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124 rows where experiment.library_layout = "SINGLE" and experiment.library_selection = "RT-PCR"

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tissue_curation >10

devstage_curation_coarse 6

devstage_curation 6

experiment.platform 3

experiment.library_strategy 3

technology 1

experiment.library_source 1

experiment.library_selection 1

  • RT-PCR · 124 ✖

experiment.library_layout 1

  • SINGLE · 124 ✖
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
282 282 DRR179616 DRX170142 DRS185505 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 2 Fin xanthophore 03 SAMD00172019   sample name:Zebrafish pigment cell 06|cell type:Xanthophore|collection date:2015 11 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172019 DRX170142 Zebrafish fin xanthophore 01 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>232</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP007318 Ion Torrent PGM sequencing of SAMD00172019       376558775.0 1624500.0 DRR179616 0:231.80 A:107837072;C:79508449;G:79372899;T:109840355;N:0 231       107837072 79508449 79372899 109840355 0 DRX170142 DRS185505 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.86944   0.10951   0.90425   0.59385   311   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
283 283 DRR179615 DRX170141 DRS185504 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 1 Fin xanthophore 02 SAMD00172018   sample name:Zebrafish pigment cell 05|cell type:Xanthophore|collection date:2015 09 10|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172018 DRX170141 Zebrafish fin xanthophore 01 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>243</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP007318 Ion Torrent PGM sequencing of SAMD00172018       515115515.0 2124170.0 DRR179615 0:242.50 A:138421982;C:119032803;G:119412227;T:138248503;N:0 242       138421982 119032803 119412227 138248503 0 DRX170141 DRS185504 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.88998   0.05858   0.88051   0.50917   284   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
284 284 DRR179614 DRX170140 DRS185503 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 1 Fin xanthophore 01 SAMD00172017   sample name:Zebrafish pigment cell 04|cell type:Xanthophore|collection date:2015 09 10|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172017 DRX170140 Zebrafish fin xanthophore 01 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>247</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP007318 Ion Torrent PGM sequencing of SAMD00172017       371242152.0 1504407.0 DRR179614 0:246.77 A:99341086;C:86126839;G:86264882;T:99509345;N:0 246       99341086 86126839 86264882 99509345 0 DRX170140 DRS185503 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.88672   0.06422   0.85679   0.5066   56   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
285 285 DRR179613 DRX170139 DRS185502 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 2 Fin melanophore 03 SAMD00172016   sample name:Zebrafish pigment cell 03|cell type:Melanophore|collection date:2015 11 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172016 DRX170139 Zebrafish fin melanophore 03 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>248</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP007318 Ion Torrent PGM sequencing of SAMD00172016       342802993.0 1585538.0 DRR179613 0:216.21 A:90833658;C:80789744;G:80463233;T:90716358;N:0 216       90833658 80789744 80463233 90716358 0 DRX170139 DRS185502 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.8312   0.03528   0.88605   0.47299   285   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
286 286 DRR179612 DRX170138 DRS185501 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 1 Fin melanophore 02 SAMD00172015   sample name:Zebrafish pigment cell 02|cell type:Melanophore|collection date:2015 05 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172015 DRX170138 Zebrafish fin melanophore 02 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>216</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP007318 Ion Torrent PGM sequencing of SAMD00172015       538412675.0 2168231.0 DRR179612 0:248.32 A:147128403;C:121854818;G:121564109;T:147865345;N:0 248       147128403 121854818 121564109 147865345 0 DRX170138 DRS185501 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.89106   0.07081   0.89286   0.5935   283   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
287 287 DRR179611 DRX170137 DRS185500 DRP007318 PRJDB8340 Gene expression analysis of zebrafish fin melanophores and xanthophores. DRP007318 Other Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.     Biological replicate 1 Fin melanophore 01 SAMD00172014   sample name:Zebrafish pigment cell 01|cell type:Melanophore|collection date:2015 05 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin                 Ion Torrent PGM sequencing of SAMD00172014 DRX170137 Zebrafish fin melanophore 01 1 1   RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>215</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP007318 Ion Torrent PGM sequencing of SAMD00172014       282446840.0 1311431.0 DRR179611 0:215.37 A:74927237;C:66575483;G:66161471;T:74782649;N:0 215       74927237 66575483 66161471 74782649 0 DRX170137 DRS185500 DRA008445 OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University 1 0.85938   0.0335   0.89248   0.58813   274   B   usable mapping rate ion_torrent ion_torrent full_length other smarter bulk unknown unknown   Japan 2021-05-21 Adult Adult Fin Surface Structure
30599 30599 SRR27865238 SRX23527802 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 con MO 6 6 con MO     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     con-KDM_1.fq.gz con-KDM_2.fq.gz fastq fastq 7088132100.0 23627107.0 con KDM 1.fq.gz 0:150 1:150 A:1893419600;C:1649526065;G:1662549202;T:1882459200;N:178033 150 150     1893419600 1649526065 1662549202 1882459200 178033 SRX23527802 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30600 30600 SRR27865239 SRX23527801 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 KDM4C MO 5 5 KDM4C MO     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     KDM-MO_1.fq.gz KDM-MO_2.fq.gz fastq fastq 7876840500.0 26256135.0 KDM MO 1.fq.gz 0:150 1:150 A:2104173142;C:1831662159;G:1843980192;T:2096831538;N:193469 150 150     2104173142 1831662159 1843980192 2096831538 193469 SRX23527801 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30601 30601 SRR27865240 SRX23527800 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 ZNF662 MO 4 4 ZNF662 MO     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     znf547-MO_1.fq.gz znf547-MO_2.fq.gz fastq fastq 7573815300.0 25246051.0 znf547 MO 1.fq.gz 0:150 1:150 A:2014197761;C:1766587259;G:1782217029;T:2010540623;N:272628 150 150     2014197761 1766587259 1782217029 2010540623 272628 SRX23527800 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30602 30602 SRR27865241 SRX23527799 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 SEMA5A RNA 3 3 SEMA5A RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     semRNA_1.fq.gz semRNA_2.fq.gz fastq fastq 5575566000.0 18585220.0 semRNA 1.fq.gz 0:150 1:150 A:1456001758;C:1325628099;G:1339796989;T:1454076989;N:62165 150 150     1456001758 1325628099 1339796989 1454076989 62165 SRX23527799 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30603 30603 SRR27865242 SRX23527798 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 MT ATP6 RNA 2 2 MT ATP6 RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     ATP6-RNA_1.fq.gz ATP6-RNA_2.fq.gz fastq fastq 5437771200.0 18125904.0 ATP6 RNA 1.fq.gz 0:150 1:150 A:1438540045;C:1272310670;G:1290121053;T:1436739799;N:59633 150 150     1438540045 1272310670 1290121053 1436739799 59633 SRX23527798 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30604 30604 SRR27865243 SRX23527797 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 con RNA 1 1 con RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     con-RNA_1.fq.gz con-RNA_2.fq.gz fastq fastq 6733158900.0 22443863.0 con RNA 1.fq.gz 0:150 1:150 A:1766014369;C:1595337569;G:1610127771;T:1761604971;N:74220 150 150     1766014369 1595337569 1610127771 1761604971 74220 SRX23527797 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
33326 33326 SRR29962931 SRX25444536 SRS22101407 SRP521963 PRJNA1139824 Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq PRJNA1139824 Other Toxicity of sine wave on early zebrafish embryo development       Embryos m6A transcriptome Embryos m6A transcriptome of SW   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 zx150 RNAseq 4 4 zx150 RNAseq     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP521963     zx150_input_1.fq.gz zx150_input_2.fq.gz fastq fastq 11540682300.0 38468941.0 zx150 input 1.fq.gz 0:150 1:150 A:3038586049;C:2720235923;G:2771004747;T:3010645578;N:210003 150 150     3038586049 2720235923 2771004747 3010645578 210003 SRX25444536 SRS22101407 SRA1931991 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-07-24 Blastula Embryo Embryo Imprecise All anatomical structures
33327 33327 SRR29962932 SRX25444535 SRS22101407 SRP521963 PRJNA1139824 Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq PRJNA1139824 Other Toxicity of sine wave on early zebrafish embryo development       Embryos m6A transcriptome Embryos m6A transcriptome of SW   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 con RNAseq 3 3 con RNAseq     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP521963     con-zx150_input_1.fq.gz con-zx150_input_2.fq.gz fastq fastq 11610174300.0 38700581.0 con zx150 input 1.fq.gz 0:150 1:150 A:3049654977;C:2746004045;G:2795023766;T:3019280685;N:210827 150 150     3049654977 2746004045 2795023766 3019280685 210827 SRX25444535 SRS22101407 SRA1931991 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-07-24 Blastula Embryo Embryo Imprecise All anatomical structures
33328 33328 SRR29962933 SRX25444534 SRS22101407 SRP521963 PRJNA1139824 Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq PRJNA1139824 Other Toxicity of sine wave on early zebrafish embryo development       Embryos m6A transcriptome Embryos m6A transcriptome of SW   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 zx150 m6A 2 2 zx150 m6A     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP521963     zx150_IP_1.fq.gz zx150_IP_2.fq.gz fastq fastq 17410816801.0 80469610.0 zx150 IP 1.fq.gz 0:108.79 1:107.58 A:4434870667;C:3759430468;G:4812205613;T:4404166470;N:143583 108 107     4434870667 3759430468 4812205613 4404166470 143583 SRX25444534 SRS22101407 SRA1931991 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-07-24 Blastula Embryo Embryo Imprecise All anatomical structures
33329 33329 SRR29962934 SRX25444533 SRS22101407 SRP521963 PRJNA1139824 Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq PRJNA1139824 Other Toxicity of sine wave on early zebrafish embryo development       Embryos m6A transcriptome Embryos m6A transcriptome of SW   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 con m6A 1 1 con m6A     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP521963     con-zx150_IP_1.fq.gz con-zx150_IP_2.fq.gz fastq fastq 16822889423.0 77865752.0 con zx150 IP 1.fq.gz 0:108.68 1:107.37 A:4324048234;C:3668630618;G:4601614069;T:4228151501;N:445001 108 107     4324048234 3668630618 4601614069 4228151501 445001 SRX25444533 SRS22101407 SRA1931991 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-07-24 Blastula Embryo Embryo Imprecise All anatomical structures
36504 36504 SRR535848 SRX174964 SRS352998 SRP014772 PRJNA172016 Danio rerio strain:*AB Variation PRJNA172016 Other Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life however identifying the causal mutations from such screens has long been the bottleneck in the process particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons alter transcript splicing or alter gene expression levels. Furthermore we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall we show that RNA Seq is a fast reliable and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.     RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data hox20 was created from 20 pooled hoxb1bb1219 fish that were the siblings of wt20. Miller hox20.bam Miller hox20.bam                     Miller hox20.bam Miller hox20.bam 1 50 bp Paired End     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>180</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> SRP014772     hox20.bam bam 2051648571.0 22151528.0 Miller hox20.bam 0:49 1:49 A:528770281;C:501621137;G:487051170;T:534176088;N:29895 49 49     528770281 501621137 487051170 534176088 29895 SRX174964 SRS352998 SRA056859 Fred Hutchinson Cancer Research Center|Moens Fred Hutchinson Cancer Research Center 2 0.9629 0.96282 0.07314 0.07288 0.6714 0.67125 0.4665 0.4637 49 49 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2012-11-30 Undetermined Undetermined Undetermined Undetermined
36663 36663 SRR800049 SRX257156 SRS405710 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio sphere RNAseq 5azaCyD control   strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere                 sphere RNAseq 5azaCyD control sphere RNAseq 5azaCyD control 9323X2 1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP020008     sphere_RNAseq_5azaCyD_control_SE_9323X2_120628_SN141_0513_AD12CFACXX_4.txt.gz Illumina native 2563410950.0 51268219.0 9323X2 120628 SN141 0513 AD12CFACXX 4 0:50 A:663337120;C:603101927;G:752336300;T:542924123;N:1711480 50       663337120 603101927 752336300 542924123 1711480 SRX257156 SRS405710 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.65713   0.09976   0.81677   0.81063   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2013-05-07 Blastula Embryo Embryo Imprecise All anatomical structures
36664 36664 SRR800046 SRX257155 SRS405709 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio sphere RNAseq 5azaCyD treatment   strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere                 sphere RNAseq 5azaCyD treatment sphere RNAseq 5azaCyD treatment 9323X1 1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP020008     sphere_RNAseq_5azaCyD_treatment_SE_9323X1_120628_SN141_0513_AD12CFACXX_4.txt.gz Illumina native 2595654550.0 51913091.0 9323X1 120628 SN141 0513 AD12CFACXX 4 0:50 A:676999669;C:618386951;G:759497082;T:539035799;N:1735049 50       676999669 618386951 759497082 539035799 1735049 SRX257155 SRS405709 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.76926   0.12287   0.82408   0.72244   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2013-04-03 Blastula Embryo Embryo Imprecise All anatomical structures
36665 36665 SRR800045 SRX257154 SRS405708 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio muscle RNAseq totalRNARibominus   strain:Tubingen|label:PE: paired end SE: single end|development stage:muscle                 muscle RNAseq totalRNARibominus muscle RNAseq totalRNARibominus 9084X1 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 1000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP020008     muscle_RNAseq_totalRNARibominus_SE_9084X1_120420_SN141_0500_AD0TG5ACXX_5.txt.gz Illumina native 3506573750.0 70131475.0 9084X1 120420 SN141 0500 AD0TG5ACXX 5 0:50 A:872717534;C:808774955;G:1036781008;T:777391447;N:10908806 50       872717534 808774955 1036781008 777391447 10908806 SRX257154 SRS405708 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.61428   0.09813   0.89305   0.6908   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2013-05-07 Undetermined Embryo Muscle Muscular System
36666 36666 SRR800043 SRX257153 SRS405345 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio sphere RNAseq totalRNARibominus   strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere                 sphere RNAseq totalRNARibominus sphere RNAseq totalRNARibominus 7986X2 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP020008     sphere_RNAseq_totalRNARibominus_SE_7986X2_110510_SN141_0338_AB06MWABXX_7.txt.gz Illumina native 3029181300.0 60583626.0 7986X2 110510 SN141 0338 AB06MWABXX 7 0:50 A:768949744;C:733340278;G:903149841;T:623482299;N:259138 50       768949744 733340278 903149841 623482299 259138 SRX257153 SRS405345 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.83515   0.15524   0.81209   0.81031   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2015-07-22 Blastula Embryo Undetermined Embryo Imprecise
36667 36667 SRR800044 SRX257153 SRS405345 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio sphere RNAseq totalRNARibominus   strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere                 sphere RNAseq totalRNARibominus sphere RNAseq totalRNARibominus 7986X2 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP020008     sphere_RNAseq_totalRNARibominus_SE_7986X2_110606_SN141_0359_BD0D8KABXX_6.txt.gz Illumina native 3947123500.0 78942470.0 7986X2 110606 SN141 0359 BD0D8KABXX 6 0:50 A:1000468440;C:957437794;G:1171831772;T:817292633;N:92861 50       1000468440 957437794 1171831772 817292633 92861 SRX257153 SRS405345 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.81283   0.14906   0.81335   0.81698   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2015-07-22 Blastula Embryo Undetermined Embryo Imprecise
36668 36668 SRR800037 SRX257149 SRS405106 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio egg RNAseq totalRNARibominus   strain:Tubingen|label:PE: paired end SE: single end|dev stage:egg                 egg RNAseq totalRNARibominus egg RNAseq totalRNARibominus 7784X1 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP020008         3584440000.0 71688800.0 7784X1 110323 SN141 0332 A81FDVABXX 8 0:50 A:1013532157;C:812179975;G:992916103;T:765761452;N:50313 50       1013532157 812179975 992916103 765761452 50313 SRX257149 SRS405106 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.87304   0.12853   0.81988   0.80407   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2013-04-01 Undetermined Embryo Undetermined Embryo Imprecise
36669 36669 SRR800038 SRX257149 SRS405106 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio egg RNAseq totalRNARibominus   strain:Tubingen|label:PE: paired end SE: single end|dev stage:egg                 egg RNAseq totalRNARibominus egg RNAseq totalRNARibominus 7784X1 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP020008         2794240450.0 55884809.0 7784X1 110119 SN141 0323 B8162JABXX 8 0:50 A:792200981;C:632130044;G:772351331;T:596980885;N:577209 50       792200981 632130044 772351331 596980885 577209 SRX257149 SRS405106 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.86104   0.12909   0.82266   0.80894   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2013-04-01 Undetermined Embryo Undetermined Embryo Imprecise
38289 38289 SRR1731761 SRX828260 SRS807370 SRP051449 PRJNA266270 Danio rerio Transcriptome or Gene expression PRJNA266270 Other To identify molecular signals that initiate liver regeneration post 1/3 PH         sham operated liver transcriptome post 1/3 PH   breed:AB line|cultivar:AB line|strain:AB line|age:10 month|sex:female|tissue:liver|BioSampleModel:Model organism or animal                 sham operated liver transcriptome post 1/3 PH sham operated 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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> SRP051449     sham-operated_R1.fastq.gz sham-operated_R2.fastq.gz fastq fastq 2339904960.0 16249340.0 sham operated 0:72 1:72 A:639730953;C:549099184;G:603489762;T:545135156;N:2449905 72 72     639730953 549099184 603489762 545135156 2449905 SRX828260 SRS807370 SRA223828 Institute of Hydrobiology, Chinese Academy of Scie|The Key Laboratory of Aquatic Biodiversity and Con Chinese Academy of Sciences 2 0.9353 0.91074 0.02617 0.0253 0.86334 0.86387 0.35902 0.36066 72 72 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2016-02-05 Adult Adult Liver Liver and Biliary System
42181 42181 SRR5482153 SRX2765568 SRS2149771 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Large harvested line biological replicate 1 F2 offspring originating from wild caught population LS1 F2   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2008|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F2 individuals LS1 F2 LS1 F2 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     LS1-F2-10_FCC4CMHACXX_L1_WHZEBagiNCADRAAPEI-205_1.fq.gz LS1-F2-1_FCC4BKHACXX_L7_WHZEBagiNCAARAAPEI-201_1.fq.gz LS1-F2-5_FCC4BKHACXX_L7_WHZEBagiNCABRAAPEI-202_1.fq.gz LS1-F2-8_FCC4BKHACXX_L7_WHZEBagiNCACRAAPEI-203_1.fq.gz fastq fastq fastq fastq 12496905120.0 255038880.0 LS1 F2 10 FCC4CMHACXX L1 WHZEBagiNCADRAAPEI 205 1.fq.gz 0:49 A:3275093505;C:2981786839;G:2904373605;T:3334855308;N:795863 49       3275093505 2981786839 2904373605 3334855308 795863 SRX2765568 SRS2149771 SRA557107 University of Turku|Biology University of Turku 1 0.88577   0.04599   0.76469   0.48703   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42182 42182 SRR5482152 SRX2765567 SRS2149770 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Large harvested line biological replicate 2 F2 offspring originating from wild caught population LS2 F2   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2008|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F2 individuals LS2 F2 LS2 F2 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     LS2-F2-10_FCC4CMHACXX_L4_WHZEBagiNCALRAAPEI-213_1.fq.gz LS2-F2-11_FCC4CMHACXX_L4_WHZEBagiNCAMRAAPEI-214_1.fq.gz LS2-F2-14_FCC4C2AACXX_L1_WHZEBagiNCANRAAPEI-215_1.fq.gz LS2-F2-9_FCC4CMHACXX_L4_WHZEBagiNCAKRAAPEI-212_1.fq.gz fastq fastq fastq fastq 11108547205.0 226705045.0 LS2 F2 9 FCC4CMHACXX L4 WHZEBagiNCAKRAAPEI 212 1.fq.gz 0:49 A:2930693084;C:2628276474;G:2564131315;T:2984423047;N:1023285 49       2930693084 2628276474 2564131315 2984423047 1023285 SRX2765567 SRS2149770 SRA557107 University of Turku|Biology University of Turku 1 0.90013   0.04677   0.81251   0.44762   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42183 42183 SRR5482151 SRX2765565 SRS2149769 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Random harvested line biological replicate 1 F2 offspring originating from wild caught population RS1 F2   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2008|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F2 individuals RS1 F2 RS1 F2 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     RS1-F2-14_FCC4C2AACXX_L2_WHZEBagiNCAURAAPEI-223_1.fq.gz RS1-F2-16_FCC4C2AACXX_L2_WHZEBagiNCAVRAAPEI-225_1.fq.gz RS1-F2-17_FCC4C2AACXX_L3_WHZEBagiNCAWRAAPEI-227_1.fq.gz RS1-F2-19_FCC4C2AACXX_L3_WHZEBagiNCAXRAAPEI-201_1.fq.gz fastq fastq fastq fastq 12074501894.0 246418406.0 RS1 F2 16 FCC4C2AACXX L2 WHZEBagiNCAVRAAPEI 225 1.fq.gz 0:49 A:3199737416;C:2851335695;G:2767557430;T:3254746975;N:1124378 49       3199737416 2851335695 2767557430 3254746975 1124378 SRX2765565 SRS2149769 SRA557107 University of Turku|Biology University of Turku 1 0.87838   0.05071   0.81663   0.55417   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42184 42184 SRR5482150 SRX2765564 SRS2149768 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Random harvested line biological replicate 2 F2 offspring originating from wild caught population RS2 F2   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2008|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F2 individuals RS2 F2 RS2 F2 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     RS2-F2-3_FCC4CMHACXX_L2_WHZEBagiNCBFRAAPEI-210_1.fq.gz RS2-F2-6-2_FCC4CMHACXX_L2_WHZEBagiNCBGRAAPEI-211_1.fq.gz RS2-F2-8_FCC4CMHACXX_L2_WHZEBagiNCBHRABPEI-212_1.fq.gz RS2-F2-9_FCC4CMHACXX_L3_WHZEBagiNCBIRABPEI-213_1.fq.gz fastq fastq fastq fastq 11923597525.0 243338725.0 RS2 F2 9 FCC4CMHACXX L3 WHZEBagiNCBIRABPEI 213 1.fq.gz 0:49 A:3132507165;C:2819390547;G:2776793842;T:3193588286;N:1317685 49       3132507165 2819390547 2776793842 3193588286 1317685 SRX2765564 SRS2149768 SRA557107 University of Turku|Biology University of Turku 1 0.90986   0.05269   0.814   0.36827   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42185 42185 SRR5482149 SRX2765563 SRS2149767 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Large harvested line biological replicate 1 F5 offspring originating from wild caught population LS1 F5   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2010|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F5 individuals LS1 F5 LS1 F5 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     LS1-15_FCC4C3HACXX_L1_WHZEBagiNBANRAAPEI-215_1.fq.gz LS1-2_FCC4BJ2ACXX_L5_WHZEBagiNBABRAAPEI-202_1.fq.gz LS1-6_FCC4BJ2ACXX_L6_WHZEBagiNBAFRAAPEI-207_1.fq.gz LS1-8_FCC4BJ2ACXX_L8_WHZEBagiNBAJRAAPEI-211_1.fq.gz fastq fastq fastq fastq 12776192331.0 260738619.0 LS1 2 FCC4BJ2ACXX L5 WHZEBagiNBABRAAPEI 202 1.fq.gz 0:49 A:3371838433;C:3025006624;G:2934135898;T:3444117388;N:1093988 49       3371838433 3025006624 2934135898 3444117388 1093988 SRX2765563 SRS2149767 SRA557107 University of Turku|Biology University of Turku 1 0.88482   0.04932   0.813   0.51224   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42186 42186 SRR5482148 SRX2765562 SRS2149766 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Large harvested line biological replicate 2 F5 offspring originating from wild caught population LS2 F5   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2010|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F5 individuals LS2 F5 LS2 F5 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     LS2-10_FCC4BJ2ACXX_L8_WHZEBagiNBAKRAAPEI-212_1.fq.gz LS2-11_FCC4C3HACXX_L1_WHZEBagiNBAORAAPEI-216_1.fq.gz LS2-1_FCC4BJ2ACXX_L5_WHZEBagiNBACRAAPEI-203_1.fq.gz LS2-7_FCC4BVYACXX_L1_WHZEBagiNBAGRAAPEI-208_1.fq.gz fastq fastq fastq fastq 11941143935.0 243696815.0 LS2 10 FCC4BJ2ACXX L8 WHZEBagiNBAKRAAPEI 212 1.fq.gz 0:49 A:3165540142;C:2817777586;G:2733117846;T:3223679054;N:1029307 49       3165540142 2817777586 2733117846 3223679054 1029307 SRX2765562 SRS2149766 SRA557107 University of Turku|Biology University of Turku 1 0.87119   0.04752   0.80251   0.55444   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42187 42187 SRR5482147 SRX2765561 SRS2149765 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Random harvested line biological replicate 1 F5 offspring originating from wild caught population RS1 F5   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2010|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F5 individuals RS1 F5 RS1 F5 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     RS1-10_FCC4BJ2ACXX_L8_WHZEBagiNBALRAAPEI-213_1.fq.gz RS1-2_FCC4Y2GACXX_L4_WHZEBagiNCBPRABPEI-221_1.fq.gz RS1-3_FCC4BJ2ACXX_L6_WHZEBagiNBADRAAPEI-205_1.fq.gz RS1-6_FCC4BV7ACXX_L1_WHZEBagiNBAHRAAPEI-209_1.fq.gz fastq fastq fastq fastq 12149652753.0 247952097.0 RS1 6 FCC4BV7ACXX L1 WHZEBagiNBAHRAAPEI 209 1.fq.gz 0:49 A:3177681868;C:2907323525;G:2822484622;T:3241144133;N:1018605 49       3177681868 2907323525 2822484622 3241144133 1018605 SRX2765561 SRS2149765 SRA557107 University of Turku|Biology University of Turku 1 0.90495   0.04625   0.80028   0.56443   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42188 42188 SRR5482146 SRX2765560 SRS2149764 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Random harvested line biological replicate 2 F5 offspring originating from wild caught population RS2 F5   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2010|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F5 individuals RS2 F5 RS2 F5 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     RS2-10_FCC4BVYACXX_L1_WHZEBagiNBAIRAAPEI-210_1.fq.gz RS2-13_FCC4C3HACXX_L1_WHZEBagiNBAMRAAPEI-214_1.fq.gz RS2-2_FCC4BJ2ACXX_L5_WHZEBagiNBAARAAPEI-201_1.fq.gz RS2-3_FCC4C19ACXX_L5_WHZEBagiNBAERAAPEI-206_1.fq.gz fastq fastq fastq fastq 11262796951.0 229852999.0 RS2 13 FCC4C3HACXX L1 WHZEBagiNBAMRAAPEI 214 1.fq.gz 0:49 A:2931626627;C:2710523895;G:2627211912;T:2992545637;N:888880 49       2931626627 2710523895 2627211912 2992545637 888880 SRX2765560 SRS2149764 SRA557107 University of Turku|Biology University of Turku 1 0.88588   0.04266   0.8112   0.52927   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42189 42189 SRR5482145 SRX2765559 SRS2149763 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Large harvested line biological replicate 1 F11 offspring originating from wild caught population LS1 F11   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2014|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F11 individuals LS1 F11 LS1 F11 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     LS1-F11B-11_FCC4CMHACXX_L1_WHZEBagiNCAERAAPEI-206_1.fq.gz LS1-F11B-13_FCC4CMHACXX_L1_WHZEBagiNCAFRAAPEI-207_1.fq.gz LS1-F11B-16_FCC4C19ACXX_L1_WHZEBagiNCAGRBAPEI-208_1.fq.gz LS1-F11B-17_FCC4BKHACXX_L8_WHZEBagiNCAHRAAPEI-209_1.fq.gz fastq fastq fastq fastq 11326213584.0 231147216.0 LS1 F11B 16 FCC4C19ACXX L1 WHZEBagiNCAGRBAPEI 208 1.fq.gz 0:49 A:2982223592;C:2693407623;G:2622876703;T:3026833843;N:871823 49       2982223592 2693407623 2622876703 3026833843 871823 SRX2765559 SRS2149763 SRA557107 University of Turku|Biology University of Turku 1 0.90202   0.04273   0.78273   0.51238   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42190 42190 SRR5482144 SRX2765558 SRS2149762 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Large harvested line biological replicate 2 F11 offspring originating from wild caught population LS2 F11   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2014|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F11 individuals LS2 F11 LS2 F11 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     LS2-F11B-1_FCC4C2AACXX_L1_WHZEBagiNCAORAAPEI-216_1.fq.gz LS2-F11B-2_FCC4C2AACXX_L1_WHZEBagiNCAPRAAPEI-218_1.fq.gz LS2-F11B-5_FCC4CMHACXX_L5_WHZEBagiNCAQRAAPEI-219_1.fq.gz LS2-F11B-7_FCC4CMHACXX_L5_WHZEBagiNCARRAAPEI-220_1.fq.gz fastq fastq fastq fastq 12030571875.0 245521875.0 LS2 F11B 7 FCC4CMHACXX L5 WHZEBagiNCARRAAPEI 220 1.fq.gz 0:49 A:3149792862;C:2871072895;G:2795019949;T:3213514581;N:1171588 49       3149792862 2871072895 2795019949 3213514581 1171588 SRX2765558 SRS2149762 SRA557107 University of Turku|Biology University of Turku 1 0.91893   0.036   0.77429   0.38962   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42191 42191 SRR5482143 SRX2765557 SRS2149760 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Random harvested line biological replicate 1 F11 offspring originating from wild caught population RS1 F11   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2014|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F11 individuals RS1 F11 RS1 F11 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     RS1-F11B-21_FCC4C2AACXX_L3_WHZEBagiNCAYRAAPEI-202_1.fq.gz RS1-F11B-23_FCC4C2AACXX_L4_WHZEBagiNCAZRAAPEI-203_1.fq.gz RS1-F11B-27_FCC4C2AACXX_L4_WHZEBagiNCBARAAPEI-205_1.fq.gz RS1-F11B-29_FCC4C2AACXX_L4_WHZEBagiNCBBRAAPEI-206_1.fq.gz fastq fastq fastq fastq 11947679555.0 243830195.0 RS1 F11B 21 FCC4C2AACXX L3 WHZEBagiNCAYRAAPEI 202 1.fq.gz 0:49 A:3159477117;C:2827401119;G:2753495798;T:3206143470;N:1162051 49       3159477117 2827401119 2753495798 3206143470 1162051 SRX2765557 SRS2149760 SRA557107 University of Turku|Biology University of Turku 1 0.87877   0.04488   0.77445   0.50852   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42192 42192 SRR5482142 SRX2765556 SRS2149761 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Random harvested line biological replicate 2 F11 offspring originating from wild caught population RS2 F11   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2014|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F11 individuals RS2 F11 RS2 F11 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     RS2-F11B-34_FCC4CMHACXX_L3_WHZEBagiNCBJRABPEI-214_1.fq.gz RS2-F11B-36_FCC4CMHACXX_L3_WHZEBagiNCBKRABPEI-215_1.fq.gz RS2-F11B-38_FCC4BY1ACXX_L1_WHZEBagiNCBLRABPEI-216_1.fq.gz RS2-F11B-40_FCC4BY1ACXX_L1_WHZEBagiNCBMRABPEI-218_1.fq.gz fastq fastq fastq fastq 10619740698.0 216729402.0 RS2 F11B 38 FCC4BY1ACXX L1 WHZEBagiNCBLRABPEI 216 1.fq.gz 0:49 A:2799661065;C:2501316593;G:2465115836;T:2852970598;N:676606 49       2799661065 2501316593 2465115836 2852970598 676606 SRX2765556 SRS2149761 SRA557107 University of Turku|Biology University of Turku 1 0.8851   0.04865   0.80407   0.54962   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42451 42451 SRR5590336 SRX2847138 SRS2220119 SRP115073 PRJNA387549 zebrafish Raw sequence reads PRJNA387549 Metagenomics The study was to unravel the complex toxic effects of chemical contaminants on the health of organisms as based on different levels of biological profling.       without xxx and with difenoconazole CK D 50 D 500   strain:AB|isolate:embryo|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:pooled male and female|tissue:whole individual|BioSampleModel:Model organism or animal                 RNA Sequencing in zebrafish without xxx and with difenoconazole zebrafish RNA Sequencing project 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>6</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> SRP115073     CK_1_1.fq.gz CK_1_2.fq.gz CK_2_1.fq.gz CK_3_1.fq.gz CK_3_2.fq.gz D_500_1_1.fq.gz D_500_1_2.fq.gz D_500_2_1.fq.gz D_500_2_2.fq.gz D_500_3_1.fq.gz D_500_3_2.fq.gz D_50_1_1.fq.gz D_50_1_2.fq.gz D_50_3_2.fq.gz D_50_3_1.fq.gz D_50_2_2.fq.gz D_50_2_1.fq.gz CK_2_2.fq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 81797448900.0 272658163.0 zebrafish RNA Seq 0:150 1:150 A:21743331485;C:19042575463;G:19378823851;T:21630253992;N:2464109 150 150     21743331485 19042575463 19378823851 21630253992 2464109 SRX2847138 SRS2220119 SRA564978 China Agricultural University|College of Science China Agricultural University 2 0.91941 0.92018 0.10515 0.10533 0.67939 0.68552 0.46739 0.46494 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-04-14 Undetermined Embryo Whole Organism All anatomical structures
47611 47611 SRR6671794 SRX3648486 SRS2913085 SRP132190 PRJNA432942 Zebrafish genes regulated in response to Mucor circinelloides infection PRJNA432942 Other Determination of the genes that can be important for the defense of the host to infection for Mucorales fungi using zebrafish and the fungus Mucor circinelloides as host and pathogen model respectively. Total RNA was sequenced RNA seq from abdominal organs of infected fish.         PBS2   strain:AB|dev stage:Adult|sex:not determined|tissue:Abdomen|treatment:Control innoculated with PBS|BioSampleModel:Model organism or animal                 RNA seq of Darnio rerio: uninffected PBS2 PBS2 Total RNA isolated from uninfected abdominal tissue was used to generate the library using truseq kit     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP132190     PBS2_GCCAAT_L001_R1_001_BH8U70ADXX.filt.fastq.gz fastq 792892359.0 15546909.0 PBS2 GCCAAT L001 R1 001 BH8U70ADXX.filt.fastq.gz 0:51 A:207417646;C:188867370;G:187996499;T:208448675;N:162169 51       207417646 188867370 187996499 208448675 162169 SRX3648486 SRS2913085 SRA655550 University of Murcia|Genetics and Microbiology University of Murcia 1 0.92826   0.02642   0.72815   0.45776   51   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Spain 2018-09-28 Adult Adult Trunk Surface Structure
47612 47612 SRR6671795 SRX3648485 SRS2913084 SRP132190 PRJNA432942 Zebrafish genes regulated in response to Mucor circinelloides infection PRJNA432942 Other Determination of the genes that can be important for the defense of the host to infection for Mucorales fungi using zebrafish and the fungus Mucor circinelloides as host and pathogen model respectively. Total RNA was sequenced RNA seq from abdominal organs of infected fish.         RDRZ   strain:AB|dev stage:Adult|sex:not determined|tissue:Abdomen|treatment:Infected with Mucor circinelloides spores|BioSampleModel:Model organism or animal                 RNA seq of Darnio rerio: infected with Mucor circinelloides RDRZ RDRZ Total RNA isolated from abdominal tissue infected with Mucor circinelloides was used to generate the library using truseq kit     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP132190     RDRZ_TGACCA_L001_R1_001_BH8U70ADXX.filt.fastq.gz fastq 741005418.0 14529518.0 RDRZ TGACCA L001 R1 001 BH8U70ADXX.filt.fastq.gz 0:51 A:192330774;C:178252917;G:175501754;T:194766886;N:153087 51       192330774 178252917 175501754 194766886 153087 SRX3648485 SRS2913084 SRA655550 University of Murcia|Genetics and Microbiology University of Murcia 1 0.91685   0.03703   0.70873   0.49947   51   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Spain 2018-09-28 Adult Adult Trunk Surface Structure
52238 52238 SRR9044114 SRX5820656 SRS4749302 SRP197695 PRJNA542436 Regulation of hematopoiesis and endothelium function by endocytic trafficking PRJNA542436 Other Endocytic trafficking in endothelium         CT1   strain:AB|isolate:ctrl MO fluorescence activated cell sorting 1|cultivar:not applicable|ecotype:not applicable|age:1 year|sex:male and female|tissue:fli1a+ endothelium|BioSampleModel:Model organism or animal                 RNA seq of endothelial cells1 ct1 20191 ct1 20191 ctrl MO 1     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP197695     CT1.gz fastq 3222866250.0 21485775.0 CT1.gz 0:150 1:0 A:845914701;C:771891741;G:774348916;T:830705072;N:5820 150 0     845914701 771891741 774348916 830705072 5820 SRX5820656 SRS4749302 SRA885405 Chinese academy of sciences|institute of zoology Chinese academy of sciences 1 0.95232   0.09195   0.7837   0.45885   150   B   usable mapping rate illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-17 Adult Adult Endothelium Cardiovascular System
52239 52239 SRR9044115 SRX5820655 SRS4749299 SRP197695 PRJNA542436 Regulation of hematopoiesis and endothelium function by endocytic trafficking PRJNA542436 Other Endocytic trafficking in endothelium         CT2   strain:AB|isolate:ctrl MO fluorescence activated cell sorting 2|cultivar:not applicable|ecotype:not applicable|age:1 year|sex:male and female|tissue:fli1a+ endothelium|BioSampleModel:Model organism or animal                 RNA seq of endothelial cells2 ct1 20192 ct1 20192 ctrl MO 2     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP197695     CT2.gz fastq 3992117700.0 26614118.0 CT2.gz 0:150 1:0 A:1040923084;C:961956867;G:964333886;T:1024896832;N:7031 150 0     1040923084 961956867 964333886 1024896832 7031 SRX5820655 SRS4749299 SRA885405 Chinese academy of sciences|institute of zoology Chinese academy of sciences 1 0.95545   0.087   0.78488   0.46466   150   B   usable mapping rate illumina novaseq_era unknown other unknown bulk unknown unknown   China 2019-05-11 Adult Adult Endothelium Cardiovascular System
52240 52240 SRR9044116 SRX5820654 SRS4749301 SRP197695 PRJNA542436 Regulation of hematopoiesis and endothelium function by endocytic trafficking PRJNA542436 Other Endocytic trafficking in endothelium         SCMO1   strain:AB|isolate:5c MO fluorescence activated cell sorting 3|cultivar:not applicable|ecotype:not applicable|age:1 year|sex:male and female|tissue:fli1a+ endothelium|BioSampleModel:Model organism or animal                 RNA seq of endothelial cells3 5c 20191 5c 20191 5c MO 1     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP197695     SCMO1.gz fastq 2137379550.0 14249197.0 SCMO1.gz 0:150 1:0 A:558129907;C:517045618;G:515434728;T:546767387;N:1910 150 0     558129907 517045618 515434728 546767387 1910 SRX5820654 SRS4749301 SRA885405 Chinese academy of sciences|institute of zoology Chinese academy of sciences 1 0.94546   0.08686   0.78709   0.56163   150   B   usable mapping rate illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-17 Adult Adult Endothelium Cardiovascular System
52241 52241 SRR9044117 SRX5820653 SRS4749300 SRP197695 PRJNA542436 Regulation of hematopoiesis and endothelium function by endocytic trafficking PRJNA542436 Other Endocytic trafficking in endothelium         SCMO2   strain:AB|isolate:5c MO fluorescence activated cell sorting 4|cultivar:not applicable|ecotype:not applicable|age:1 year|sex:male and female|tissue:fli1a+ endothelium|BioSampleModel:Model organism or animal                 RNA seq of endothelial cells4 5c 20192 5c 20192 5c MO 2     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP197695     SCMO2.gz fastq 3909804300.0 26065362.0 SCMO2.gz 0:150 1:0 A:1033271905;C:928576644;G:928527559;T:1019420939;N:7253 150 0     1033271905 928576644 928527559 1019420939 7253 SRX5820653 SRS4749300 SRA885405 Chinese academy of sciences|institute of zoology Chinese academy of sciences 1 0.94475   0.096   0.7867   0.55845   150   B   usable mapping rate illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-17 Adult Adult Endothelium Cardiovascular System
58991 58991 SRR11577236 SRX8145127 SRS6507863 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 iso 5 20170222A 5dpf iso   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 22|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:5|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A016 A016 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170222A_5dpf_iso_S10_R1_001.fastq.gz fastq 1145417285.0 8785034.0 20170222A 5dpf iso S10 R1 001.fastq.gz 0:130.38 1:0 A:322759854;C:242145737;G:242143184;T:336959770;N:1408740 130 0     322759854 242145737 242143184 336959770 1408740 SRX8145127 SRS6507863 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93521   0.17614   0.66411   0.49656   109   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
58992 58992 SRR11577237 SRX8145126 SRS6507862 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 social 5 20170222A 5dpf soc   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 22|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:5|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A015 A015 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170222A_5dpf_soc_S9_R1_001.fastq.gz fastq 1951935848.0 15606984.0 20170222A 5dpf soc S9 R1 001.fastq.gz 0:125.07 1:0 A:546425279;C:412941736;G:422316572;T:568807662;N:1444599 125 0     546425279 412941736 422316572 568807662 1444599 SRX8145126 SRS6507862 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93665   0.17342   0.65971   0.50276   135   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
58993 58993 SRR11577238 SRX8145125 SRS6507861 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 iso 4 20170210B 5dpf iso   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 10|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:4|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A014 A014 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170210B_5dpf_iso_S8_R1_001.fastq.gz fastq 1438281543.0 10175957.0 20170210B 5dpf iso S8 R1 001.fastq.gz 0:141.34 1:0 A:405893769;C:302927323;G:299208098;T:428334452;N:1917901 141 0     405893769 302927323 299208098 428334452 1917901 SRX8145125 SRS6507861 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.9398   0.14632   0.66225   0.50935   150   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
58994 58994 SRR11577239 SRX8145124 SRS6507860 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 social 4 20170210B 5dpf soc   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 10|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:4|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A013 A013 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170210B_5dpf_soc_S7_R1_001.fastq.gz fastq 2086284546.0 17392851.0 20170210B 5dpf soc S7 R1 001.fastq.gz 0:119.95 1:0 A:564323359;C:455998854;G:458642653;T:599704356;N:7615324 119 0     564323359 455998854 458642653 599704356 7615324 SRX8145124 SRS6507860 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94679   0.14294   0.66724   0.49719   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
58995 58995 SRR11577240 SRX8145123 SRS6507859 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 iso 3 20170210A 5dpf iso   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 10|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:3|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A012 A012 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170210A_5dpf_iso_S6_R1_001.fastq.gz fastq 1518854121.0 12280862.0 20170210A 5dpf iso S6 R1 001.fastq.gz 0:123.68 1:0 A:416560027;C:326775060;G:324773078;T:444339405;N:6406551 123 0     416560027 326775060 324773078 444339405 6406551 SRX8145123 SRS6507859 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94696   0.13785   0.65969   0.50295   93   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
58996 58996 SRR11577241 SRX8145122 SRS6507858 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       21 va 4 20170906 21dpf va   breed:Konstanz Wildtype|age:21 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 06|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:visual access|replicate:4|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D712 D503 D712 D503 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170906_21dpf_va_S33_R1_001.fastq.gz fastq 1661935649.0 12040839.0 20170906 21dpf va S33 R1 001.fastq.gz 0:138.02 1:0 A:512672438;C:325062238;G:324522459;T:499578935;N:99579 138 0     512672438 325062238 324522459 499578935 99579 SRX8145122 SRS6507858 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92534   0.20642   0.71415   0.50058   149   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
58997 58997 SRR11577242 SRX8145121 SRS6507857 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       21 social 4 20170906 21dpf soc   breed:Konstanz Wildtype|age:21 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 06|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:4|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D712 D502 D712 D502 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170906_21dpf_soc_S32_R1_001.fastq.gz fastq 1794859081.0 13268077.0 20170906 21dpf soc S32 R1 001.fastq.gz 0:135.28 1:0 A:540408588;C:359901078;G:360448696;T:532610170;N:1490549 135 0     540408588 359901078 360448696 532610170 1490549 SRX8145121 SRS6507857 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92777   0.20003   0.70836   0.49772   150   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
58998 58998 SRR11577243 SRX8145120 SRS6507856 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       21 iso 4 20170906 21dpf iso   breed:Konstanz Wildtype|age:21 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 06|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:4|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D712 D501 D712 D501 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170906_21dpf_iso_S31_R1_001.fastq.gz fastq 1873301073.0 13752080.0 20170906 21dpf iso S31 R1 001.fastq.gz 0:136.22 1:0 A:542725908;C:393749236;G:391185289;T:545475931;N:164709 136 0     542725908 393749236 391185289 545475931 164709 SRX8145120 SRS6507856 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93526   0.1792   0.70449   0.5011   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
58999 58999 SRR11577244 SRX8145119 SRS6507855 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       21 va 3 20170830 21dpf va   breed:Konstanz Wildtype|age:21 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 08 30|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:visual access|replicate:3|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D711 D508 D711 D508 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170830_21dpf_va_S30_R1_001.fastq.gz fastq 1665561578.0 12239078.0 20170830 21dpf va S30 R1 001.fastq.gz 0:136.09 1:0 A:523851621;C:320222311;G:318423760;T:502879358;N:184528 136 0     523851621 320222311 318423760 502879358 184528 SRX8145119 SRS6507855 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92268   0.22072   0.7167   0.50583   150   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59000 59000 SRR11577245 SRX8145118 SRS6507854 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       21 social 3 20170830 21dpf soc   breed:Konstanz Wildtype|age:21 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2018 08 30|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:3|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D711 D507 D711 D507 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170830_21dpf_soc_S29_R1_001.fastq.gz fastq 1587516569.0 11532068.0 20170830 21dpf soc S29 R1 001.fastq.gz 0:137.66 1:0 A:505388701;C:300044293;G:297465254;T:484459426;N:158895 137 0     505388701 300044293 297465254 484459426 158895 SRX8145118 SRS6507854 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92277   0.22348   0.7237   0.50214   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59001 59001 SRR11577246 SRX8145117 SRS6507853 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 social 3 20170210A 5dpf soc   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 10|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:3|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A007 A007 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170210A_5dpf_soc_S5_R1_001.fastq.gz fastq 1726237934.0 14278894.0 20170210A 5dpf soc S5 R1 001.fastq.gz 0:120.89 1:0 A:463605810;C:370696125;G:372572642;T:495475185;N:23888172 120 0     463605810 370696125 372572642 495475185 23888172 SRX8145117 SRS6507853 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94821   0.14237   0.66689   0.48963   136   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59002 59002 SRR11577247 SRX8145116 SRS6507852 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       21 iso 3 20170830 21dpf iso   breed:Konstanz Wildtype|age:21 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 08 30|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:3|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D711 D506 D711 D506 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170830_21dpf_iso_S28_R1_001.fastq.gz fastq 1502071856.0 11108454.0 20170830 21dpf iso S28 R1 001.fastq.gz 0:135.22 1:0 A:465590927;C:293070754;G:290713397;T:452388232;N:308546 135 0     465590927 293070754 290713397 452388232 308546 SRX8145116 SRS6507852 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.9282   0.21564   0.71735   0.48929   122   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59003 59003 SRR11577248 SRX8145115 SRS6507851 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       14 iso 5 20171019 14dpf iso   breed:Konstanz Wildtype|age:14 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 10 19|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:5|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D711 D505 D711 D505 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171019_14dpf_iso_S27_R1_001.fastq.gz fastq 1768205560.0 12917483.0 20171019 14dpf iso S27 R1 001.fastq.gz 0:136.88 1:0 A:555603588;C:338259364;G:332890369;T:541226785;N:225454 136 0     555603588 338259364 332890369 541226785 225454 SRX8145115 SRS6507851 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92237   0.22542   0.7189   0.49571   137   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59004 59004 SRR11577249 SRX8145114 SRS6507850 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       14 social 5 20171019 14dpf soc   breed:Konstanz Wildtype|age:14 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 10 19|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:5|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D711 D504 D711 D504 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171019_14dpf_soc_S26_R1_001.fastq.gz fastq 2449724667.0 17539539.0 20171019 14dpf soc S26 R1 001.fastq.gz 0:139.67 1:0 A:770396759;C:469506555;G:460464367;T:749061593;N:295393 139 0     770396759 469506555 460464367 749061593 295393 SRX8145114 SRS6507850 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92149   0.22074   0.72176   0.48648   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59005 59005 SRR11577250 SRX8145113 SRS6507849 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       14 iso 4 20170927 14dpf iso   breed:Konstanz Wildtype|age:14 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 27|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:4|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D711 D503 D711 D503 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170927_14dpf_iso_S25_R1_001.fastq.gz fastq 2024375395.0 14714506.0 20170927 14dpf iso S25 R1 001.fastq.gz 0:137.58 1:0 A:630956852;C:392021593;G:387382117;T:613569631;N:445202 137 0     630956852 392021593 387382117 613569631 445202 SRX8145113 SRS6507849 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92636   0.22205   0.71334   0.46764   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59006 59006 SRR11577251 SRX8145112 SRS6507848 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       14 iso 3 20170912 14dpf iso   breed:Konstanz Wildtype|age:14 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 12|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:3|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D711 D502 D711 D502 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170912_14dpf_iso_S24_R1_001.fastq.gz fastq 1539139897.0 11503089.0 20170912 14dpf iso S24 R1 001.fastq.gz 0:133.80 1:0 A:462339700;C:309696226;G:308140729;T:457996565;N:966677 133 0     462339700 309696226 308140729 457996565 966677 SRX8145112 SRS6507848 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93509   0.18982   0.70745   0.49473   125   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59007 59007 SRR11577252 SRX8145111 SRS6507847 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       14 social 3 20170912 14dpf soc   breed:Konstanz Wildtype|age:14 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 12|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:3|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D711 D501 D711 D501 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170912_14dpf_soc_S23_R1_001.fastq.gz fastq 1846815763.0 13311290.0 20170912 14dpf soc S23 R1 001.fastq.gz 0:138.74 1:0 A:532697843;C:390098289;G:387302654;T:536566282;N:150695 138 0     532697843 390098289 387302654 536566282 150695 SRX8145111 SRS6507847 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94078   0.16787   0.70345   0.50462   150   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59008 59008 SRR11577253 SRX8145110 SRS6507846 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 iso 6 20171109 8dpf iso B   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 11 09|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:6|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D508 D710 D508 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171109_8dpf_iso_B_S22_R1_001.fastq.gz fastq 1700207946.0 12434052.0 20171109 8dpf iso B S22 R1 001.fastq.gz 0:136.74 1:0 A:521541858;C:336119080;G:332771490;T:509018316;N:757202 136 0     521541858 336119080 332771490 509018316 757202 SRX8145110 SRS6507846 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93058   0.19578   0.68868   0.50184   139   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59009 59009 SRR11577254 SRX8145109 SRS6507845 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 social 6 20171109 8dpf soc B   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 11 09|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:6|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D507 D710 D507 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171109_8dpf_soc_B_S21_R1_001.fastq.gz fastq 2564439613.0 18763192.0 20171109 8dpf soc B S21 R1 001.fastq.gz 0:136.67 1:0 A:790757790;C:503826332;G:501530520;T:767769522;N:555449 136 0     790757790 503826332 501530520 767769522 555449 SRX8145109 SRS6507845 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92839   0.1986   0.68885   0.50483   131   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59010 59010 SRR11577255 SRX8145108 SRS6507844 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 iso 5 20171026 8dpf iso   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 10 26|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:5|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D506 D710 D506 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171026_8dpf_iso_S20_R1_001.fastq.gz fastq 2826413292.0 20452973.0 20171026 8dpf iso S20 R1 001.fastq.gz 0:138.19 1:0 A:865014614;C:559489084;G:552925517;T:847716596;N:1267481 138 0     865014614 559489084 552925517 847716596 1267481 SRX8145108 SRS6507844 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92608   0.2105   0.67903   0.49051   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59011 59011 SRR11577256 SRX8145107 SRS6507843 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 social 5 20171026 8dpf soc   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 10 26|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:5|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D505 D710 D505 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171026_8dpf_soc_S19_R1_001.fastq.gz fastq 2392544953.0 17491839.0 20171026 8dpf soc S19 R1 001.fastq.gz 0:136.78 1:0 A:742679673;C:465343974;G:462989237;T:721074201;N:457868 136 0     742679673 465343974 462989237 721074201 457868 SRX8145107 SRS6507843 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92316   0.21835   0.68655   0.48878   98   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59012 59012 SRR11577257 SRX8145106 SRS6507842 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 iso 2 20170209 5dpf iso   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 09|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:2|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A006 A006 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170209_5dpf_iso_S4_R1_001.fastq.gz fastq 1425974682.0 10933160.0 20170209 5dpf iso S4 R1 001.fastq.gz 0:130.43 1:0 A:384119497;C:314204651;G:311289822;T:412270680;N:4090032 130 0     384119497 314204651 311289822 412270680 4090032 SRX8145106 SRS6507842 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94694   0.14009   0.66271   0.50186   35   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59013 59013 SRR11577258 SRX8145105 SRS6507841 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 iso 4 20171019 8dpf iso   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 10 19|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:4|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D504 D710 D504 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171019_8dpf_iso_S18_R1_001.fastq.gz fastq 1983037322.0 14462095.0 20171019 8dpf iso S18 R1 001.fastq.gz 0:137.12 1:0 A:615819850;C:385988693;G:385056417;T:595787232;N:385130 137 0     615819850 385988693 385056417 595787232 385130 SRX8145105 SRS6507841 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92714   0.20602   0.68387   0.49262   150   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59014 59014 SRR11577259 SRX8145104 SRS6507840 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 social 4 20171019 8dpf soc   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 10 19|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:4|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D503 D710 D503 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171019_8dpf_soc_S17_R1_001.fastq.gz fastq 2128354590.0 15330724.0 20171019 8dpf soc S17 R1 001.fastq.gz 0:138.83 1:0 A:664838663;C:412783437;G:406007808;T:644520130;N:204552 138 0     664838663 412783437 406007808 644520130 204552 SRX8145104 SRS6507840 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92294   0.21336   0.68907   0.48677   112   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59015 59015 SRR11577260 SRX8145103 SRS6507839 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 iso 3 20170921 8dpf iso   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 21|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:3|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D502 D710 D502 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170921_8dpf_iso_S16_R1_001.fastq.gz fastq 1715158999.0 12523396.0 20170921 8dpf iso S16 R1 001.fastq.gz 0:136.96 1:0 A:517292645;C:345214588;G:340081628;T:512406926;N:163212 136 0     517292645 345214588 340081628 512406926 163212 SRX8145103 SRS6507839 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93065   0.1956   0.67543   0.48715   112   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59016 59016 SRR11577261 SRX8145102 SRS6507838 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 social 3 20170921 8dpf soc   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 21|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:3|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D501 D710 D501 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170921_8dpf_soc_S15_R1_001.fastq.gz fastq 1903374830.0 13985406.0 20170921 8dpf soc S15 R1 001.fastq.gz 0:136.10 1:0 A:576312482;C:382917713;G:376058448;T:567672351;N:413836 136 0     576312482 382917713 376058448 567672351 413836 SRX8145102 SRS6507838 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.928   0.20225   0.68079   0.47235   139   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59017 59017 SRR11577262 SRX8145101 SRS6507837 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       21 va 2 20170912 21dpf va   breed:Konstanz Wildtype|age:21 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 12|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:visual access|replicate:2|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D709 D508 D709 D508 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170912_21dpf_va_S14_R1_001.fastq.gz fastq 1672012701.0 12141814.0 20170912 21dpf va S14 R1 001.fastq.gz 0:137.71 1:0 A:476642379;C:357414674;G:356006342;T:480630478;N:1318828 137 0     476642379 357414674 356006342 480630478 1318828 SRX8145101 SRS6507837 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94024   0.16163   0.69779   0.49063   150   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59018 59018 SRR11577263 SRX8145100 SRS6507836 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       21 social 2 20170912 21dpf soc   breed:Konstanz Wildtype|age:21 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 12|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:2|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D709 D507 D709 D507 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170912_21dpf_soc_S13_R1_001.fastq.gz fastq 2080939075.0 14649700.0 20170912 21dpf soc S13 R1 001.fastq.gz 0:142.05 1:0 A:597966503;C:441812252;G:438654868;T:601449778;N:1055674 142 0     597966503 441812252 438654868 601449778 1055674 SRX8145100 SRS6507836 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93757   0.1703   0.70061   0.49625   148   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59019 59019 SRR11577264 SRX8145099 SRS6507835 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       21 iso 2 20170912 21dpf iso   breed:Konstanz Wildtype|age:21 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 12|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:2|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D709 D506 D709 D506 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170912_21dpf_iso_S12_R1_001.fastq.gz fastq 3489258082.0 25226043.0 20170912 21dpf iso S12 R1 001.fastq.gz 0:138.32 1:0 A:1004881001;C:740475054;G:734330793;T:1008365272;N:1205962 138 0     1004881001 740475054 734330793 1008365272 1205962 SRX8145099 SRS6507835 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.9401   0.16556   0.69848   0.48682   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59020 59020 SRR11577265 SRX8145098 SRS6507834 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       21 va 1 20170816 21dpf va   breed:Konstanz Wildtype|age:21 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 08 16|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:visual access|replicate:1|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D709 D505 D709 D505 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170816_21dpf_va_S11_R1_001.fastq.gz fastq 2357126069.0 17284572.0 20170816 21dpf va S11 R1 001.fastq.gz 0:136.37 1:0 A:673543974;C:503174130;G:502244040;T:676474372;N:1689553 136 0     673543974 503174130 502244040 676474372 1689553 SRX8145098 SRS6507834 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94094   0.16335   0.69718   0.50833   150   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59021 59021 SRR11577266 SRX8145097 SRS6507833 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       21 social 1 20170816 21dpf soc   breed:Konstanz Wildtype|age:21 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 08 16|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:1|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D709 D504 D709 D504 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170816_21dpf_soc_S10_R1_001.fastq.gz fastq 1891180488.0 13827534.0 20170816 21dpf soc S10 R1 001.fastq.gz 0:136.77 1:0 A:533386853;C:409970181;G:408848698;T:536931439;N:2043317 136 0     533386853 409970181 408848698 536931439 2043317 SRX8145097 SRS6507833 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94486   0.15116   0.70007   0.50715   86   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59022 59022 SRR11577267 SRX8145096 SRS6507832 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       21 iso 1 20170816 21dpf iso   breed:Konstanz Wildtype|age:21 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 08 16|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:1|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D709 D503 D709 D503 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170816_21dpf_iso_S9_R1_001.fastq.gz fastq 1787118538.0 12892680.0 20170816 21dpf iso S9 R1 001.fastq.gz 0:138.61 1:0 A:524315938;C:372386070;G:371250402;T:518145923;N:1020205 138 0     524315938 372386070 371250402 518145923 1020205 SRX8145096 SRS6507832 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93597   0.18637   0.70185   0.50951   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59023 59023 SRR11577268 SRX8145095 SRS6507831 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 social 2 20170209 5dpf soc   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 09|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:2|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A005 A005 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170209_5dpf_soc_S3_R1_001.fastq.gz fastq 932021340.0 8105951.0 20170209 5dpf soc S3 R1 001.fastq.gz 0:114.98 1:0 A:242483339;C:210201362;G:210814912;T:264386634;N:4135093 114 0     242483339 210201362 210814912 264386634 4135093 SRX8145095 SRS6507831 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.95059   0.13154   0.66099   0.48071   86   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59024 59024 SRR11577269 SRX8145094 SRS6507830 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       14 social 2 20171102 14dpf soc   breed:Konstanz Wildtype|age:14 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 11 02|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:2|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D709 D502 D709 D502 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171102_14dpf_soc_S8_R1_001.fastq.gz fastq 1822206481.0 13207373.0 20171102 14dpf soc S8 R1 001.fastq.gz 0:137.97 1:0 A:521401675;C:390638985;G:384942844;T:524801703;N:421274 137 0     521401675 390638985 384942844 524801703 421274 SRX8145094 SRS6507830 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93965   0.1632   0.70406   0.49414   137   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59025 59025 SRR11577270 SRX8145093 SRS6507829 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       14 iso 2 20171102 14dpf iso   breed:Konstanz Wildtype|age:14 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 11 02|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:2|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D709D 501 D709D 501 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171102_14dpf_iso_S7_R1_001.fastq.gz fastq 1654915081.0 12110608.0 20171102 14dpf iso S7 R1 001.fastq.gz 0:136.65 1:0 A:453654237;C:368578514;G:366570763;T:464593788;N:1517779 136 0     453654237 368578514 366570763 464593788 1517779 SRX8145093 SRS6507829 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94734   0.14469   0.69976   0.48909   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59026 59026 SRR11577271 SRX8145092 SRS6507828 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       14 social 1 20170921 14dpf soc   breed:Konstanz Wildtype|age:14 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 21|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:1|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D708 D506 D708 D506 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170921__14dpf_soc_S6_R1_001.fastq.gz fastq 2318687589.0 16884467.0 20170921 14dpf soc S6 R1 001.fastq.gz 0:137.33 1:0 A:670856703;C:490885071;G:485692957;T:670107300;N:1145558 137 0     670856703 490885071 485692957 670107300 1145558 SRX8145092 SRS6507828 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94232   0.14969   0.69846   0.50741   136   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59027 59027 SRR11577272 SRX8145091 SRS6507827 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       14 iso 1 20170921 14dpf iso   breed:Konstanz Wildtype|age:14 dpf|dev stage:juvenile|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 21|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:1|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D708 D505 D708 D505 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170921__14dpf_iso_S5_R1_001.fastq.gz fastq 2786167106.0 20134934.0 20170921 14dpf iso S5 R1 001.fastq.gz 0:138.37 1:0 A:830172483;C:576374466;G:571085075;T:807339855;N:1195227 138 0     830172483 576374466 571085075 807339855 1195227 SRX8145091 SRS6507827 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.9363   0.16883   0.70325   0.50421   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Multi-stage Multi-stage Brain Nervous System
59028 59028 SRR11577273 SRX8145090 SRS6507826 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 social 2 20171109 8dpf soc   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 11 09|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:2|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D708 D504 D708 D504 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171109__8dpf_soc_S4_R1_001.fastq.gz fastq 3315005132.0 25084324.0 20171109 8dpf soc S4 R1 001.fastq.gz 0:132.15 1:0 A:943965767;C:716020466;G:709793117;T:943523271;N:1702511 132 0     943965767 716020466 709793117 943523271 1702511 SRX8145090 SRS6507826 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94089   0.15844   0.68314   0.48662   150   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59029 59029 SRR11577274 SRX8145089 SRS6507825 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 iso 2 20171109 8dpf iso   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 11 09|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:2|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D708 D503 D708 D503 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171109__8dpf_iso_S3_R1_001.fastq.gz fastq 2050353509.0 15447845.0 20171109 8dpf iso S3 R1 001.fastq.gz 0:132.73 1:0 A:587865535;C:439314529;G:435742480;T:586757262;N:673703 132 0     587865535 439314529 435742480 586757262 673703 SRX8145089 SRS6507825 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93978   0.1602   0.67381   0.48469   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59030 59030 SRR11577275 SRX8145088 SRS6507824 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 social 1 20171102 8dpf soc   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 11 02|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:1|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D708 D502 D708 D502 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171102__8dpf_soc_S2_R1_001.fastq.gz fastq 1343770858.0 9948770.0 20171102 8dpf soc S2 R1 001.fastq.gz 0:135.07 1:0 A:393209270;C:281371562;G:280065221;T:388373414;N:751391 135 0     393209270 281371562 280065221 388373414 751391 SRX8145088 SRS6507824 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93753   0.16528   0.67478   0.48859   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59031 59031 SRR11577276 SRX8145087 SRS6507823 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 iso 1 20171102 8dpf iso   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 11 02|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:1|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D708 D501 D708 D501 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171102__8dpf_iso_S1_R1_001.fastq.gz fastq 2222891523.0 16512518.0 20171102 8dpf iso S1 R1 001.fastq.gz 0:134.62 1:0 A:612900253;C:492583648;G:489352034;T:626301202;N:1754386 134 0     612900253 492583648 489352034 626301202 1754386 SRX8145087 SRS6507823 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94375   0.14492   0.67117   0.4862   150   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59032 59032 SRR11577277 SRX8145086 SRS6507822 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 iso 6 20170222B 5dpf iso   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 22|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:6|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A019 A019 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170222B_5dpf_iso_S12_R1_001.fastq.gz fastq 1384115190.0 10880190.0 20170222B 5dpf iso S12 R1 001.fastq.gz 0:127.21 1:0 A:374024483;C:300637678;G:306091186;T:396608297;N:6753546 127 0     374024483 300637678 306091186 396608297 6753546 SRX8145086 SRS6507822 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93966   0.14845   0.66145   0.49277   135   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59033 59033 SRR11577278 SRX8145085 SRS6507821 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 social 6 20170222B 5dpf soc   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 22|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:6|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A018 A018 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170222B_5dpf_soc_S11_R1_001.fastq.gz fastq 1509062868.0 11709685.0 20170222B 5dpf soc S11 R1 001.fastq.gz 0:128.87 1:0 A:424881841;C:317025415;G:321339469;T:440828991;N:4987152 128 0     424881841 317025415 321339469 440828991 4987152 SRX8145085 SRS6507821 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92918   0.18084   0.67067   0.48693   113   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59034 59034 SRR11577279 SRX8145084 SRS6507820 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 iso 1 20170201 5pdf iso   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 01|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:1|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A004 A004 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170201_5pdf_iso_S2_R1_001.fastq.gz fastq 2182551927.0 16660472.0 20170201 5pdf iso S2 R1 001.fastq.gz 0:131.00 1:0 A:585229301;C:487317339;G:480857079;T:626932180;N:2216028 131 0     585229301 487317339 480857079 626932180 2216028 SRX8145084 SRS6507820 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94677   0.13688   0.6633   0.47121   145   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59035 59035 SRR11577280 SRX8145083 SRS6507819 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 social 1 20170201 5dpf soc   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 01|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:1|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A002 A002 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170201_5dpf_soc_S1_R1_001.fastq.gz fastq 1713105557.0 13585484.0 20170201 5dpf soc S1 R1 001.fastq.gz 0:126.10 1:0 A:446628660;C:370803315;G:376374066;T:481602204;N:37697312 126 0     446628660 370803315 376374066 481602204 37697312 SRX8145083 SRS6507819 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94527   0.13591   0.66302   0.48385   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
60007 60007 SRR12109607 SRX8633610 SRS6920345 SRP269241 PRJNA641989 Zebrafish intestinal SmallRNA PRJNA641989 Other A model of streptococcus agalactiae infected zebrafish was established to determine intestinal small RNA of zebrafish.To explore the molecular mechanism of antibacterial immunity of zebrafish.         Drt3   strain:Streptococcus agalactiae|age:adult|sex:male|tissue:gut|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish intestine F F BGISEQ     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE BGISEQ BGISEQ-500   SRP269241   loader:fastq load.py Drt3.fq.gz fastq 953116651.0 39450392.0 Drt3.fq.gz 0:24.16 A:165275545;C:266933722;G:285524079;T:235383107;N:198 24       165275545 266933722 285524079 235383107 198 SRX8633610 SRS6920345 SRA1092425 Kunming University of Science and Technology|faculty of life science and technology Kunming University of Science and Technology 1 0.86243   0.21541   0.80294   0.67181   29   B   usable mapping rate bgi bgi unknown small_rna unknown bulk unknown unknown   China 2020-07-10 Adult Adult Gut Digestive System
60008 60008 SRR12109608 SRX8633609 SRS6920344 SRP269241 PRJNA641989 Zebrafish intestinal SmallRNA PRJNA641989 Other A model of streptococcus agalactiae infected zebrafish was established to determine intestinal small RNA of zebrafish.To explore the molecular mechanism of antibacterial immunity of zebrafish.         Drt2   strain:Streptococcus agalactiae|age:adult|sex:male|tissue:gut|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish intestine E E BGISEQ     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE BGISEQ BGISEQ-500   SRP269241   loader:fastq load.py Drt2.fq.gz fastq 629335361.0 26037543.0 Drt2.fq.gz 0:24.17 A:111827613;C:172564695;G:192159133;T:152783892;N:28 24       111827613 172564695 192159133 152783892 28 SRX8633609 SRS6920344 SRA1092425 Kunming University of Science and Technology|faculty of life science and technology Kunming University of Science and Technology 1 0.86328   0.21943   0.7992   0.64786   26   B   usable mapping rate bgi bgi unknown small_rna unknown bulk unknown unknown   China 2020-07-10 Adult Adult Gut Digestive System
60009 60009 SRR12109609 SRX8633608 SRS6920343 SRP269241 PRJNA641989 Zebrafish intestinal SmallRNA PRJNA641989 Other A model of streptococcus agalactiae infected zebrafish was established to determine intestinal small RNA of zebrafish.To explore the molecular mechanism of antibacterial immunity of zebrafish.         Drt1   strain:Streptococcus agalactiae|age:adult|sex:male|tissue:gut|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish intestine D D BGISEQ     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE BGISEQ BGISEQ-500   SRP269241   loader:fastq load.py Drt1.fq.gz fastq 898185854.0 37273958.0 Drt1.fq.gz 0:24.10 A:155257170;C:247725871;G:276963807;T:218238980;N:26 24       155257170 247725871 276963807 218238980 26 SRX8633608 SRS6920343 SRA1092425 Kunming University of Science and Technology|faculty of life science and technology Kunming University of Science and Technology 1 0.86686   0.21764   0.79508   0.6694   24   B   usable mapping rate bgi bgi unknown small_rna unknown bulk unknown unknown   China 2020-07-10 Adult Adult Gut Digestive System
60010 60010 SRR12109610 SRX8633607 SRS6920342 SRP269241 PRJNA641989 Zebrafish intestinal SmallRNA PRJNA641989 Other A model of streptococcus agalactiae infected zebrafish was established to determine intestinal small RNA of zebrafish.To explore the molecular mechanism of antibacterial immunity of zebrafish.         Drc3   strain:Streptococcus agalactiae|age:adult|sex:male|tissue:gut|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish intestine C C BGISEQ     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE BGISEQ BGISEQ-500   SRP269241   loader:fastq load.py Drc3.fq.gz fastq 912782161.0 35931507.0 Drc3.fq.gz 0:25.40 A:153448479;C:252628189;G:280829895;T:225874586;N:1012 25       153448479 252628189 280829895 225874586 1012 SRX8633607 SRS6920342 SRA1092425 Kunming University of Science and Technology|faculty of life science and technology Kunming University of Science and Technology 1 0.89797   0.21308   0.80823   0.62611   23   B   usable mapping rate bgi bgi unknown small_rna unknown bulk unknown unknown   China 2020-07-10 Adult Adult Gut Digestive System
60011 60011 SRR12109611 SRX8633606 SRS6920341 SRP269241 PRJNA641989 Zebrafish intestinal SmallRNA PRJNA641989 Other A model of streptococcus agalactiae infected zebrafish was established to determine intestinal small RNA of zebrafish.To explore the molecular mechanism of antibacterial immunity of zebrafish.         Drc2   strain:Streptococcus agalactiae|age:adult|sex:male|tissue:gut|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish intestine B B BGISEQ     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE BGISEQ BGISEQ-500   SRP269241   loader:fastq load.py Drc2.fq.gz fastq 784553020.0 31429473.0 Drc2.fq.gz 0:24.96 A:128271350;C:223302609;G:241310233;T:191668193;N:635 24       128271350 223302609 241310233 191668193 635 SRX8633606 SRS6920341 SRA1092425 Kunming University of Science and Technology|faculty of life science and technology Kunming University of Science and Technology 1 0.9087   0.20487   0.80805   0.67324   30   B   usable mapping rate bgi bgi unknown small_rna unknown bulk unknown unknown   China 2020-07-10 Adult Adult Gut Digestive System
60012 60012 SRR12109612 SRX8633605 SRS6920340 SRP269241 PRJNA641989 Zebrafish intestinal SmallRNA PRJNA641989 Other A model of streptococcus agalactiae infected zebrafish was established to determine intestinal small RNA of zebrafish.To explore the molecular mechanism of antibacterial immunity of zebrafish.         Drc1   strain:Streptococcus agalactiae|age:adult|sex:male|tissue:gut|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish intestine A A BGISEQ     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE BGISEQ BGISEQ-500   SRP269241   loader:fastq load.py Drc1.fq.gz fastq 814894343.0 32234530.0 Drc1.fq.gz 0:25.28 A:133616147;C:230834630;G:253965304;T:196477437;N:825 25       133616147 230834630 253965304 196477437 825 SRX8633605 SRS6920340 SRA1092425 Kunming University of Science and Technology|faculty of life science and technology Kunming University of Science and Technology 1 0.89344   0.21273   0.80738   0.66815   28   B   usable mapping rate bgi bgi unknown small_rna unknown bulk unknown unknown   China 2020-07-10 Adult Adult Gut Digestive System
61655 61655 SRR12903379 SRX9368290 SRS7590200 SRP288657 PRJNA672138 RNA seq of zebrafish HSCs of cftr mutant at 48hpf PRJNA672138 Other To reveal the role of cftr in HSC of zebrafish embryo at 48hpf       cmyb+GFP HSC cmyb+GFP HSC   strain:AB|isolate:FACS|breed:Egg water|age:0.8year|dev stage:48hpf|sex:not applicable|tissue:HSC|cell line:HSC|cell type:HSC|collected by:FACS|BioSampleModel:Model organism or animal                 RNA Seq of cftr mutant cmyb+GFP HSC 2 2 cftr mutant cmyb+GFP HSC     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP288657     CF-HSC_L4_Q803604.R1.fastq.gz CF-HSC_L4_Q803604.R2.fastq.gz fastq fastq 9923396100.0 33077987.0 CF HSC L4 Q803604.R1.fastq.gz 0:150 1:150 A:2814592323;C:2140796492;G:2161622902;T:2806345512;N:38871 150 150     2814592323 2140796492 2161622902 2806345512 38871 SRX9368290 SRS7590200 SRA1148101 Sichuan University|West China Second University Hospital Sichuan University 2 0.92974 0.93014 0.25254 0.25232 0.739 0.73933 0.51947 0.51997 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-10-26 Multi-stage Multi-stage Cell Line Cell Line
61656 61656 SRR12903380 SRX9368289 SRS7590200 SRP288657 PRJNA672138 RNA seq of zebrafish HSCs of cftr mutant at 48hpf PRJNA672138 Other To reveal the role of cftr in HSC of zebrafish embryo at 48hpf       cmyb+GFP HSC cmyb+GFP HSC   strain:AB|isolate:FACS|breed:Egg water|age:0.8year|dev stage:48hpf|sex:not applicable|tissue:HSC|cell line:HSC|cell type:HSC|collected by:FACS|BioSampleModel:Model organism or animal                 RNA Seq of WT cmyb+GFP HSC 1 1 WT cmyb+GFP HSC     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP288657     WT-HSC_L4_Q802604.R1.fastq.gz WT-HSC_L4_Q802604.R2.fastq.gz fastq fastq 10530660600.0 35102202.0 WT HSC L4 Q802604.R1.fastq.gz 0:150 1:150 A:2977953142;C:2283045134;G:2298868821;T:2970751970;N:41533 150 150     2977953142 2283045134 2298868821 2970751970 41533 SRX9368289 SRS7590200 SRA1148101 Sichuan University|West China Second University Hospital Sichuan University 2 0.93722 0.93625 0.21368 0.21331 0.72859 0.729 0.49389 0.49309 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-10-26 Multi-stage Multi-stage Cell Line Cell Line
65669 65669 SRR15498138 SRX11797853 SRS9797787 SRP332839 PRJNA755482 miRNA sequencing from zebrafish testes and ovaries exposed to normal and high temperatures PRJNA755482 Other We exposed zebrafish to elevated temperatures during early development a treatment that is known to result in male skewed sex ratios in order to understand the role of the epigenetic regulation mediated by miRNAs in the gonads.       Ovary High Temperature ZF 36 G12F   strain:AB|age:90 dpf|sex:female|tissue:Ovary|replicate:Biological replicate OHT 2|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult treated ovary 36 G12 36 G12 NEBNext Small RNA Library Prep Set for Illumina was used on total RNA isolated from zebrafish ovary using Qiagen RNeasy mini kit. Library was constructed using sequencing Lane 1x50 v4 HiSeq single end mode with a read length of 50 bp     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_36_G12_22313_ATGAGC.fastq ZF_36_G12_24794_ATGAGC.fastq fastq fastq 385298900.0 7705978.0 ZF 36 G12 22313 ATGAGC.fastq 0:50 1:0 A:115879319;C:84755497;G:100335882;T:84312716;N:15486 50 0     115879319 84755497 100335882 84312716 15486 SRX11797853 SRS9797787 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.76472   0.49644   0.83287   0.51149   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65670 65670 SRR15498139 SRX11797852 SRS9797788 SRP332839 PRJNA755482 miRNA sequencing from zebrafish testes and ovaries exposed to normal and high temperatures PRJNA755482 Other We exposed zebrafish to elevated temperatures during early development a treatment that is known to result in male skewed sex ratios in order to understand the role of the epigenetic regulation mediated by miRNAs in the gonads.       Ovary High Temperature ZF 36 G9F   strain:AB|age:90 dpf|sex:female|tissue:Ovary|replicate:Biological replicate OHT 1|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult treated ovary 36 G9 36 G9 NEBNext Small RNA Library Prep Set for Illumina was used on total RNA isolated from zebrafish ovary using Qiagen RNeasy mini kit. Library was constructed using sequencing Lane 1x50 v4 HiSeq single end mode with a read length of 50 bp     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_36_G9_22313_ACTGAT.fastq ZF_36_G9_24794_ACTGAT.fastq fastq fastq 448040450.0 8960809.0 ZF 36 G9 22313 ACTGAT.fastq 0:50 1:0 A:134152732;C:98754272;G:116124383;T:98987716;N:21347 50 0     134152732 98754272 116124383 98987716 21347 SRX11797852 SRS9797788 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.73407   0.52835   0.83092   0.53201   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65671 65671 SRR15498140 SRX11797851 SRS9797786 SRP332839 PRJNA755482 miRNA sequencing from zebrafish testes and ovaries exposed to normal and high temperatures PRJNA755482 Other We exposed zebrafish to elevated temperatures during early development a treatment that is known to result in male skewed sex ratios in order to understand the role of the epigenetic regulation mediated by miRNAs in the gonads.       Testis Low Temperature ZF 28 G11M   strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate TLT 2|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult untreated testis 28 G11 28 G11 NEBNext Small RNA Library Prep Set for Illumina was used on total RNA isolated from zebrafish testis using Qiagen RNeasy mini kit. Library was constructed using sequencing Lane 1x50 v4 HiSeq single end mode with a read length of 50 bp     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_28_G11_22312_CACCGG.fastq fastq 397315650.0 7946313.0 ZF 28 G11 22312 CACCGG.fastq 0:50 1:0 A:117553892;C:87676340;G:103796431;T:88242064;N:46923 50 0     117553892 87676340 103796431 88242064 46923 SRX11797851 SRS9797786 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.7153   0.45777   0.85131   0.51595   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System

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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");;