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run_metadata

114 rows where devstage_curation = "Adult" and tissue_curation_coarse = "Undetermined"

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technology 3

experiment.platform 3

experiment.library_source 3

experiment.library_selection 3

experiment.library_strategy 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Undetermined · 114 ✖

tissue_curation 1

devstage_curation_coarse 1

devstage_curation 1

  • Adult · 114 ✖
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
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
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
15531 15531 ERR647627 ERX604063 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 12 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_012.fastq.gz fastq 135155439.0 6123293.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 12 0:22.07 A:35870227;C:27070386;G:34401412;T:37813414;N:0 22       35870227 27070386 34401412 37813414 0 ERX604063 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.69126   0.12647   0.91695   0.46572   25   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15532 15532 ERR647626 ERX604062 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 11 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_011.fastq.gz fastq 138836612.0 5648801.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 11 0:24.58 A:36426455;C:28359755;G:34985736;T:39064666;N:0 24       36426455 28359755 34985736 39064666 0 ERX604062 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.73565   0.15718   0.90382   0.45772   67   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15533 15533 ERR647625 ERX604061 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 10 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_010.fastq.gz fastq 182404716.0 6612019.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 10 0:27.59 A:47718609;C:38775928;G:45637186;T:50272993;N:0 27       47718609 38775928 45637186 50272993 0 ERX604061 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.75246   0.19746   0.88544   0.48212   36   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15534 15534 ERR647616 ERX604052 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 15:08:22:086 1 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_001.fastq.gz fastq 137653436.0 5155975.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 1 0:26.70 A:34561717;C:29961559;G:35320222;T:37809938;N:0 26       34561717 29961559 35320222 37809938 0 ERX604052 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.71887   0.15223   0.90824   0.49462   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15535 15535 ERR647630 ERX604066 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 15 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_015.fastq.gz fastq 101714594.0 4045987.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 15 0:25.14 A:26518632;C:20741074;G:25853629;T:28601259;N:0 25       26518632 20741074 25853629 28601259 0 ERX604066 ERS557914 ERA363851 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.74566   0.16455   0.89534   0.48977   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15536 15536 ERR647610 ERX604046 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 PGM sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 1 RID0023 1     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM   ERP007147 Ion Torrent PGM sequencing ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 RID0023_009.fastq.gz fastq 114880508.0 4321457.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 1 0:26.58 A:31499097;C:23030789;G:27803371;T:32547251;N:0 26       31499097 23030789 27803371 32547251 0 ERX604046 ERS557914 ERA363850 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.7932   0.2086   0.89045   0.49364   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15537 15537 ERR647611 ERX604047 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 14:59:02:785 2 RID0023 1     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 RID0023_010.fastq.gz fastq 124380158.0 4885304.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 2 0:25.46 A:33809369;C:25116497;G:30529372;T:34924920;N:0 25       33809369 25116497 30529372 34924920 0 ERX604047 ERS557914 ERA363850 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.78302   0.1944   0.89398   0.50469   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15538 15538 ERR647612 ERX604048 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 14:59:02:785 3 RID0023 1     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 RID0023_011.fastq.gz fastq 122081664.0 4959591.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 3 0:24.62 A:33452935;C:24151113;G:29942213;T:34535403;N:0 24       33452935 24151113 29942213 34535403 0 ERX604048 ERS557914 ERA363850 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.77425   0.18982   0.8911   0.46046   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15539 15539 ERR647615 ERX604051 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 14:59:02:785 6 RID0023 1     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 RID0023_014.fastq.gz fastq 120491210.0 4564333.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 6 0:26.40 A:33116448;C:24416657;G:29447901;T:33510204;N:0 26       33116448 24416657 29447901 33510204 0 ERX604051 ERS557914 ERA363850 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.77843   0.20568   0.88605   0.51892   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15540 15540 ERR647614 ERX604050 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 14:59:02:785 5 RID0023 1     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 RID0023_013.fastq.gz fastq 108193052.0 4221217.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 5 0:25.63 A:29795112;C:21481151;G:26281164;T:30635625;N:0 25       29795112 21481151 26281164 30635625 0 ERX604050 ERS557914 ERA363850 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.78861   0.19966   0.89207   0.49332   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15541 15541 ERR647613 ERX604049 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 14:59:02:785 4 RID0023 1     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 RID0023_012.fastq.gz fastq 134807115.0 5232713.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 4 0:25.76 A:37141537;C:27086121;G:32486547;T:38092910;N:0 25       37141537 27086121 32486547 38092910 0 ERX604049 ERS557914 ERA363850 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.78328   0.20061   0.88903   0.51655   32   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15542 15542 ERR647603 ERX604039 ERS557923 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.       Female 016 SAMEA2796308 UNIVERSITY OF AMSTERDAM Alias:Female 016|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 01T14:38:25Z|INSDC status:public|SRA accession:ERS557923|Sample Name:ERS557923|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 8 RID0035 1     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 RID0035_010.fastq.gz fastq 186445198.0 6054478.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 8 0:30.79 A:51431122;C:41043403;G:44213690;T:49756983;N:0 30       51431122 41043403 44213690 49756983 0 ERX604039 ERS557923 ERA363846 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.74649   0.44738   0.84254   0.55199   13   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15543 15543 ERR647602 ERX604038 ERS557922 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.       Female 014 SAMEA2796307 UNIVERSITY OF AMSTERDAM Alias:Female 014|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 01T14:38:25Z|INSDC status:public|SRA accession:ERS557922|Sample Name:ERS557922|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 7 RID0035 1     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 RID0035_009.fastq.gz fastq 199860614.0 6227225.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 7 0:32.09 A:53999848;C:44698032;G:48251471;T:52911263;N:0 32       53999848 44698032 48251471 52911263 0 ERX604038 ERS557922 ERA363846 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.75262   0.42794   0.83619   0.5624   29   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15544 15544 ERR647601 ERX604037 ERS557921 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.       Female 008 SAMEA2796306 UNIVERSITY OF AMSTERDAM Alias:Female 008|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 01T14:38:25Z|INSDC status:public|SRA accession:ERS557921|Sample Name:ERS557921|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 6 RID0035 1     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 RID0035_008.fastq.gz fastq 190251948.0 6082600.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 6 0:31.28 A:50176174;C:43027879;G:47458847;T:49589048;N:0 31       50176174 43027879 47458847 49589048 0 ERX604037 ERS557921 ERA363846 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.72654   0.373   0.82785   0.52436   25   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15545 15545 ERR647600 ERX604036 ERS557920 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.       Female 007 SAMEA2796305 UNIVERSITY OF AMSTERDAM Alias:Female 007|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 01T14:38:24Z|INSDC status:public|SRA accession:ERS557920|Sample Name:ERS557920|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 5 RID0035 1     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 RID0035_007.fastq.gz fastq 214503694.0 6990446.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 5 0:30.69 A:59354819;C:47472262;G:51306173;T:56370440;N:0 30       59354819 47472262 51306173 56370440 0 ERX604036 ERS557920 ERA363846 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.74272   0.45587   0.83161   0.53444   22   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15546 15546 ERR647599 ERX604035 ERS557919 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 014 SAMEA2796304 UNIVERSITY OF AMSTERDAM Alias:Male 014|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 01T14:38:24Z|INSDC status:public|SRA accession:ERS557919|Sample Name:ERS557919|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 4 RID0035 1     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 RID0035_005.fastq.gz fastq 235098531.0 7522781.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 4 0:31.25 A:58178492;C:54009752;G:64159987;T:58750300;N:0 31       58178492 54009752 64159987 58750300 0 ERX604035 ERS557919 ERA363846 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.73752   0.19698   0.86665   0.58697   13   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15547 15547 ERR647598 ERX604034 ERS557918 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 011 SAMEA2796303 UNIVERSITY OF AMSTERDAM Alias:Male 011|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 01T14:38:24Z|INSDC status:public|SRA accession:ERS557918|Sample Name:ERS557918|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 3 RID0035 1     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 RID0035_004.fastq.gz fastq 223142261.0 6553993.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 3 0:34.05 A:55488952;C:50941034;G:58123716;T:58588559;N:0 34       55488952 50941034 58123716 58588559 0 ERX604034 ERS557918 ERA363846 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.74686   0.2139   0.86996   0.55375   11   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15548 15548 ERR647597 ERX604033 ERS557917 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 006 SAMEA2796302 UNIVERSITY OF AMSTERDAM Alias:Male 006|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 01T14:38:24Z|INSDC status:public|SRA accession:ERS557917|Sample Name:ERS557917|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 2 RID0035 1     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 RID0035_002.fastq.gz fastq 166401146.0 5656405.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 2 0:29.42 A:41137490;C:38824883;G:44865980;T:41572793;N:0 29       41137490 38824883 44865980 41572793 0 ERX604033 ERS557917 ERA363846 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.69452   0.18245   0.87044   0.58162   11   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15549 15549 ERR647596 ERX604032 ERS557916 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 003 SAMEA2796301 UNIVERSITY OF AMSTERDAM Alias:Male 003|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 01T14:38:23Z|INSDC status:public|SRA accession:ERS557916|Sample Name:ERS557916|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 1 RID0035 1     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 RID0035_001.fastq.gz fastq 167146177.0 6380638.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 1 0:26.20 A:43620211;C:36811253;G:43301042;T:43413671;N:0 26       43620211 36811253 43301042 43413671 0 ERX604032 ERS557916 ERA363846 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.70048   0.18034   0.88075   0.55658   11   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15551 15551 ERR647594 ERX604030 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 14:02:18:976 6 RID0011 1     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 RID0011_015.fastq.gz fastq 273349184.0 9019669.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 6 0:30.31 A:74069549;C:59041449;G:64551451;T:75686735;N:0 30       74069549 59041449 64551451 75686735 0 ERX604030 ERS557914 ERA363842 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.78759   0.26081   0.90989   0.51416   29   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15552 15552 ERR647589 ERX604025 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 14:02:18:976 1 RID0011 1     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 RID0011_010.fastq.gz fastq 54651692.0 2000589.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 1 0:27.32 A:16624629;C:13894132;G:10557585;T:13575346;N:0 27       16624629 13894132 10557585 13575346 0 ERX604025 ERS557914 ERA363842 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.11072   0.02655   0.97749   0.53916   26   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15553 15553 ERR647590 ERX604026 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 14:02:18:976 2 RID0011 1     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 RID0011_011.fastq.gz fastq 47051190.0 1414933.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 2 0:33.25 A:12984359;C:11329853;G:10330928;T:12406050;N:0 33       12984359 11329853 10330928 12406050 0 ERX604026 ERS557914 ERA363842 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.36871   0.10094   0.9483   0.51008   40   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15554 15554 ERR647592 ERX604028 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 14:02:18:976 4 RID0011 1     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 RID0011_013.fastq.gz fastq 394812059.0 13329274.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 4 0:29.62 A:108705027;C:84131955;G:92090437;T:109884640;N:0 29       108705027 84131955 92090437 109884640 0 ERX604028 ERS557914 ERA363842 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.65205   0.21183   0.91977   0.52643   21   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15555 15555 ERR647593 ERX604029 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 14:02:18:976 5 RID0011 1     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 RID0011_014.fastq.gz fastq 143238806.0 4225461.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 5 0:33.90 A:38374880;C:31424768;G:33687670;T:39751488;N:0 33       38374880 31424768 33687670 39751488 0 ERX604029 ERS557914 ERA363842 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.78469   0.26587   0.92178   0.51694   80   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
15556 15556 ERR647591 ERX604027 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 14:02:18:976 3 RID0011 1     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 RID0011_012.fastq.gz fastq 55541174.0 1649692.0 ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 3 0:33.67 A:16076639;C:14164415;G:11139997;T:14160123;N:0 33       16076639 14164415 11139997 14160123 0 ERX604027 ERS557914 ERA363842 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.16692   0.04528   0.96384   0.52823   17   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Adult Adult Undetermined Undetermined
33007 33007 SRR29551178 SRX25058395 SRS21755348 SRP516116 PRJNA1128236 The axillary lymphoid organ an external experimentally accessible immune organ in the zebrafish GSE270797 Other Lymph nodes and other secondary lymphoid organs play critical roles in immune surveillance and immune activation in mammals but the deep internal locations of these organs makes it challenging to study dynamic cellular mechanisms of immune cell interaction with pathogens or other host tissues such as the vasculature in living animals. Here we describe a previously uncharacterized external immune organ located near the base of the zebrafish pectoral fin the pectoral axillary lobe PAL with a variety of features that make it ideally suited for studying immune cell dynamics in vivo. This small transparent organ consists of an outer cortex teeming with immune cells and an inner medulla with a mesh like network of fibroblastic reticular cells along which immune cells migrate and a network of lymphatic vessels draining to a large adjacent lymph sac. Noninvasive high resolution imaging of transgenically marked immune cells can be carried out in the lobes of living animals and the PAL is readily accessible to external treatment with antigens or pathogens. This newly discovered tissue provides a superb model for dynamic live imaging of immune cells and their interaction with pathogens and surrounding tissues including blood and lymphatic vessels. Overall design: Single cell expression profiling by high throughput sequencing   pubmed:39091802   Pectoral axillary lobe scRNA GSM8352182   source name:Pectoral axillary lobe|tissue:Pectoral axillary lobe|geo loc name:missing|collection date:missing Pectoral axillary lobe scRNA cellranger count v7.0.0 Assembly: zv11 Supplementary files format and content: TSV value and matrix files Pectoral axillary lobe   Cell suspension prepared from 4 pectoral axillary lobes 2 from males 2 from females removed from adult zebrafish comprising 10k cells 10X 3.1 GEM kits following manufacturer recommendations   tissue:Pectoral axillary lobe GSM8352182 GSM8352182: Pectoral axillary lobe scRNA; Danio rerio; RNA Seq GSM8352182 r1 GSM8352182 1 Cell suspension prepared from 4 pectoral axillary lobes 2 from males 2 from females removed from adult zebrafish comprising 10k cells 10X 3.1 GEM kits following manufacturer recommendations   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP516116     LCK1_S3_L001_R1_001.fastq.gz LCK1_S3_L001_R2_001.fastq.gz LCK1_S3_L002_R1_001.fastq.gz LCK1_S3_L002_R2_001.fastq.gz fastq fastq fastq fastq 21583802440.0 182913580.0 GSM8352182 r1 0:28 1:90 A:6079984051;C:4913875575;G:5182513698;T:5406578531;N:850585 28 90     6079984051 4913875575 5182513698 5406578531 850585 SRX25058395 SRS21755348 SRA1909244 BG 10 RM 8S261, NICHD, NIH BG 10 RM 8S261, NICHD, NIH                       T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-06-25 Adult Adult Undetermined Undetermined
34961 34961 SRR32588718 SRX27895233 SRS24266235 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from Danio rerio C2 F2 F IE   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:inner ear|BioSampleModel:Model organism or animal                 Iso Seq RNA from inner ear C2 F2 F IE C2 F2 F IE The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m84270_240904_152521_s2.skera.flnc.fastq.gz fastq 93609779073.0 46650644.0 m84270 240904 152521 s2.skera.flnc.fastq.gz 0:2006.61 A:27359819621;C:19471270902;G:20218480457;T:26560208093;N:0 2006       27359819621 19471270902 20218480457 26560208093 0 SRX27895233 SRS24266235 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Undetermined Undetermined
53150 53150 SRR9692020 SRX6451054 SRS5104325 SRP214773 PRJNA554788 Gene expression analysis in the zebrafish fractured scale GSE134330 Transcriptome Analysis Bone is a connective tissue which undergoes continuous remodeling including bone resorption and formation by osteoclasts OCs and osteoblasts OBs respectively. Recently extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs OCs and bone matrix providing an elegant model to visualize OC OB communication. Here we developed a double transgenic zebrafish line trap:GFP; osterix:mCherry which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer respectively. Utilizing this double transgenic line in combination with Hoechst 33342 Hoe staining we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry GFP– mCh+ Hoehigh OB fraction GFPlow mCh+ Hoehigh OC precursor pOC fraction GFPhigh Hoehigh mature OC mOC fraction and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each fraction. Overall design: mRNA profiles of isolated OBs pOCs mOCs and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.   pubmed:32327701   mOC 2 GSM3942346   source name:mature osteoclasts|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:mature osteoclasts|molecule type:Amplified RNA mOC 2 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. mature osteoclasts   Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.   age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:mature osteoclasts|molecule type:Amplified RNA GSM3942346 GSM3942346: mOC 2; Danio rerio; RNA Seq GSM3942346   1 Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP214773     mOC_2_R1.fastq.gz mOC_2_R2.fastq.gz fastq fastq 3442034400.0 11473448.0 GSM3942346 r1 0:150 1:150 A:874790081;C:854584498;G:837659746;T:874907519;N:92556 150 150     874790081 854584498 837659746 874907519 92556 SRX6451054 SRS5104325 SRA921382 GEO Kanazawa University 2 0.94546 0.94169 0.03234 0.03643 0.79845 0.81132 0.49852 0.47127 150 150 B B biological fallback assumption illumina nextseq 3prime poly_a nextera sc single_cell_plate quartzseq   Japan 2019-07-16 Adult Adult Undetermined Undetermined
53151 53151 SRR9692019 SRX6451053 SRS5104324 SRP214773 PRJNA554788 Gene expression analysis in the zebrafish fractured scale GSE134330 Transcriptome Analysis Bone is a connective tissue which undergoes continuous remodeling including bone resorption and formation by osteoclasts OCs and osteoblasts OBs respectively. Recently extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs OCs and bone matrix providing an elegant model to visualize OC OB communication. Here we developed a double transgenic zebrafish line trap:GFP; osterix:mCherry which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer respectively. Utilizing this double transgenic line in combination with Hoechst 33342 Hoe staining we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry GFP– mCh+ Hoehigh OB fraction GFPlow mCh+ Hoehigh OC precursor pOC fraction GFPhigh Hoehigh mature OC mOC fraction and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each fraction. Overall design: mRNA profiles of isolated OBs pOCs mOCs and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.   pubmed:32327701   mOC 1 GSM3942345   source name:mature osteoclasts|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:mature osteoclasts|molecule type:Amplified RNA mOC 1 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. mature osteoclasts   Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.   age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:mature osteoclasts|molecule type:Amplified RNA GSM3942345 GSM3942345: mOC 1; Danio rerio; RNA Seq GSM3942345   1 Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP214773     mOC_1_R1.fastq.gz mOC_1_R2.fastq.gz fastq fastq 3725202300.0 12417341.0 GSM3942345 r1 0:150 1:150 A:939287270;C:932158020;G:913434023;T:940223484;N:99503 150 150     939287270 932158020 913434023 940223484 99503 SRX6451053 SRS5104324 SRA921382 GEO Kanazawa University 2 0.95139 0.94882 0.0326 0.03471 0.79393 0.80507 0.4667 0.49924 150 150 B B biological fallback assumption illumina nextseq 3prime poly_a nextera sc single_cell_plate quartzseq   Japan 2019-07-16 Adult Adult Undetermined Undetermined
53152 53152 SRR9692018 SRX6451052 SRS5104323 SRP214773 PRJNA554788 Gene expression analysis in the zebrafish fractured scale GSE134330 Transcriptome Analysis Bone is a connective tissue which undergoes continuous remodeling including bone resorption and formation by osteoclasts OCs and osteoblasts OBs respectively. Recently extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs OCs and bone matrix providing an elegant model to visualize OC OB communication. Here we developed a double transgenic zebrafish line trap:GFP; osterix:mCherry which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer respectively. Utilizing this double transgenic line in combination with Hoechst 33342 Hoe staining we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry GFP– mCh+ Hoehigh OB fraction GFPlow mCh+ Hoehigh OC precursor pOC fraction GFPhigh Hoehigh mature OC mOC fraction and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each fraction. Overall design: mRNA profiles of isolated OBs pOCs mOCs and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.   pubmed:32327701   pOC 2 GSM3942344   source name:osteoclast precursors|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoclast precursors|molecule type:Amplified RNA pOC 2 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. osteoclast precursors   Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.   age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoclast precursors|molecule type:Amplified RNA GSM3942344 GSM3942344: pOC 2; Danio rerio; RNA Seq GSM3942344   1 Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP214773     pOC_2_R1.fastq.gz pOC_2_R2.fastq.gz fastq fastq 8180901900.0 27269673.0 GSM3942344 r1 0:150 1:150 A:2045941714;C:2067950267;G:1981277316;T:2085490817;N:241786 150 150     2045941714 2067950267 1981277316 2085490817 241786 SRX6451052 SRS5104323 SRA921382 GEO Kanazawa University 2 0.94075 0.93872 0.04606 0.04832 0.77847 0.78482 0.50377 0.50525 150 150 B B biological fallback assumption illumina nextseq 3prime poly_a nextera sc single_cell_plate quartzseq   Japan 2019-07-16 Adult Adult Undetermined Undetermined
53153 53153 SRR9692017 SRX6451051 SRS5104322 SRP214773 PRJNA554788 Gene expression analysis in the zebrafish fractured scale GSE134330 Transcriptome Analysis Bone is a connective tissue which undergoes continuous remodeling including bone resorption and formation by osteoclasts OCs and osteoblasts OBs respectively. Recently extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs OCs and bone matrix providing an elegant model to visualize OC OB communication. Here we developed a double transgenic zebrafish line trap:GFP; osterix:mCherry which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer respectively. Utilizing this double transgenic line in combination with Hoechst 33342 Hoe staining we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry GFP– mCh+ Hoehigh OB fraction GFPlow mCh+ Hoehigh OC precursor pOC fraction GFPhigh Hoehigh mature OC mOC fraction and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each fraction. Overall design: mRNA profiles of isolated OBs pOCs mOCs and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.   pubmed:32327701   pOC 1 GSM3942343   source name:osteoclast precursors|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoclast precursors|molecule type:Amplified RNA pOC 1 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. osteoclast precursors   Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.   age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoclast precursors|molecule type:Amplified RNA GSM3942343 GSM3942343: pOC 1; Danio rerio; RNA Seq GSM3942343   1 Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP214773     pOC_1_R1.fastq.gz pOC_1_R2.fastq.gz fastq fastq 8119854000.0 27066180.0 GSM3942343 r1 0:150 1:150 A:2022941314;C:2067331062;G:1960663076;T:2068678318;N:240230 150 150     2022941314 2067331062 1960663076 2068678318 240230 SRX6451051 SRS5104322 SRA921382 GEO Kanazawa University 2 0.94544 0.94406 0.04202 0.04348 0.77979 0.78624 0.50479 0.48269 150 150 B B biological fallback assumption illumina nextseq 3prime poly_a nextera sc single_cell_plate quartzseq   Japan 2019-07-16 Adult Adult Undetermined Undetermined
68979 68979 SRR18278279 SRX14416139 SRS12225417 SRP363191 PRJNA814235 Profiling the cancer prone microenvironment in a zebrafish model for MPNST GSE198220 Transcriptome Analysis Microenvironmental contributions to soft tissue sarcoma progression are relatively undefined particularly in the context of sarcoma onset. Use of animal models to reveal these contributions is impeded by 1 the difficulty in discriminating between microenvironmental precancerous and cancer cells; and 2 the challenge in defining a precancerous microenvironment. We developed a zebrafish model that allows segregation of microenvironmental precancerous and cancerous cell populations by fluorescence activated cell sorting. This model exhibits high predilection for malignant peripheral nerve sheath tumor MPNST a type of soft tissue sarcoma that exhibits rapid aggressive growth. Using RNA seq we profiled the transcriptomes of microenvironmental cells from our zebrafish MPNST model. We show broad activation of inflammatory and immune associated signaling networks and significant upregulation of tumor promoting ligands in both precancerous and cancerous microenvironments. We also identify specific ligand receptor pairs that may promote sarcomagenesis. This work provides insight into how the microenvironment may promote MPNST initiation and progression. Overall design: N = 3 4 SAMPLES PER TREATMENT GROUP: Pre Cancerous Sox10 High Pre Cancerous Sox10 Low Control Sox10 Low Cancer Sox10 High Cancer Sox10 Low       Control Sox10 Low rep3 GSM5941033   source name:Control|strain:tgsox10:RFP|tissue:Control Microenvironment|age:5.0 months|treatment:Control|geo loc name:missing|collection date:missing Control Sox10 Low rep3 The quality of sequenced data was assessed using fastqc application and 10 poor quality bases were trimmed from the 5’ end. The remaining good quality reads were aligned to the Zebrafish reference genome danRer10 downloaded from the Ensembl database using STAR aligner. Per gene counts of uniquely mapped reads were calculated using htseq count script from the HTSeq Python package for each replicate. Gene counts were imported to R and features with at least 2 counts in 8 or more samples were retained. Zebrafish ensemble gene IDs were mapped to unique ZF  gene symbol and summed. DESeq2 was used to estimate size factors and generate normalized counts for downstream analyses as well as log2FC and adjusted pvalues for treatment comparions Assembly: danRer10 Supplementary files format and content: csv format read count Control Ocular tissues were removed enzymatically dissociated and processed by FACS RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended Zebrafish housed and maintained under standard conditions strain:tgsox10:RFP|tissue:Control Microenvironment|age:5.0 months|treatment:Control GSM5941033 GSM5941033: Control Sox10 Low rep3; Danio rerio; RNA Seq GSM5941033 r1 GSM5941033 1 RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP363191   loader:fastq load.py ONP8_RFPminus_S5_R2_001.fastq.gz ONP8_RFPminus_S5_R1_001.fastq.gz fastq fastq 7810043784.0 51381867.0 GSM5941033 r1 0:76 1:76 A:2092382937;C:1802045263;G:1839565399;T:2073221662;N:2828523 76 76     2092382937 1802045263 1839565399 2073221662 2828523 SRX14416139 SRS12225417 SRA1386032 Center for Human Health and the Environment (CHHE) and Bioinformatics Research Center (BRC), North Carolina State University CHHE, NCSU 2 0.9118 0.91256 0.14354 0.14146 0.72419 0.72663 0.51189 0.50262 76 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   United States 2022-03-09 Adult Adult Undetermined Undetermined
68980 68980 SRR18278280 SRX14416138 SRS12225416 SRP363191 PRJNA814235 Profiling the cancer prone microenvironment in a zebrafish model for MPNST GSE198220 Transcriptome Analysis Microenvironmental contributions to soft tissue sarcoma progression are relatively undefined particularly in the context of sarcoma onset. Use of animal models to reveal these contributions is impeded by 1 the difficulty in discriminating between microenvironmental precancerous and cancer cells; and 2 the challenge in defining a precancerous microenvironment. We developed a zebrafish model that allows segregation of microenvironmental precancerous and cancerous cell populations by fluorescence activated cell sorting. This model exhibits high predilection for malignant peripheral nerve sheath tumor MPNST a type of soft tissue sarcoma that exhibits rapid aggressive growth. Using RNA seq we profiled the transcriptomes of microenvironmental cells from our zebrafish MPNST model. We show broad activation of inflammatory and immune associated signaling networks and significant upregulation of tumor promoting ligands in both precancerous and cancerous microenvironments. We also identify specific ligand receptor pairs that may promote sarcomagenesis. This work provides insight into how the microenvironment may promote MPNST initiation and progression. Overall design: N = 3 4 SAMPLES PER TREATMENT GROUP: Pre Cancerous Sox10 High Pre Cancerous Sox10 Low Control Sox10 Low Cancer Sox10 High Cancer Sox10 Low       Control Sox10 Low rep2 GSM5941032   source name:Control|strain:tgsox10:RFP|tissue:Control Microenvironment|age:5.0 months|treatment:Control|geo loc name:missing|collection date:missing Control Sox10 Low rep2 The quality of sequenced data was assessed using fastqc application and 10 poor quality bases were trimmed from the 5’ end. The remaining good quality reads were aligned to the Zebrafish reference genome danRer10 downloaded from the Ensembl database using STAR aligner. Per gene counts of uniquely mapped reads were calculated using htseq count script from the HTSeq Python package for each replicate. Gene counts were imported to R and features with at least 2 counts in 8 or more samples were retained. Zebrafish ensemble gene IDs were mapped to unique ZF  gene symbol and summed. DESeq2 was used to estimate size factors and generate normalized counts for downstream analyses as well as log2FC and adjusted pvalues for treatment comparions Assembly: danRer10 Supplementary files format and content: csv format read count Control Ocular tissues were removed enzymatically dissociated and processed by FACS RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended Zebrafish housed and maintained under standard conditions strain:tgsox10:RFP|tissue:Control Microenvironment|age:5.0 months|treatment:Control GSM5941032 GSM5941032: Control Sox10 Low rep2; Danio rerio; RNA Seq GSM5941032 r1 GSM5941032 1 RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP363191   loader:fastq load.py ONP7_RFPminus_S9_R2_001.fastq.gz ONP7_RFPminus_S9_R1_001.fastq.gz fastq fastq 7603890288.0 50025594.0 GSM5941032 r1 0:76 1:76 A:2093368388;C:1700220526;G:1731925604;T:2075633834;N:2741936 76 76     2093368388 1700220526 1731925604 2075633834 2741936 SRX14416138 SRS12225416 SRA1386032 Center for Human Health and the Environment (CHHE) and Bioinformatics Research Center (BRC), North Carolina State University CHHE, NCSU 2 0.91228 0.91613 0.13849 0.13679 0.72555 0.72874 0.50816 0.5168 76 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   United States 2022-03-09 Adult Adult Undetermined Undetermined
68981 68981 SRR18278281 SRX14416137 SRS12225415 SRP363191 PRJNA814235 Profiling the cancer prone microenvironment in a zebrafish model for MPNST GSE198220 Transcriptome Analysis Microenvironmental contributions to soft tissue sarcoma progression are relatively undefined particularly in the context of sarcoma onset. Use of animal models to reveal these contributions is impeded by 1 the difficulty in discriminating between microenvironmental precancerous and cancer cells; and 2 the challenge in defining a precancerous microenvironment. We developed a zebrafish model that allows segregation of microenvironmental precancerous and cancerous cell populations by fluorescence activated cell sorting. This model exhibits high predilection for malignant peripheral nerve sheath tumor MPNST a type of soft tissue sarcoma that exhibits rapid aggressive growth. Using RNA seq we profiled the transcriptomes of microenvironmental cells from our zebrafish MPNST model. We show broad activation of inflammatory and immune associated signaling networks and significant upregulation of tumor promoting ligands in both precancerous and cancerous microenvironments. We also identify specific ligand receptor pairs that may promote sarcomagenesis. This work provides insight into how the microenvironment may promote MPNST initiation and progression. Overall design: N = 3 4 SAMPLES PER TREATMENT GROUP: Pre Cancerous Sox10 High Pre Cancerous Sox10 Low Control Sox10 Low Cancer Sox10 High Cancer Sox10 Low       Control Sox10 Low rep1 GSM5941031   source name:Control|strain:tgsox10:RFP|tissue:Control Microenvironment|age:4.6 months|treatment:Control|geo loc name:missing|collection date:missing Control Sox10 Low rep1 The quality of sequenced data was assessed using fastqc application and 10 poor quality bases were trimmed from the 5’ end. The remaining good quality reads were aligned to the Zebrafish reference genome danRer10 downloaded from the Ensembl database using STAR aligner. Per gene counts of uniquely mapped reads were calculated using htseq count script from the HTSeq Python package for each replicate. Gene counts were imported to R and features with at least 2 counts in 8 or more samples were retained. Zebrafish ensemble gene IDs were mapped to unique ZF  gene symbol and summed. DESeq2 was used to estimate size factors and generate normalized counts for downstream analyses as well as log2FC and adjusted pvalues for treatment comparions Assembly: danRer10 Supplementary files format and content: csv format read count Control Ocular tissues were removed enzymatically dissociated and processed by FACS RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended Zebrafish housed and maintained under standard conditions strain:tgsox10:RFP|tissue:Control Microenvironment|age:4.6 months|treatment:Control GSM5941031 GSM5941031: Control Sox10 Low rep1; Danio rerio; RNA Seq GSM5941031 r1 GSM5941031 1 RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP363191   loader:fastq load.py ONP6_RFPminus_S3_R2_001.fastq.gz ONP6_RFPminus_S3_R1_001.fastq.gz fastq fastq 7354811536.0 48386918.0 GSM5941031 r1 0:76 1:76 A:1961381686;C:1710025545;G:1743343438;T:1937463525;N:2597342 76 76     1961381686 1710025545 1743343438 1937463525 2597342 SRX14416137 SRS12225415 SRA1386032 Center for Human Health and the Environment (CHHE) and Bioinformatics Research Center (BRC), North Carolina State University CHHE, NCSU 2 0.87064 0.87046 0.14974 0.14605 0.7542 0.75767 0.56111 0.5346 76 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   United States 2022-03-09 Adult Adult Undetermined Undetermined
68982 68982 SRR18278282 SRX14416136 SRS12225413 SRP363191 PRJNA814235 Profiling the cancer prone microenvironment in a zebrafish model for MPNST GSE198220 Transcriptome Analysis Microenvironmental contributions to soft tissue sarcoma progression are relatively undefined particularly in the context of sarcoma onset. Use of animal models to reveal these contributions is impeded by 1 the difficulty in discriminating between microenvironmental precancerous and cancer cells; and 2 the challenge in defining a precancerous microenvironment. We developed a zebrafish model that allows segregation of microenvironmental precancerous and cancerous cell populations by fluorescence activated cell sorting. This model exhibits high predilection for malignant peripheral nerve sheath tumor MPNST a type of soft tissue sarcoma that exhibits rapid aggressive growth. Using RNA seq we profiled the transcriptomes of microenvironmental cells from our zebrafish MPNST model. We show broad activation of inflammatory and immune associated signaling networks and significant upregulation of tumor promoting ligands in both precancerous and cancerous microenvironments. We also identify specific ligand receptor pairs that may promote sarcomagenesis. This work provides insight into how the microenvironment may promote MPNST initiation and progression. Overall design: N = 3 4 SAMPLES PER TREATMENT GROUP: Pre Cancerous Sox10 High Pre Cancerous Sox10 Low Control Sox10 Low Cancer Sox10 High Cancer Sox10 Low       Pre Cancerous Sox10 Low rep3 GSM5941030   source name:PreC Sox10 Low|strain:tgsox10:RFP; brca2hg5/hg5; tp53zdf1/zdf1|tissue:Precancerous Microenvironment|age:4.7 months|treatment:Sox10 Low|geo loc name:missing|collection date:missing Pre Cancerous Sox10 Low rep3 The quality of sequenced data was assessed using fastqc application and 10 poor quality bases were trimmed from the 5’ end. The remaining good quality reads were aligned to the Zebrafish reference genome danRer10 downloaded from the Ensembl database using STAR aligner. Per gene counts of uniquely mapped reads were calculated using htseq count script from the HTSeq Python package for each replicate. Gene counts were imported to R and features with at least 2 counts in 8 or more samples were retained. Zebrafish ensemble gene IDs were mapped to unique ZF  gene symbol and summed. DESeq2 was used to estimate size factors and generate normalized counts for downstream analyses as well as log2FC and adjusted pvalues for treatment comparions Assembly: danRer10 Supplementary files format and content: csv format read count PreC Sox10 Low Ocular tissues were removed enzymatically dissociated and processed by FACS RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended Zebrafish housed and maintained under standard conditions strain:tgsox10:RFP;brca2hg5/hg5;tp53zdf1/zdf1|tissue:Precancerous Microenvironment|age:4.7 months|treatment:Sox10 Low GSM5941030 GSM5941030: Pre Cancerous Sox10 Low rep3; Danio rerio; RNA Seq GSM5941030 r1 GSM5941030 1 RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP363191   loader:fastq load.py ONP3_RFPminus_S8_R2_001.fastq.gz ONP3_RFPminus_S8_R1_001.fastq.gz fastq fastq 8529685960.0 56116355.0 GSM5941030 r1 0:76 1:76 A:2284306669;C:1971218562;G:2010991772;T:2260056039;N:3112918 76 76     2284306669 1971218562 2010991772 2260056039 3112918 SRX14416136 SRS12225413 SRA1386032 Center for Human Health and the Environment (CHHE) and Bioinformatics Research Center (BRC), North Carolina State University CHHE, NCSU 2 0.91189 0.91382 0.13779 0.13518 0.71106 0.71561 0.51476 0.52531 76 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   United States 2022-03-09 Adult Adult Undetermined Undetermined
68983 68983 SRR18278283 SRX14416135 SRS12225414 SRP363191 PRJNA814235 Profiling the cancer prone microenvironment in a zebrafish model for MPNST GSE198220 Transcriptome Analysis Microenvironmental contributions to soft tissue sarcoma progression are relatively undefined particularly in the context of sarcoma onset. Use of animal models to reveal these contributions is impeded by 1 the difficulty in discriminating between microenvironmental precancerous and cancer cells; and 2 the challenge in defining a precancerous microenvironment. We developed a zebrafish model that allows segregation of microenvironmental precancerous and cancerous cell populations by fluorescence activated cell sorting. This model exhibits high predilection for malignant peripheral nerve sheath tumor MPNST a type of soft tissue sarcoma that exhibits rapid aggressive growth. Using RNA seq we profiled the transcriptomes of microenvironmental cells from our zebrafish MPNST model. We show broad activation of inflammatory and immune associated signaling networks and significant upregulation of tumor promoting ligands in both precancerous and cancerous microenvironments. We also identify specific ligand receptor pairs that may promote sarcomagenesis. This work provides insight into how the microenvironment may promote MPNST initiation and progression. Overall design: N = 3 4 SAMPLES PER TREATMENT GROUP: Pre Cancerous Sox10 High Pre Cancerous Sox10 Low Control Sox10 Low Cancer Sox10 High Cancer Sox10 Low       Pre Cancerous Sox10 Low rep2 GSM5941029   source name:PreC Sox10 Low|strain:tgsox10:RFP; brca2hg5/hg5; tp53zdf1/zdf1|tissue:Precancerous Microenvironment|age:4.5 months|treatment:Sox10 Low|geo loc name:missing|collection date:missing Pre Cancerous Sox10 Low rep2 The quality of sequenced data was assessed using fastqc application and 10 poor quality bases were trimmed from the 5’ end. The remaining good quality reads were aligned to the Zebrafish reference genome danRer10 downloaded from the Ensembl database using STAR aligner. Per gene counts of uniquely mapped reads were calculated using htseq count script from the HTSeq Python package for each replicate. Gene counts were imported to R and features with at least 2 counts in 8 or more samples were retained. Zebrafish ensemble gene IDs were mapped to unique ZF  gene symbol and summed. DESeq2 was used to estimate size factors and generate normalized counts for downstream analyses as well as log2FC and adjusted pvalues for treatment comparions Assembly: danRer10 Supplementary files format and content: csv format read count PreC Sox10 Low Ocular tissues were removed enzymatically dissociated and processed by FACS RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended Zebrafish housed and maintained under standard conditions strain:tgsox10:RFP;brca2hg5/hg5;tp53zdf1/zdf1|tissue:Precancerous Microenvironment|age:4.5 months|treatment:Sox10 Low GSM5941029 GSM5941029: Pre Cancerous Sox10 Low rep2; Danio rerio; RNA Seq GSM5941029 r1 GSM5941029 1 RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP363191   loader:fastq load.py ONP2_RFPminus_S4_R1_001.fastq.gz ONP2_RFPminus_S4_R2_001.fastq.gz fastq fastq 8038248528.0 52883214.0 GSM5941029 r1 0:76 1:76 A:2158083548;C:1851314393;G:1891780473;T:2134167471;N:2902643 76 76     2158083548 1851314393 1891780473 2134167471 2902643 SRX14416135 SRS12225414 SRA1386032 Center for Human Health and the Environment (CHHE) and Bioinformatics Research Center (BRC), North Carolina State University CHHE, NCSU 2 0.89222 0.892 0.14543 0.14175 0.72604 0.7292 0.54391 0.56194 76 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   United States 2022-03-09 Adult Adult Undetermined Undetermined
68984 68984 SRR18278284 SRX14416134 SRS12225412 SRP363191 PRJNA814235 Profiling the cancer prone microenvironment in a zebrafish model for MPNST GSE198220 Transcriptome Analysis Microenvironmental contributions to soft tissue sarcoma progression are relatively undefined particularly in the context of sarcoma onset. Use of animal models to reveal these contributions is impeded by 1 the difficulty in discriminating between microenvironmental precancerous and cancer cells; and 2 the challenge in defining a precancerous microenvironment. We developed a zebrafish model that allows segregation of microenvironmental precancerous and cancerous cell populations by fluorescence activated cell sorting. This model exhibits high predilection for malignant peripheral nerve sheath tumor MPNST a type of soft tissue sarcoma that exhibits rapid aggressive growth. Using RNA seq we profiled the transcriptomes of microenvironmental cells from our zebrafish MPNST model. We show broad activation of inflammatory and immune associated signaling networks and significant upregulation of tumor promoting ligands in both precancerous and cancerous microenvironments. We also identify specific ligand receptor pairs that may promote sarcomagenesis. This work provides insight into how the microenvironment may promote MPNST initiation and progression. Overall design: N = 3 4 SAMPLES PER TREATMENT GROUP: Pre Cancerous Sox10 High Pre Cancerous Sox10 Low Control Sox10 Low Cancer Sox10 High Cancer Sox10 Low       Pre Cancerous Sox10 Low rep1 GSM5941028   source name:PreC Sox10 Low|strain:tgsox10:RFP; brca2hg5/hg5; tp53zdf1/zdf1|tissue:Precancerous Microenvironment|age:4.5 months|treatment:Sox10 Low|geo loc name:missing|collection date:missing Pre Cancerous Sox10 Low rep1 The quality of sequenced data was assessed using fastqc application and 10 poor quality bases were trimmed from the 5’ end. The remaining good quality reads were aligned to the Zebrafish reference genome danRer10 downloaded from the Ensembl database using STAR aligner. Per gene counts of uniquely mapped reads were calculated using htseq count script from the HTSeq Python package for each replicate. Gene counts were imported to R and features with at least 2 counts in 8 or more samples were retained. Zebrafish ensemble gene IDs were mapped to unique ZF  gene symbol and summed. DESeq2 was used to estimate size factors and generate normalized counts for downstream analyses as well as log2FC and adjusted pvalues for treatment comparions Assembly: danRer10 Supplementary files format and content: csv format read count PreC Sox10 Low Ocular tissues were removed enzymatically dissociated and processed by FACS RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended Zebrafish housed and maintained under standard conditions strain:tgsox10:RFP;brca2hg5/hg5;tp53zdf1/zdf1|tissue:Precancerous Microenvironment|age:4.5 months|treatment:Sox10 Low GSM5941028 GSM5941028: Pre Cancerous Sox10 Low rep1; Danio rerio; RNA Seq GSM5941028 r1 GSM5941028 1 RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP363191   loader:fastq load.py ONP1_RFPminus_S6_R2_001.fastq.gz ONP1_RFPminus_S6_R1_001.fastq.gz fastq fastq 8449095256.0 55586153.0 GSM5941028 r1 0:76 1:76 A:2285725917;C:1928716547;G:1967054415;T:2264542755;N:3055622 76 76     2285725917 1928716547 1967054415 2264542755 3055622 SRX14416134 SRS12225412 SRA1386032 Center for Human Health and the Environment (CHHE) and Bioinformatics Research Center (BRC), North Carolina State University CHHE, NCSU 2 0.92533 0.92685 0.14583 0.14304 0.72082 0.72466 0.5591 0.56338 76 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   United States 2022-03-09 Adult Adult Undetermined Undetermined
68985 68985 SRR18278285 SRX14416133 SRS12225410 SRP363191 PRJNA814235 Profiling the cancer prone microenvironment in a zebrafish model for MPNST GSE198220 Transcriptome Analysis Microenvironmental contributions to soft tissue sarcoma progression are relatively undefined particularly in the context of sarcoma onset. Use of animal models to reveal these contributions is impeded by 1 the difficulty in discriminating between microenvironmental precancerous and cancer cells; and 2 the challenge in defining a precancerous microenvironment. We developed a zebrafish model that allows segregation of microenvironmental precancerous and cancerous cell populations by fluorescence activated cell sorting. This model exhibits high predilection for malignant peripheral nerve sheath tumor MPNST a type of soft tissue sarcoma that exhibits rapid aggressive growth. Using RNA seq we profiled the transcriptomes of microenvironmental cells from our zebrafish MPNST model. We show broad activation of inflammatory and immune associated signaling networks and significant upregulation of tumor promoting ligands in both precancerous and cancerous microenvironments. We also identify specific ligand receptor pairs that may promote sarcomagenesis. This work provides insight into how the microenvironment may promote MPNST initiation and progression. Overall design: N = 3 4 SAMPLES PER TREATMENT GROUP: Pre Cancerous Sox10 High Pre Cancerous Sox10 Low Control Sox10 Low Cancer Sox10 High Cancer Sox10 Low       Pre Cancerous Sox10 High rep3 GSM5941027   source name:PreC Sox10 High|strain:tgsox10:RFP; brca2hg5/hg5; tp53zdf1/zdf1|tissue:Precancerous Cells|age:4.7 months|treatment:Sox10 High|geo loc name:missing|collection date:missing Pre Cancerous Sox10 High rep3 The quality of sequenced data was assessed using fastqc application and 10 poor quality bases were trimmed from the 5’ end. The remaining good quality reads were aligned to the Zebrafish reference genome danRer10 downloaded from the Ensembl database using STAR aligner. Per gene counts of uniquely mapped reads were calculated using htseq count script from the HTSeq Python package for each replicate. Gene counts were imported to R and features with at least 2 counts in 8 or more samples were retained. Zebrafish ensemble gene IDs were mapped to unique ZF  gene symbol and summed. DESeq2 was used to estimate size factors and generate normalized counts for downstream analyses as well as log2FC and adjusted pvalues for treatment comparions Assembly: danRer10 Supplementary files format and content: csv format read count PreC Sox10 High Ocular tissues were removed enzymatically dissociated and processed by FACS RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended Zebrafish housed and maintained under standard conditions strain:tgsox10:RFP;brca2hg5/hg5;tp53zdf1/zdf1|tissue:Precancerous Cells|age:4.7 months|treatment:Sox10 High GSM5941027 GSM5941027: Pre Cancerous Sox10 High rep3; Danio rerio; RNA Seq GSM5941027 r1 GSM5941027 1 RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP363191   loader:fastq load.py ONP3_RFPplus_S1_R1_001.fastq.gz ONP3_RFPplus_S1_R2_001.fastq.gz fastq fastq 8057004264.0 53006607.0 GSM5941027 r1 0:76 1:76 A:2152864798;C:1869556956;G:1910834804;T:2120825212;N:2922494 76 76     2152864798 1869556956 1910834804 2120825212 2922494 SRX14416133 SRS12225410 SRA1386032 Center for Human Health and the Environment (CHHE) and Bioinformatics Research Center (BRC), North Carolina State University CHHE, NCSU 2 0.74916 0.75171 0.11452 0.11138 0.74838 0.75008 0.50912 0.50906 76 76 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   United States 2022-03-09 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");;