run_metadata
239 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" and tissue_curation = "Undetermined"
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| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 14 | 14 | DRR334977 | DRX323973 | DRS217313 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 28 degrees rep 3 | SAMD00422597 | sample name:rRNA mock community 28 degrees rep 3|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:28|treatment:rRNA | NextSeq 2000 sequencing of SAMD00422597 | DRX323973 | t28 3 tRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422597 | 3791170746.0 | 37701921.0 | DRR334977 | 0:100.56 1:0 | A:967477491;C:926887571;G:898697642;T:998107868;N:174 | 100 | 0 | 967477491 | 926887571 | 898697642 | 998107868 | 174 | DRX323973 | DRS217313 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.31527 | 0.06446 | 0.88844 | 0.62118 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 15 | 15 | DRR334976 | DRX323972 | DRS217312 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 28 degrees rep 2 | SAMD00422596 | sample name:rRNA mock community 28 degrees rep 2|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:28|treatment:rRNA | NextSeq 2000 sequencing of SAMD00422596 | DRX323972 | t28 2 tRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422596 | 2801693695.0 | 27860658.0 | DRR334976 | 0:100.56 1:0 | A:700189496;C:702936549;G:679920984;T:718646067;N:599 | 100 | 0 | 700189496 | 702936549 | 679920984 | 718646067 | 599 | DRX323972 | DRS217312 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.43508 | 0.08819 | 0.85859 | 0.69447 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 16 | 16 | DRR334975 | DRX323971 | DRS217311 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 28 degrees rep 1 | SAMD00422595 | sample name:rRNA mock community 28 degrees rep 1|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:28|treatment:rRNA | NextSeq 2000 sequencing of SAMD00422595 | DRX323971 | t28 1 tRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422595 | 3148691934.0 | 31307464.0 | DRR334975 | 0:100.57 1:0 | A:785000734;C:791315678;G:766594599;T:805780465;N:458 | 100 | 0 | 785000734 | 791315678 | 766594599 | 805780465 | 458 | DRX323971 | DRS217311 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.37139 | 0.09061 | 0.94065 | 0.74047 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 17 | 17 | DRR334974 | DRX323970 | DRS217310 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 19 degrees rep 3 | SAMD00422594 | sample name:rRNA mock community 19 degrees rep 3|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:19|treatment:rRNA | NextSeq 2000 sequencing of SAMD00422594 | DRX323970 | t19 3 tRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422594 | 2856186273.0 | 28400524.0 | DRR334974 | 0:100.57 1:0 | A:695685787;C:733754277;G:715270279;T:711475544;N:386 | 100 | 0 | 695685787 | 733754277 | 715270279 | 711475544 | 386 | DRX323970 | DRS217310 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.48152 | 0.10933 | 0.87105 | 0.7287 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 18 | 18 | DRR334973 | DRX323969 | DRS217309 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 19 degrees rep 2 | SAMD00422593 | sample name:rRNA mock community 19 degrees rep 2|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:19|treatment:rRNA | NextSeq 2000 sequencing of SAMD00422593 | DRX323969 | t19 2 tRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422593 | 3199929804.0 | 31816971.0 | DRR334973 | 0:100.57 1:0 | A:777149590;C:825478743;G:804835148;T:792466124;N:199 | 100 | 0 | 777149590 | 825478743 | 804835148 | 792466124 | 199 | DRX323969 | DRS217309 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.4418 | 0.10282 | 0.89706 | 0.74667 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 19 | 19 | DRR334972 | DRX323968 | DRS217308 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 19 degrees rep 1 | SAMD00422592 | sample name:rRNA mock community 19 degrees rep 1|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:19|treatment:rRNA | NextSeq 2000 sequencing of SAMD00422592 | DRX323968 | t19 1 tRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422592 | 3658675391.0 | 36374718.0 | DRR334972 | 0:100.58 1:0 | A:879342063;C:954687406;G:929537615;T:895107890;N:417 | 100 | 0 | 879342063 | 954687406 | 929537615 | 895107890 | 417 | DRX323968 | DRS217308 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.49439 | 0.11691 | 0.88239 | 0.73925 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 20 | 20 | DRR334971 | DRX323967 | DRS217307 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 10 degrees rep 3 | SAMD00422591 | sample name:rRNA mock community 10 degrees rep 3|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:10|treatment:rRNA | NextSeq 2000 sequencing of SAMD00422591 | DRX323967 | t10 3 tRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422591 | 3017524690.0 | 30006334.0 | DRR334971 | 0:100.56 1:0 | A:771967717;C:738814269;G:712866126;T:793876235;N:343 | 100 | 0 | 771967717 | 738814269 | 712866126 | 793876235 | 343 | DRX323967 | DRS217307 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.33157 | 0.07363 | 0.9093 | 0.73422 | 100 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 21 | 21 | DRR334970 | DRX323966 | DRS217306 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 10 degrees rep 2 | SAMD00422590 | sample name:rRNA mock community 10 degrees rep 2|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:10|treatment:rRNA | NextSeq 2000 sequencing of SAMD00422590 | DRX323966 | t10 2 tRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422590 | 3115915184.0 | 30982336.0 | DRR334970 | 0:100.57 1:0 | A:765727966;C:794741415;G:771082024;T:784363609;N:170 | 100 | 0 | 765727966 | 794741415 | 771082024 | 784363609 | 170 | DRX323966 | DRS217306 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.45458 | 0.10504 | 0.89357 | 0.749 | 100 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 22 | 22 | DRR334969 | DRX323965 | DRS217305 | DRP008001 | PRJDB12578 | Allometric scaling of RNA abundance from genes to communities | DRP008001 | Other | The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes. | totalRNA metatranscriptomic sequences from mock communities consist of five model species | rRNA mock community at 10 degrees rep 1 | SAMD00422589 | sample name:rRNA mock community 10 degrees rep 1|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:10|treatment:rRNA | NextSeq 2000 sequencing of SAMD00422589 | DRX323965 | t10 1 tRNA.fastq | 1 | NEBNext Kit for Illumina | RNA-Seq | METATRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP008001 | NextSeq 2000 sequencing of SAMD00422589 | 3206657309.0 | 31883532.0 | DRR334969 | 0:100.57 1:0 | A:792874386;C:814578518;G:787469614;T:811734581;N:210 | 100 | 0 | 792874386 | 814578518 | 787469614 | 811734581 | 210 | DRX323965 | DRS217305 | DRA013226 | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica | 1 | 0.40156 | 0.09664 | 0.92898 | 0.74114 | 101 | B | usable mapping rate | illumina | nextseq_v2 | unknown | random_priming | nebnext | bulk | unknown | unknown | Taiwan | 2021-12-23 | Adult | Adult | Undetermined | Undetermined | ||||||||||||||||||||||||
| 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 | ||||||||||||||||||||||||
| 24546 | 24546 | ERR964671 | ERX1041634 | ERS792101 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484816 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484816|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 1cell|common name:zebrafish|dev stage:1cell|sample name:KI BN JKE DRERIO RNASEQ 2009 1cell|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 5 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20091014-1cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-1cell_F3_QV.qual.gz | SOLiD_native SOLiD_native | 2625510200.0 | 52510204.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 5 | 0:50 | 0:677149824;1:606769571;2:761187530;3:578170290;.:2232985 | 50 | ERX1041634 | ERS792101 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.71662 | 0.0994 | 0.91644 | 0.74578 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Zygote | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 24547 | 24547 | ERR964670 | ERX1041633 | ERS792104 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484819 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484819|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 50epiboly|common name:zebrafish|dev stage:50% epiboly|sample name:KI BN JKE DRERIO RNASEQ 2009 50epiboly|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 4 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20090709-50epiboly_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-50epiboly_F3_QV.qual.gz | SOLiD_native SOLiD_native | 5325942150.0 | 106518843.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 4 | 0:50 | 0:1376469323;1:1227617853;2:1499234750;3:1210700143;.:11920081 | 50 | ERX1041633 | ERS792104 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.7059 | 0.10511 | 0.91492 | 0.75125 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Gastrula | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 24548 | 24548 | ERR964669 | ERX1041632 | ERS792103 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484818 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484818|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 512cell|common name:zebrafish|dev stage:512 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 512cell|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 3 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20090709-512cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-512cell_F3_QV.qual.gz | SOLiD_native SOLiD_native | 5452772750.0 | 109055455.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 3 | 0:50 | 0:1391108289;1:1312099760;2:1551659810;3:1179923010;.:17981881 | 50 | ERX1041632 | ERS792103 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.73133 | 0.07897 | 0.88057 | 0.63645 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Blastula | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 24549 | 24549 | ERR964667 | ERX1041630 | ERS792101 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484816 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484816|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 1cell|common name:zebrafish|dev stage:1cell|sample name:KI BN JKE DRERIO RNASEQ 2009 1cell|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 1 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20090709-1cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-1cell_F3_QV.qual.gz | SOLiD_native SOLiD_native | 5717685400.0 | 114353708.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 1 | 0:50 | 0:1643444976;1:1261570333;2:1504304496;3:1282815913;.:25549682 | 50 | ERX1041630 | ERS792101 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.72274 | 0.11151 | 0.92348 | 0.71904 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Zygote | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 24550 | 24550 | ERR964668 | ERX1041631 | ERS792102 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484817 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484817|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 16cell|common name:zebrafish|dev stage:16 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 16cell|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 2 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20090709-16cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-16cell_F3_QV.qual.gz | SOLiD_native SOLiD_native | 5278508300.0 | 105570166.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 2 | 0:50 | 0:1410981717;1:1203936808;2:1415708111;3:1223403795;.:24477869 | 50 | ERX1041631 | ERS792102 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.71371 | 0.09346 | 0.91539 | 0.73015 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Cleavage | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 24551 | 24551 | ERR964674 | ERX1041637 | ERS792104 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484819 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484819|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 50epiboly|common name:zebrafish|dev stage:50% epiboly|sample name:KI BN JKE DRERIO RNASEQ 2009 50epiboly|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:873 8 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20091014-50epiboly_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-50epiboly_F3_QV.qual.gz | SOLiD_native SOLiD_native | 2541596650.0 | 50831933.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:873 8 | 0:50 | 0:670988333;1:585266057;2:708634642;3:574052618;.:2655000 | 50 | ERX1041637 | ERS792104 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.72135 | 0.10529 | 0.90997 | 0.76049 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Gastrula | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 24552 | 24552 | ERR964673 | ERX1041636 | ERS792103 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484818 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484818|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 512cell|common name:zebrafish|dev stage:512 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 512cell|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 7 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20091014-512cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-512cell_F3_QV.qual.gz | SOLiD_native SOLiD_native | 2027760000.0 | 40555200.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 7 | 0:50 | 0:511413081;1:492642968;2:594959353;3:426692118;.:2052480 | 50 | ERX1041636 | ERS792103 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.77106 | 0.08154 | 0.85675 | 0.64875 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Blastula | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 24553 | 24553 | ERR964672 | ERX1041635 | ERS792102 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484817 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484817|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 16cell|common name:zebrafish|dev stage:16 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 16cell|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 6 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20091014-16cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-16cell_F3_QV.qual.gz | SOLiD_native SOLiD_native | 2719433200.0 | 54388664.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 6 | 0:50 | 0:699731678;1:628745158;2:754903505;3:633574679;.:2478180 | 50 | ERX1041635 | ERS792102 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.73214 | 0.09566 | 0.90836 | 0.74043 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Cleavage | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 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 | |||||||||||||||||||||||||||||||||
| 37961 | 37961 | SRR1205174 | SRX501301 | SRS582373 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | cntl neo 5hr 3 | GSM1357182 | tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012 | cntl neo 5hr 3 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP negative cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012 | GSM1357182 | GSM1357182: cntl neo 5hr 3; Danio rerio; RNA Seq | GSM1357182 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357182 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | cntl_neo_5_3.fastq.gz | fastq | 1630216750.0 | 32604335.0 | GSM1357182 r1 | 0:50 1:0 | A:435441738;C:384703554;G:377838654;T:432163463;N:69341 | 50 | 0 | 435441738 | 384703554 | 377838654 | 432163463 | 69341 | SRX501301 | SRS582373 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93632 | 0.20492 | 0.67551 | 0.50281 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37962 | 37962 | SRR1205173 | SRX501300 | SRS582372 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | cntl neo 5hr 2 | GSM1357181 | tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012 | cntl neo 5hr 2 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP negative cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012 | GSM1357181 | GSM1357181: cntl neo 5hr 2; Danio rerio; RNA Seq | GSM1357181 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357181 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | cntl_neo_5_2.fastq.gz | fastq | 1812797550.0 | 36255951.0 | GSM1357181 r1 | 0:50 1:0 | A:484800524;C:426109547;G:417833682;T:483968870;N:84927 | 50 | 0 | 484800524 | 426109547 | 417833682 | 483968870 | 84927 | SRX501300 | SRS582372 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93602 | 0.21513 | 0.67517 | 0.49404 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37963 | 37963 | SRR1205172 | SRX501299 | SRS582371 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | cntl neo 5hr 1 | GSM1357180 | tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012 | cntl neo 5hr 1 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP negative cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012 | GSM1357180 | GSM1357180: cntl neo 5hr 1; Danio rerio; RNA Seq | GSM1357180 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357180 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | cntl_neo_5_1.fastq.gz | fastq | 1616736500.0 | 32334730.0 | GSM1357180 r1 | 0:50 1:0 | A:425328931;C:388105733;G:379129548;T:424100489;N:71799 | 50 | 0 | 425328931 | 388105733 | 379129548 | 424100489 | 71799 | SRX501299 | SRS582371 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.9361 | 0.23516 | 0.68091 | 0.50961 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37964 | 37964 | SRR1205171 | SRX501298 | SRS582370 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | gfp neo 5hr 3 | GSM1357179 | tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012 | gfp neo 5hr 3 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP positive cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012 | GSM1357179 | GSM1357179: gfp neo 5hr 3; Danio rerio; RNA Seq | GSM1357179 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357179 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | gfp_neo_5_3.fastq.gz | fastq | 1856512100.0 | 37130242.0 | GSM1357179 r1 | 0:50 1:0 | A:492227117;C:440944515;G:431529818;T:491731276;N:79374 | 50 | 0 | 492227117 | 440944515 | 431529818 | 491731276 | 79374 | SRX501298 | SRS582370 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93677 | 0.28732 | 0.71435 | 0.50496 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37965 | 37965 | SRR1205170 | SRX501297 | SRS582369 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | gfp neo 5hr 2 | GSM1357178 | tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012 | gfp neo 5hr 2 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP positive cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012 | GSM1357178 | GSM1357178: gfp neo 5hr 2; Danio rerio; RNA Seq | GSM1357178 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357178 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | gfp_neo_5_2.fastq.gz | fastq | 1605154400.0 | 32103088.0 | GSM1357178 r1 | 0:50 1:0 | A:431076570;C:373656204;G:367046732;T:433299718;N:75176 | 50 | 0 | 431076570 | 373656204 | 367046732 | 433299718 | 75176 | SRX501297 | SRS582369 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93022 | 0.29198 | 0.69656 | 0.47675 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37966 | 37966 | SRR1205169 | SRX501296 | SRS582368 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | gfp neo 5hr 1 | GSM1357177 | tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012 | gfp neo 5hr 1 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP positive cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012 | GSM1357177 | GSM1357177: gfp neo 5hr 1; Danio rerio; RNA Seq | GSM1357177 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357177 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | gfp_neo_5_1.fastq.gz | fastq | 1902899900.0 | 38057998.0 | GSM1357177 r1 | 0:50 1:0 | A:511489376;C:443148505;G:433716076;T:514461324;N:84619 | 50 | 0 | 511489376 | 443148505 | 433716076 | 514461324 | 84619 | SRX501296 | SRS582368 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.92977 | 0.29647 | 0.69583 | 0.48582 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37967 | 37967 | SRR1205168 | SRX501295 | SRS582367 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | cntl neo 3hr 3 | GSM1357176 | tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012 | cntl neo 3hr 3 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP negative cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012 | GSM1357176 | GSM1357176: cntl neo 3hr 3; Danio rerio; RNA Seq | GSM1357176 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357176 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | cntl_neo_3_3.fastq.gz | fastq | 1555198750.0 | 31103975.0 | GSM1357176 r1 | 0:50 1:0 | A:416734314;C:365733903;G:359113904;T:413549150;N:67479 | 50 | 0 | 416734314 | 365733903 | 359113904 | 413549150 | 67479 | SRX501295 | SRS582367 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93432 | 0.21789 | 0.67363 | 0.49063 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37968 | 37968 | SRR1205167 | SRX501294 | SRS582366 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | cntl neo 3hr 2 | GSM1357175 | tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012 | cntl neo 3hr 2 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP negative cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012 | GSM1357175 | GSM1357175: cntl neo 3hr 2; Danio rerio; RNA Seq | GSM1357175 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357175 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | cntl_neo_3_2.fastq.gz | fastq | 1701011300.0 | 34020226.0 | GSM1357175 r1 | 0:50 1:0 | A:453767169;C:401144167;G:392795706;T:453224665;N:79593 | 50 | 0 | 453767169 | 401144167 | 392795706 | 453224665 | 79593 | SRX501294 | SRS582366 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93437 | 0.19214 | 0.66884 | 0.48995 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37969 | 37969 | SRR1205166 | SRX501293 | SRS582365 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | cntl neo 3hr 1 | GSM1357174 | tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012 | cntl neo 3hr 1 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP negative cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012 | GSM1357174 | GSM1357174: cntl neo 3hr 1; Danio rerio; RNA Seq | GSM1357174 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357174 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | cntl_neo_3_1.fastq.gz | fastq | 1228792200.0 | 24575844.0 | GSM1357174 r1 | 0:50 1:0 | A:328509222;C:288306723;G:283185002;T:328736353;N:54900 | 50 | 0 | 328509222 | 288306723 | 283185002 | 328736353 | 54900 | SRX501293 | SRS582365 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93269 | 0.21003 | 0.66592 | 0.48875 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37970 | 37970 | SRR1205165 | SRX501292 | SRS582364 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | gfp neo 3hr 3 | GSM1357173 | tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012 | gfp neo 3hr 3 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP positive cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012 | GSM1357173 | GSM1357173: gfp neo 3hr 3; Danio rerio; RNA Seq | GSM1357173 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357173 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | gfp_neo_3_3.fastq.gz | fastq | 1406657700.0 | 28133154.0 | GSM1357173 r1 | 0:50 1:0 | A:379997165;C:326224852;G:320555458;T:379818406;N:61819 | 50 | 0 | 379997165 | 326224852 | 320555458 | 379818406 | 61819 | SRX501292 | SRS582364 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.9327 | 0.3167 | 0.70709 | 0.48722 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37971 | 37971 | SRR1205164 | SRX501291 | SRS582363 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | gfp neo 3hr 2 | GSM1357172 | tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012 | gfp neo 3hr 2 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP positive cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012 | GSM1357172 | GSM1357172: gfp neo 3hr 2; Danio rerio; RNA Seq | GSM1357172 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357172 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | gfp_neo_3_2.fastq.gz | fastq | 1409177900.0 | 28183558.0 | GSM1357172 r1 | 0:50 1:0 | A:377366991;C:329654609;G:322942817;T:379147506;N:65977 | 50 | 0 | 377366991 | 329654609 | 322942817 | 379147506 | 65977 | SRX501291 | SRS582363 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.92559 | 0.27573 | 0.69968 | 0.48668 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37972 | 37972 | SRR1205163 | SRX501290 | SRS582362 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | gfp neo 3hr 1 | GSM1357171 | tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012 | gfp neo 3hr 1 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP positive cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012 | GSM1357171 | GSM1357171: gfp neo 3hr 1; Danio rerio; RNA Seq | GSM1357171 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357171 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | gfp_neo_3_1.fastq.gz | fastq | 1364255100.0 | 27285102.0 | GSM1357171 r1 | 0:50 1:0 | A:367031933;C:317262942;G:311363762;T:368536308;N:60155 | 50 | 0 | 367031933 | 317262942 | 311363762 | 368536308 | 60155 | SRX501290 | SRS582362 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93433 | 0.34822 | 0.70504 | 0.49052 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37973 | 37973 | SRR1205162 | SRX501289 | SRS582361 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | gfp nt 1hr 3 | GSM1357170 | tissue:GFP positive cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012 | gfp nt 1hr 3 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP positive cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012 | GSM1357170 | GSM1357170: gfp nt 1hr 3; Danio rerio; RNA Seq | GSM1357170 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357170 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | gfp_nt_1_3.fastq.gz | fastq | 2032585500.0 | 40651710.0 | GSM1357170 r1 | 0:50 1:0 | A:540423336;C:478257444;G:470055372;T:543729414;N:119934 | 50 | 0 | 540423336 | 478257444 | 470055372 | 543729414 | 119934 | SRX501289 | SRS582361 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93511 | 0.2696 | 0.70425 | 0.49291 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37974 | 37974 | SRR1205161 | SRX501288 | SRS582360 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | gfp nt 1hr 2 | GSM1357169 | tissue:GFP positive cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012 | gfp nt 1hr 2 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP positive cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012 | GSM1357169 | GSM1357169: gfp nt 1hr 2; Danio rerio; RNA Seq | GSM1357169 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357169 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | gfp_nt_1_2.fastq.gz | fastq | 1562346650.0 | 31246933.0 | GSM1357169 r1 | 0:50 1:0 | A:414164641;C:369142355;G:361974997;T:416978503;N:86154 | 50 | 0 | 414164641 | 369142355 | 361974997 | 416978503 | 86154 | SRX501288 | SRS582360 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93897 | 0.31695 | 0.70991 | 0.50448 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37975 | 37975 | SRR1205160 | SRX501287 | SRS582359 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | gfp nt 1hr 1 | GSM1357168 | tissue:GFP positive cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012 | gfp nt 1hr 1 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP positive cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012 | GSM1357168 | GSM1357168: gfp nt 1hr 1; Danio rerio; RNA Seq | GSM1357168 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357168 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | gfp_nt_1_1.fastq.gz | fastq | 1689050050.0 | 33781001.0 | GSM1357168 r1 | 0:50 1:0 | A:453271567;C:394505701;G:386090706;T:455068897;N:113179 | 50 | 0 | 453271567 | 394505701 | 386090706 | 455068897 | 113179 | SRX501287 | SRS582359 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93627 | 0.28408 | 0.70585 | 0.48065 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37976 | 37976 | SRR1205159 | SRX501286 | SRS582358 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | gfp neo 1hr 3 | GSM1357167 | tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012 | gfp neo 1hr 3 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP positive cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012 | GSM1357167 | GSM1357167: gfp neo 1hr 3; Danio rerio; RNA Seq | GSM1357167 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357167 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | gfp_neo_1_3.fastq.gz | fastq | 1611919200.0 | 32238384.0 | GSM1357167 r1 | 0:50 1:0 | A:428150047;C:380113504;G:372605259;T:430955158;N:95232 | 50 | 0 | 428150047 | 380113504 | 372605259 | 430955158 | 95232 | SRX501286 | SRS582358 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.94024 | 0.31287 | 0.71601 | 0.50103 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37977 | 37977 | SRR1205158 | SRX501285 | SRS582357 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | gfp neo 1hr 2 | GSM1357166 | tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012 | gfp neo 1hr 2 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP positive cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012 | GSM1357166 | GSM1357166: gfp neo 1hr 2; Danio rerio; RNA Seq | GSM1357166 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357166 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | gfp_neo_1_2.fastq.gz | fastq | 1653679950.0 | 33073599.0 | GSM1357166 r1 | 0:50 1:0 | A:439492851;C:388625865;G:381772828;T:443698911;N:89495 | 50 | 0 | 439492851 | 388625865 | 381772828 | 443698911 | 89495 | SRX501285 | SRS582357 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.94345 | 0.38847 | 0.7357 | 0.50373 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37978 | 37978 | SRR1205157 | SRX501284 | SRS582356 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | gfp neo 1hr 1 | GSM1357165 | tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012 | gfp neo 1hr 1 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP positive cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012 | GSM1357165 | GSM1357165: gfp neo 1hr 1; Danio rerio; RNA Seq | GSM1357165 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357165 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | gfp_neo_1_1.fastq.gz | fastq | 1873022200.0 | 37460444.0 | GSM1357165 r1 | 0:50 1:0 | A:501397145;C:438845045;G:428481612;T:504171995;N:126403 | 50 | 0 | 501397145 | 438845045 | 428481612 | 504171995 | 126403 | SRX501284 | SRS582356 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.933 | 0.24769 | 0.70591 | 0.50587 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37979 | 37979 | SRR1205156 | SRX501283 | SRS582355 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | cntl nt 1hr 3 | GSM1357164 | tissue:GFP negative cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012 | cntl nt 1hr 3 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP negative cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012 | GSM1357164 | GSM1357164: cntl nt 1hr 3; Danio rerio; RNA Seq | GSM1357164 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357164 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | cntl_nt_1_3.fastq.gz | fastq | 1523970250.0 | 30479405.0 | GSM1357164 r1 | 0:50 1:0 | A:404458518;C:360948466;G:353690676;T:404782977;N:89613 | 50 | 0 | 404458518 | 360948466 | 353690676 | 404782977 | 89613 | SRX501283 | SRS582355 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93995 | 0.21232 | 0.66772 | 0.48499 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37980 | 37980 | SRR1205155 | SRX501282 | SRS582354 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | cntl nt 1hr 2 | GSM1357163 | tissue:GFP negative cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012 | cntl nt 1hr 2 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP negative cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012 | GSM1357163 | GSM1357163: cntl nt 1hr 2; Danio rerio; RNA Seq | GSM1357163 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357163 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | cntl_nt_1_2.fastq.gz | fastq | 1649622150.0 | 32992443.0 | GSM1357163 r1 | 0:50 1:0 | A:434980357;C:392949654;G:385359402;T:436242531;N:90206 | 50 | 0 | 434980357 | 392949654 | 385359402 | 436242531 | 90206 | SRX501282 | SRS582354 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.94128 | 0.24395 | 0.67549 | 0.50787 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37981 | 37981 | SRR1205154 | SRX501281 | SRS582353 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | cntl nt 1hr 1 | GSM1357162 | tissue:GFP negative cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012 | cntl nt 1hr 1 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP negative cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012 | GSM1357162 | GSM1357162: cntl nt 1hr 1; Danio rerio; RNA Seq | GSM1357162 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357162 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | cntl_nt_1_1.fastq.gz | fastq | 1953710600.0 | 39074212.0 | GSM1357162 r1 | 0:50 1:0 | A:518489677;C:462970545;G:452495723;T:519623507;N:131148 | 50 | 0 | 518489677 | 462970545 | 452495723 | 519623507 | 131148 | SRX501281 | SRS582353 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93818 | 0.2175 | 0.66229 | 0.50468 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37982 | 37982 | SRR1205153 | SRX501280 | SRS582352 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | cntl neo 1hr 3 | GSM1357161 | tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012 | cntl neo 1hr 3 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP negative cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012 | GSM1357161 | GSM1357161: cntl neo 1hr 3; Danio rerio; RNA Seq | GSM1357161 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357161 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | cntl_neo_1_3.fastq.gz | fastq | 1934085200.0 | 38681704.0 | GSM1357161 r1 | 0:50 1:0 | A:513203802;C:458221455;G:449581302;T:512967391;N:111250 | 50 | 0 | 513203802 | 458221455 | 449581302 | 512967391 | 111250 | SRX501280 | SRS582352 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93811 | 0.22613 | 0.66671 | 0.49681 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37983 | 37983 | SRR1205152 | SRX501279 | SRS582351 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | cntl neo 1hr 2 | GSM1357160 | tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012 | cntl neo 1hr 2 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP negative cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012 | GSM1357160 | GSM1357160: cntl neo 1hr 2; Danio rerio; RNA Seq | GSM1357160 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357160 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | cntl_neo_1_2.fastq.gz | fastq | 1836127900.0 | 36722558.0 | GSM1357160 r1 | 0:50 1:0 | A:485828745;C:436091545;G:426562682;T:487543575;N:101353 | 50 | 0 | 485828745 | 436091545 | 426562682 | 487543575 | 101353 | SRX501279 | SRS582351 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93856 | 0.23223 | 0.67154 | 0.5021 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 37984 | 37984 | SRR1205151 | SRX501278 | SRS582350 | SRP040561 | PRJNA242641 | Gene expression analysis of hair cell regeneration in the zebrafish lateral line | GSE56176 | Transcriptome Analysis | Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples. | pubmed:24706903 | cntl neo 1hr 1 | GSM1357159 | tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012 | cntl neo 1hr 1 | Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene. | GFP negative cells from 5 dpf larvae | For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time. | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope. | drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012 | GSM1357159 | GSM1357159: cntl neo 1hr 1; Danio rerio; RNA Seq | GSM1357159 | 1 | Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies. | GEO Accession:GSM1357159 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP040561 | loader:latf load | cntl_neo_1_1.fastq.gz | fastq | 1687481850.0 | 33749637.0 | GSM1357159 r1 | 0:50 1:0 | A:448529802;C:398804686;G:391019451;T:449013498;N:114413 | 50 | 0 | 448529802 | 398804686 | 391019451 | 449013498 | 114413 | SRX501278 | SRS582350 | SRA149178 | GEO | Seidel, Genomics, Stowers Institute | 1 | 0.93698 | 0.21557 | 0.66436 | 0.49756 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-03-25 | Multi-stage | Multi-stage | Undetermined | Undetermined | |||||||||||||||
| 41420 | 41420 | SRR4423116 | SRX2245300 | SRS1745858 | SRP091534 | PRJNA347637 | Danio rerio and Xenopus laevis Raw sequence reads | PRJNA347637 | Other | To study the transcriptome during development | egg pools from three different mothers | Egg pool Dr | strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Egg|sex:not applicable|tissue:eggs|BioSampleModel:Model organism or animal | miRNA Seq of Zebrafish: Egg pool | 94 4 | 94 4 | Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol. | miRNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent Proton | SRP091534 | eggRID0094BC04smallZF.fastq | fastq | 1392075126.0 | 18333358.0 | eggRID0094BC04smallZF.fastq | 0:75.93 | A:323480979;C:386272283;G:377777594;T:304544270;N:0 | 75 | 323480979 | 386272283 | 377777594 | 304544270 | 0 | SRX2245300 | SRS1745858 | SRA485147 | Universiteit van Amsterdam|SILS | Universiteit van Amsterdam | 1 | 0.68028 | 0.1685 | 0.89982 | 0.84521 | 83 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | small_rna | unknown | bulk | unknown | unknown | Netherlands | 2016-10-19 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 41422 | 41422 | SRR4423114 | SRX2245298 | SRS1745858 | SRP091534 | PRJNA347637 | Danio rerio and Xenopus laevis Raw sequence reads | PRJNA347637 | Other | To study the transcriptome during development | egg pools from three different mothers | Egg pool Dr | strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Egg|sex:not applicable|tissue:eggs|BioSampleModel:Model organism or animal | RNA Seq of Zebrafish: Egg pool | 99 6 | 99 6 | Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent Proton | SRP091534 | eggRID0099BC06LargeZF.fastq | fastq | 4454090954.0 | 48098559.0 | eggRID0099BC06LargeZF.fastq | 0:92.60 | A:1084275872;C:1151665265;G:1338679196;T:879470621;N:0 | 92 | 1084275872 | 1151665265 | 1338679196 | 879470621 | 0 | SRX2245298 | SRS1745858 | SRA485147 | Universiteit van Amsterdam|SILS | Universiteit van Amsterdam | 1 | 0.91346 | 0.27222 | 0.96694 | 0.91118 | 144 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Netherlands | 2016-10-19 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 41424 | 41424 | SRR4423112 | SRX2245296 | SRS1745858 | SRP091534 | PRJNA347637 | Danio rerio and Xenopus laevis Raw sequence reads | PRJNA347637 | Other | To study the transcriptome during development | egg pools from three different mothers | Egg pool Dr | strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Egg|sex:not applicable|tissue:eggs|BioSampleModel:Model organism or animal | miRNA Seq of Zebrafish: Egg pool | 88 4 | 88 4 | Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol. | miRNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent Proton | SRP091534 | eggRID0088BC04smallZF.fastq | fastq | 1063934659.0 | 14422089.0 | eggRID0088BC04smallZF.fastq | 0:73.77 | A:248885216;C:293368431;G:288043879;T:233637133;N:0 | 73 | 248885216 | 293368431 | 288043879 | 233637133 | 0 | SRX2245296 | SRS1745858 | SRA485147 | Universiteit van Amsterdam|SILS | Universiteit van Amsterdam | 1 | 0.66115 | 0.18031 | 0.89546 | 0.78468 | 72 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | small_rna | unknown | bulk | unknown | unknown | Netherlands | 2016-10-19 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 41426 | 41426 | SRR4423110 | SRX2245294 | SRS1745858 | SRP091534 | PRJNA347637 | Danio rerio and Xenopus laevis Raw sequence reads | PRJNA347637 | Other | To study the transcriptome during development | egg pools from three different mothers | Egg pool Dr | strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Egg|sex:not applicable|tissue:eggs|BioSampleModel:Model organism or animal | miRNA Seq of Zebrafish: Egg pool | 93 4 | 93 4 | Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol. | miRNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent Proton | SRP091534 | eggRID0093BC04smallZF.fastq | fastq | 1382951404.0 | 18190154.0 | eggRID0093BC04smallZF.fastq | 0:76.03 | A:322536095;C:383176934;G:374216039;T:303022336;N:0 | 76 | 322536095 | 383176934 | 374216039 | 303022336 | 0 | SRX2245294 | SRS1745858 | SRA485147 | Universiteit van Amsterdam|SILS | Universiteit van Amsterdam | 1 | 0.66399 | 0.17461 | 0.90134 | 0.82432 | 156 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | small_rna | unknown | bulk | unknown | unknown | Netherlands | 2016-10-19 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 50533 | 50533 | SRR8129704 | SRX4950826 | SRS3993016 | SRP167139 | PRJNA499073 | Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes | GSE121917 | Transcriptome Analysis | We provide a method for high quality RNA purification out of a small number 5000 100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo. | pubmed:30894119 | RNeasy sorted 2 | GSM3449965 | tissue:Fli:GFP sorted 3 days RNeasy sample 1|cell type:fli:GFP GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit | RNeasy sorted 2 | Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data | Fli:GFP sorted 3 days RNeasy sample 1 | polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina | cell type:fli:GFP GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit | GSM3449965 | GSM3449965: RNeasy sorted 2; Danio rerio; RNA Seq | GSM3449965 | 1 | polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina | GEO Accession:GSM3449965 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP167139 | Q_1.fastq.gz | fastq | 1059463914.0 | 14029229.0 | GSM3449965 r1 | 0:75.52 1:0 | A:284634446;C:242976410;G:245781627;T:286026099;N:45332 | 75 | 0 | 284634446 | 242976410 | 245781627 | 286026099 | 45332 | SRX4950826 | SRS3993016 | SRA800291 | GEO | Center for Medical Genetics, Ghent University | 1 | 0.91903 | 0.09754 | 0.73537 | 0.48738 | 76 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | nextera | sc | single_cell_plate | smartseq | Belgium | 2018-10-29 | Larval | Larval | Undetermined | Undetermined | ||||||||||||||||||
| 50534 | 50534 | SRR8129703 | SRX4950825 | SRS3993017 | SRP167139 | PRJNA499073 | Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes | GSE121917 | Transcriptome Analysis | We provide a method for high quality RNA purification out of a small number 5000 100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo. | pubmed:30894119 | RNAqueous sorted 1 | GSM3449964 | tissue:Fli:GFP sorted 3 days RNAqueous sample 1|cell type:fli:GFP GFP sorted|age:3 days|rna isolation kit:RNAqueous micro | RNAqueous sorted 1 | Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data | Fli:GFP sorted 3 days RNAqueous sample 1 | polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina | cell type:fli:GFP GFP sorted|age:3 days|rna isolation kit:RNAqueous micro | GSM3449964 | GSM3449964: RNAqueous sorted 1; Danio rerio; RNA Seq | GSM3449964 | 1 | polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina | GEO Accession:GSM3449964 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP167139 | A_1.fastq.gz | fastq | 1477268521.0 | 19562904.0 | GSM3449964 r1 | 0:75.51 1:0 | A:399601730;C:333778207;G:337372866;T:406448608;N:67110 | 75 | 0 | 399601730 | 333778207 | 337372866 | 406448608 | 67110 | SRX4950825 | SRS3993017 | SRA800291 | GEO | Center for Medical Genetics, Ghent University | 1 | 0.90617 | 0.09373 | 0.74558 | 0.49316 | 76 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | nextera | sc | single_cell_plate | smartseq | Belgium | 2018-10-29 | Larval | Larval | 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");;