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 GFP_001_R1.fastq.gz GFP_001_R2.fastq.gz fastq fastq 2873485447.0 19035162.0 webin reads GFP 001 0:75.52 1:75.44 A:746120172;C:687054955;G:682142981;T:757435799;N:731540 75 75     746120172 687054955 682142981 757435799 731540 ERX8083633 ERS10517664 ERA8935703 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96176 0.96461 0.07014 0.06932 0.68672 0.68913 0.47006 0.46794 75 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10387 10387 ERR8517115 ERX8083589 ERS10517671 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Modifier rescue 91S hnRNPK 003 SAMEA12918521 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918521|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S hnRNPK 003|common name:zebrafish|sample name:91S hnRNPK 003                 NextSeq 500 paired end sequencing; Raw reads: 91S hnRNPK 003 webin reads 91S hnRNPK 003   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: 91S hnRNPK 003 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 91S_hnRNPK_003_R1.fastq.gz 91S_hnRNPK_003_R2.fastq.gz fastq fastq 2853403405.0 18902398.0 webin reads 91S hnRNPK 003 0:75.52 1:75.44 A:739541111;C:681340573;G:681790014;T:750013318;N:718389 75 75     739541111 681340573 681790014 750013318 718389 ERX8083589 ERS10517671 ERA8935191 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96234 0.96429 0.0679 0.06627 0.68984 0.69126 0.46434 0.47087 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10388 10388 ERR8517082 ERX8083556 ERS10517667 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Modifier rescue 91S hnRNPK 001 SAMEA12918517 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918517|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S hnRNPK 001|common name:zebrafish|sample name:91S hnRNPK 001                 NextSeq 500 paired end sequencing; Raw reads: 91S hnRNPK 001 webin reads 91S hnRNPK 001   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: 91S hnRNPK 001 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 91S_hnRNPK_001_R1.fastq.gz 91S_hnRNPK_001_R2.fastq.gz fastq fastq 2795603091.0 18519699.0 webin reads 91S hnRNPK 001 0:75.52 1:75.43 A:722724564;C:672552332;G:664566386;T:735058575;N:701234 75 75     722724564 672552332 664566386 735058575 701234 ERX8083556 ERS10517667 ERA8934579 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96307 0.96547 0.06551 0.06458 0.68714 0.68856 0.46817 0.46555 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10389 10389 ERR8517039 ERX8083513 ERS10517670 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Toxic condition 91S GFP 003 SAMEA12918520 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918520|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S GFP 003|common name:zebrafish|sample name:91S GFP 003                 NextSeq 500 paired end sequencing; Raw reads: 91S GFP 003 webin reads 91S GFP 003   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: 91S GFP 003 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 91S_GFP_003_R1.fastq.gz 91S_GFP_003_R2.fastq.gz fastq fastq 2946600193.0 19521826.0 webin reads 91S GFP 003 0:75.51 1:75.43 A:763284580;C:704439363;G:702989767;T:775149110;N:737373 75 75     763284580 704439363 702989767 775149110 737373 ERX8083513 ERS10517670 ERA8933888 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96151 0.96295 0.06621 0.06481 0.68807 0.69092 0.46928 0.46982 75 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
10390 10390 ERR8516998 ERX8083472 ERS10517666 ERP135370 PRJEB50765 HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS 69e2093b-755e-4be3-88b8-5b4a761258fe Other A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA which is dependent on its subcellular localization and on RNA recognition and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue we discovered an increased nuclear translocation but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2 a downstream target of HNRNPK involved in DNA damage response. Finally we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response opening novel therapeutic strategies for C9 ALS/FTD. ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 PUBMED:29302778;PUBMED:35895140 Toxic condition 91S GFP 001 SAMEA12918516 vib-ku leuven ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918516|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S GFP 001|common name:zebrafish|sample name:91S GFP 001                 NextSeq 500 paired end sequencing; Raw reads: 91S GFP 001 webin reads 91S GFP 001   unspecified     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP135370 Raw reads: 91S GFP 001 ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22 91S_GFP_001_R1.fastq.gz 91S_GFP_001_R2.fastq.gz fastq fastq 2821113913.0 18686946.0 webin reads 91S GFP 001 0:75.52 1:75.44 A:726676187;C:676899384;G:676400816;T:740427303;N:710223 75 75     726676187 676899384 676400816 740427303 710223 ERX8083472 ERS10517666 ERA8933211 vib-ku leuven|European Nucleotide Archive vib-ku leuven 2 0.96147 0.96465 0.07106 0.06991 0.68822 0.69556 0.47261 0.47451 75 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Belgium 2022-08-22 Undetermined Undetermined Undetermined Undetermined
15504 15504 ERR757154 ERX701784 ERS659467 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Normalization across length SAMEA3251321 UNIVERSITY OF AMSTERDAM ENA first public:2015 02 12|ENA last update:2015 02 12|External Id:SAMEA3251321|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2015 02 12T17:06:49Z|INSDC last update:2015 02 12T09:52:20Z|INSDC status:public|Submitter Id:Female X|common name:zebrafish|dev stage:Adult|sample name:Female X|sex:female                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 2 RID0035 1     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2015 02 12|ENA LAST UPDATE:2018 11 16 RID0035_003.fastq.gz fastq 275591336.0 7611054.0 ena RUN UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 2 0:36.21 A:72212971;C:63331647;G:68054270;T:71992448;N:0 36       72212971 63331647 68054270 71992448 0 ERX701784 ERS659467 ERA410345 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.76262   0.4273   0.8101   0.56676   8   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2015-02-12 Adult Adult Undetermined Undetermined
15505 15505 ERR757153 ERX701783 ERS659466 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Normalization across length SAMEA3251320 UNIVERSITY OF AMSTERDAM ENA first public:2015 02 12|ENA last update:2015 02 12|External Id:SAMEA3251320|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2015 02 12T17:06:49Z|INSDC last update:2015 02 12T09:52:20Z|INSDC status:public|Submitter Id:Female 002|common name:zebrafish|dev stage:Adult|sample name:Female 002|sex:female                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 1 RID0035 1     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2015 02 12|ENA LAST UPDATE:2018 11 16 RID0035_006.fastq.gz fastq 193706106.0 6343893.0 ena RUN UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 1 0:30.53 A:52756888;C:42895374;G:46979869;T:51073975;N:0 30       52756888 42895374 46979869 51073975 0 ERX701783 ERS659466 ERA410345 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.74991   0.41319   0.83002   0.55823   8   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2015-02-12 Adult Adult Undetermined Undetermined
15506 15506 ERR647638 ERX604074 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 7 RID0015 Fold Change     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0015_007.fastq.gz fastq 181485343.0 7581675.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 7 0:23.94 A:49408107;C:35660562;G:44520624;T:51896050;N:0 23       49408107 35660562 44520624 51896050 0 ERX604074 ERS557914 ERA363852 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.75831   0.16017   0.90723   0.48684   13   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15507 15507 ERR647632 ERX604068 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 1 RID0015 Fold Change     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0015_001.fastq.gz fastq 158714692.0 5407747.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 1 0:29.35 A:42098161;C:32991434;G:38596553;T:45028544;N:0 29       42098161 32991434 38596553 45028544 0 ERX604068 ERS557914 ERA363852 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.75901   0.20293   0.89505   0.48215   24   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15508 15508 ERR647636 ERX604072 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 5 RID0015 Fold Change     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0015_005.fastq.gz fastq 124167412.0 4838491.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 5 0:25.66 A:33439510;C:24728035;G:30897675;T:35102192;N:0 25       33439510 24728035 30897675 35102192 0 ERX604072 ERS557914 ERA363852 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.76027   0.17783   0.89692   0.48421   30   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15509 15509 ERR647635 ERX604071 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 4 RID0015 Fold Change     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0015_004.fastq.gz fastq 124786630.0 4701452.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 4 0:26.54 A:33803418;C:24800330;G:30482560;T:35700322;N:0 26       33803418 24800330 30482560 35700322 0 ERX604071 ERS557914 ERA363852 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.74872   0.18448   0.89789   0.50377   12   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15510 15510 ERR647634 ERX604070 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 3 RID0015 Fold Change     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0015_003.fastq.gz fastq 110526752.0 4078127.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 3 0:27.10 A:29453167;C:22981184;G:27444083;T:30648318;N:0 27       29453167 22981184 27444083 30648318 0 ERX604070 ERS557914 ERA363852 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.73961   0.1804   0.89686   0.50069   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15511 15511 ERR647633 ERX604069 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 2 RID0015 Fold Change     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0015_002.fastq.gz fastq 114721515.0 4468497.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 2 0:25.67 A:31387085;C:22123581;G:28270438;T:32940411;N:0 25       31387085 22123581 28270438 32940411 0 ERX604069 ERS557914 ERA363852 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.75767   0.17199   0.90118   0.49949   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15512 15512 ERR647645 ERX604081 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 14 RID0015 Reproducibility     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0015_014.fastq.gz fastq 127742942.0 5487454.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 14 0:23.28 A:35700746;C:25577569;G:31187339;T:35277288;N:0 23       35700746 25577569 31187339 35277288 0 ERX604081 ERS557914 ERA363852 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.72451   0.1507   0.91078   0.47283   30   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15513 15513 ERR647644 ERX604080 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 13 RID0015 Reproducibility     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0015_013.fastq.gz fastq 175319872.0 7193103.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 13 0:24.37 A:48008107;C:34657005;G:43047489;T:49607271;N:0 24       48008107 34657005 43047489 49607271 0 ERX604080 ERS557914 ERA363852 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.75539   0.16288   0.90388   0.47538   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15514 15514 ERR647643 ERX604079 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 12 RID0015 Reproducibility     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0015_012.fastq.gz fastq 177443752.0 7567733.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 12 0:23.45 A:48143286;C:36300870;G:44060167;T:48939429;N:0 23       48143286 36300870 44060167 48939429 0 ERX604079 ERS557914 ERA363852 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.74839   0.15018   0.90782   0.49076   27   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15515 15515 ERR647642 ERX604078 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 11 RID0015 Reproducibility     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0015_011.fastq.gz fastq 163389373.0 6320373.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 11 0:25.85 A:44540588;C:32608476;G:40066295;T:46174014;N:0 25       44540588 32608476 40066295 46174014 0 ERX604078 ERS557914 ERA363852 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.75948   0.17375   0.90252   0.47536   33   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15516 15516 ERR647641 ERX604077 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 10 RID0015 Reproducibility     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0015_010.fastq.gz fastq 128059692.0 5701206.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 10 0:22.46 A:35418188;C:24802528;G:31593786;T:36245190;N:0 22       35418188 24802528 31593786 36245190 0 ERX604077 ERS557914 ERA363852 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.72586   0.1331   0.92514   0.4216   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15517 15517 ERR647637 ERX604073 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 6 RID0015 Fold Change     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0015_006.fastq.gz fastq 165327404.0 6835740.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 6 0:24.19 A:45252916;C:32442683;G:40306020;T:47325785;N:0 24       45252916 32442683 40306020 47325785 0 ERX604073 ERS557914 ERA363852 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.74944   0.16   0.91068   0.47704   21   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15518 15518 ERR647640 ERX604076 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 9 RID0015 Reproducibility     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0015_009.fastq.gz fastq 134426587.0 5846482.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 9 0:22.99 A:36803811;C:26283055;G:33442229;T:37897492;N:0 22       36803811 26283055 33442229 37897492 0 ERX604076 ERS557914 ERA363852 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.74219   0.13958   0.91837   0.47819   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15519 15519 ERR647639 ERX604075 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 8 RID0015 Fold Change     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0015_008.fastq.gz fastq 164369360.0 6762174.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 8 0:24.31 A:44826982;C:33030972;G:40615427;T:45895979;N:0 24       44826982 33030972 40615427 45895979 0 ERX604075 ERS557914 ERA363852 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.75513   0.16254   0.90534   0.50535   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15520 15520 ERR647623 ERX604059 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 8 RID0017 EtOH conc. experiment     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0017_008.fastq.gz fastq 198146766.0 7373392.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 8 0:26.87 A:50518864;C:42346985;G:50683068;T:54597849;N:0 26       50518864 42346985 50683068 54597849 0 ERX604059 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.73719   0.16567   0.89869   0.49695   76   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15521 15521 ERR647622 ERX604058 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 7 RID0017 EtOH conc. experiment     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0017_007.fastq.gz fastq 240260456.0 9194064.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 7 0:26.13 A:62434032;C:50861577;G:60916218;T:66048629;N:0 26       62434032 50861577 60916218 66048629 0 ERX604058 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.73042   0.17017   0.89509   0.51784   44   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15522 15522 ERR647620 ERX604056 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 5 RID0017 EtOH conc. experiment     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0017_005.fastq.gz fastq 140470735.0 4903805.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 5 0:28.65 A:35312706;C:29191443;G:36788541;T:39178045;N:0 28       35312706 29191443 36788541 39178045 0 ERX604056 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.76081   0.16609   0.90216   0.48155   72   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15523 15523 ERR647617 ERX604053 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 2 RID0017 EtOH conc. experiment     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0017_002.fastq.gz fastq 113953599.0 4875815.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 2 0:23.37 A:29576305;C:23096908;G:29656780;T:31623606;N:0 23       29576305 23096908 29656780 31623606 0 ERX604053 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.70891   0.13528   0.91208   0.4622   24   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15524 15524 ERR647624 ERX604060 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 9 RID0017 EtOH conc. experiment     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0017_009.fastq.gz fastq 127769435.0 5492615.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 9 0:23.26 A:34397217;C:25332113;G:31991788;T:36048317;N:0 23       34397217 25332113 31991788 36048317 0 ERX604060 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.71147   0.1472   0.91015   0.49014   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15525 15525 ERR647629 ERX604065 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 14 RID0017 EtOH conc. experiment     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0017_014.fastq.gz fastq 83983757.0 3823842.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 14 0:21.96 A:22501534;C:16455147;G:21619305;T:23407771;N:0 21       22501534 16455147 21619305 23407771 0 ERX604065 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.70211   0.13351   0.92038   0.45898   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15526 15526 ERR647631 ERX604067 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 16 RID0017 EtOH conc. experiment     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0017_016.fastq.gz fastq 117220472.0 4272650.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 16 0:27.44 A:29509123;C:25768315;G:30220006;T:31723028;N:0 27       29509123 25768315 30220006 31723028 0 ERX604067 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.68585   0.14679   0.90778   0.49492   20   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15527 15527 ERR647618 ERX604054 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 3 RID0017 EtOH conc. experiment     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0017_003.fastq.gz fastq 165279016.0 5211580.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 3 0:31.71 A:41451579;C:36699133;G:41477197;T:45651107;N:0 31       41451579 36699133 41477197 45651107 0 ERX604054 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.71827   0.17456   0.90554   0.50274   18   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15528 15528 ERR647621 ERX604057 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 6 RID0017 EtOH conc. experiment     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0017_006.fastq.gz fastq 181164500.0 7686285.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 6 0:23.57 A:48622049;C:36019225;G:45318073;T:51205153;N:0 23       48622049 36019225 45318073 51205153 0 ERX604057 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.73267   0.15948   0.9026   0.483   14   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15529 15529 ERR647619 ERX604055 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 4 RID0017 EtOH conc. experiment     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0017_004.fastq.gz fastq 131702671.0 4688094.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 4 0:28.09 A:32537215;C:28853793;G:34317576;T:35994087;N:0 28       32537215 28853793 34317576 35994087 0 ERX604055 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.68635   0.14911   0.90532   0.50027   31   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15530 15530 ERR647628 ERX604064 ERS557914 ERP007147 PRJEB7420 Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 Other There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.       Male 001 SAMEA2796299 UNIVERSITY OF AMSTERDAM Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 13 RID0017 EtOH conc. experiment     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   ERP007147 Ion Torrent Proton sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0017_013.fastq.gz fastq 123881257.0 5143681.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 13 0:24.08 A:32852368;C:25503683;G:31339781;T:34185425;N:0 24       32852368 25503683 31339781 34185425 0 ERX604064 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.72384   0.15147   0.90648   0.46   24   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined

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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");;