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814 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "unknown" and tissue_curation = "Multi-tissue"

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experiment.library_selection 10

devstage_curation 7

experiment.library_strategy 5

devstage_curation_coarse 4

experiment.platform 3

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Multi-tissue · 814 ✖

technology 1

  • unknown · 814 ✖

experiment.library_source 1

  • TRANSCRIPTOMIC · 814 ✖
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
51 51 DRR029943 DRX026961 DRS086501 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     oocyte maturation duirng natural paring zebrafish ovary isolated from adult fish at oocyte maturation duirng natural paring. [RNAseq] SAMD00025433   sample name:5 OM|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025433 DRX026961 5 OM 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025433       573617016.0 15933806.0 DRR029943 0:36 A:130606804;C:141376330;G:145891720;T:155734276;N:7886 36       130606804 141376330 145891720 155734276 7886 DRX026961 DRS086501 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91108   0.0173   0.76205   0.46319   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Multi-tissue Multi-system
168 168 DRR075402 DRX069316 DRS075497 DRP004473 PRJDB5226 Effects of local gut tumor on whole organismal gene expressions in zebrafish DRP004473 Other How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.     The liver of tumor fish 7dpf Tumor liver SAMD00065416   sample name:6 Tumor liver 150701 Hiseq3A l3 022|tissue type:Liver                 Illumina HiSeq 2500 sequencing of SAMD00065416 DRX069316 Tumor liver 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004473 Illumina HiSeq 2500 sequencing of SAMD00065416       1091167236.0 30310201.0 DRR075402 0:36 A:272216839;C:257523620;G:259746158;T:301642763;N:37856 36       272216839 257523620 259746158 301642763 37856 DRX069316 DRS075497 DRA005199 ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International 1 0.90443   0.08935   0.71863   0.51145   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2018-09-19 Larval Larval Multi-tissue Multi-system
169 169 DRR075401 DRX069315 DRS075496 DRP004473 PRJDB5226 Effects of local gut tumor on whole organismal gene expressions in zebrafish DRP004473 Other How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.     The gut of tumor fish 7dpf Tumor gut SAMD00065415   sample name:5 Tumor gut 150701 Hiseq3A l3 021|tissue type:Gut                 Illumina HiSeq 2500 sequencing of SAMD00065415 DRX069315 Tumor gut 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004473 Illumina HiSeq 2500 sequencing of SAMD00065415       1423792872.0 39549802.0 DRR075401 0:36 A:342328685;C:346616167;G:341519547;T:393278536;N:49937 36       342328685 346616167 341519547 393278536 49937 DRX069315 DRS075496 DRA005199 ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International 1 0.91303   0.0869   0.70494   0.44332   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2018-09-19 Larval Larval Multi-tissue Multi-system
170 170 DRR075400 DRX069314 DRS075495 DRP004473 PRJDB5226 Effects of local gut tumor on whole organismal gene expressions in zebrafish DRP004473 Other How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.     The remaining part of body of tumor fish 7dpf Tumor body SAMD00065414   sample name:4 Tumor body 150701 Hiseq3A l3 020|tissue type:Body                 Illumina HiSeq 2500 sequencing of SAMD00065414 DRX069314 Tumor body 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004473 Illumina HiSeq 2500 sequencing of SAMD00065414       1168514964.0 32458749.0 DRR075400 0:36 A:286579925;C:275496498;G:278133055;T:328265078;N:40408 36       286579925 275496498 278133055 328265078 40408 DRX069314 DRS075495 DRA005199 ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International 1 0.89927   0.15051   0.66714   0.47579   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2018-09-19 Larval Larval Multi-tissue Multi-system
175 175 DRR084197 DRX078028 DRS086522 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     natural paring early sample zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate2] SAMD00073604   sample name:M 4th|replicate:biological replicate 2                 Illumina HiSeq 2500 sequencing of SAMD00073604 DRX078028 zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate2] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073604       1389837888.0 38606608.0 DRR084197 0:36 A:320671418;C:336948866;G:347550258;T:381720581;N:2946765 36       320671418 336948866 347550258 381720581 2946765 DRX078028 DRS086522 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.89763   0.02235   0.76445   0.46381   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Zygote Embryo Multi-tissue Multi-system
181 181 DRR084191 DRX078022 DRS086516 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     natural paring early sample zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate1] SAMD00073598   sample name:M|replicate:biological replicate 1                 Illumina HiSeq 2500 sequencing of SAMD00073598 DRX078022 zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate1] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073598       1050981012.0 29193917.0 DRR084191 0:36 A:241048832;C:256186268;G:260277071;T:293299597;N:169244 36       241048832 256186268 260277071 293299597 169244 DRX078022 DRS086516 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.9088   0.02369   0.7624   0.47998   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Zygote Embryo Multi-tissue Multi-system
3703 3703 ERR1397087 ERX1468346 ERS1023493 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 186 1 8 SAMEA3716344 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 9 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716344|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:44Z|INSDC status:public|Submitter Id:2362a210 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 9 mpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TCTCTTCA is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph186|sample name:2362a210 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#56 15566396 Illumina sequencing of library 15566396 constructed from sample accession ERS1023493 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TCTCTTCA. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#56.cram cram 707144490.0 5439573.0 SC RUN 18715 8#56 0:55 1:75 A:188121373;C:125159654;G:138365161;T:255495006;N:3296 55 75     188121373 125159654 138365161 255495006 3296 ERX1468346 ERS1023493 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.25954 0.84737 0.1072 0.10684 0.96889 0.90337 0.7843 0.68587 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3704 3704 ERR1397086 ERX1468345 ERS1023492 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 186 1 7 SAMEA3716343 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 9 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716343|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:43Z|INSDC status:public|Submitter Id:2359a160 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 9 mpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TGTGAAGA is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph186|sample name:2359a160 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#55 15566395 Illumina sequencing of library 15566395 constructed from sample accession ERS1023492 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TGTGAAGA. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#55.cram cram 618409870.0 4756999.0 SC RUN 18715 8#55 0:55 1:75 A:169528505;C:106711234;G:111143607;T:231024694;N:1830 55 75     169528505 106711234 111143607 231024694 1830 ERX1468345 ERS1023492 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.31798 0.81356 0.1471 0.11489 0.9707 0.89708 0.48844 0.54567 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3705 3705 ERR1397085 ERX1468344 ERS1023491 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 186 1 6 SAMEA3716342 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 9 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716342|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:43Z|INSDC status:public|Submitter Id:2350a0b0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 9 mpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TAGACGGA is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph186|sample name:2350a0b0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#54 15566394 Illumina sequencing of library 15566394 constructed from sample accession ERS1023491 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TAGACGGA. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#54.cram cram 714746240.0 5498048.0 SC RUN 18715 8#54 0:55 1:75 A:192003042;C:125908202;G:130551705;T:266281416;N:1875 55 75     192003042 125908202 130551705 266281416 1875 ERX1468344 ERS1023491 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.28492 0.84395 0.14733 0.11571 0.9727 0.90149 0.81768 0.65432 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3706 3706 ERR1397084 ERX1468343 ERS1023490 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 186 1 5 SAMEA3716341 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 9 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716341|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:43Z|INSDC status:public|Submitter Id:234778f0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 9 mpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TGCTGATA is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph186|sample name:234778f0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#53 15566393 Illumina sequencing of library 15566393 constructed from sample accession ERS1023490 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TGCTGATA. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#53.cram cram 746119400.0 5739380.0 SC RUN 18715 8#53 0:55 1:75 A:202741777;C:128874768;G:133432494;T:281067099;N:3262 55 75     202741777 128874768 133432494 281067099 3262 ERX1468343 ERS1023490 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.28545 0.827 0.17591 0.11992 0.97165 0.89483 0.77417 0.62382 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3707 3707 ERR1397083 ERX1468342 ERS1023489 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 186 1 4 SAMEA3716340 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 9 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716340|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:42Z|INSDC status:public|Submitter Id:233e7840 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 9 mpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TCGTTAGC is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph186|sample name:233e7840 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#52 15566392 Illumina sequencing of library 15566392 constructed from sample accession ERS1023489 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TCGTTAGC. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#52.cram cram 776598680.0 5973836.0 SC RUN 18715 8#52 0:55 1:75 A:207406716;C:137168865;G:146112068;T:285908651;N:2380 55 75     207406716 137168865 146112068 285908651 2380 ERX1468342 ERS1023489 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.27793 0.8492 0.1319 0.11351 0.97145 0.90366 0.80649 0.66871 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3708 3708 ERR1397082 ERX1468341 ERS1023488 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 186 1 3 SAMEA3716339 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 9 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716339|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:42Z|INSDC status:public|Submitter Id:23355080 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 9 mpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TTACTCGC is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph186|sample name:23355080 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#51 15566391 Illumina sequencing of library 15566391 constructed from sample accession ERS1023488 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TTACTCGC. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#51.cram cram 636459330.0 4895841.0 SC RUN 18715 8#51 0:55 1:75 A:170841699;C:107415456;G:118061456;T:240137938;N:2781 55 75     170841699 107415456 118061456 240137938 2781 ERX1468341 ERS1023488 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.33457 0.84812 0.16722 0.11863 0.97165 0.88755 0.82802 0.54829 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3709 3709 ERR1397081 ERX1468340 ERS1023487 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 186 1 2 SAMEA3716338 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 9 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716338|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:41Z|INSDC status:public|Submitter Id:232c01b0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 9 mpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TATGTGGC is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph186|sample name:232c01b0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#50 15566390 Illumina sequencing of library 15566390 constructed from sample accession ERS1023487 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TATGTGGC. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#50.cram cram 762887060.0 5868362.0 SC RUN 18715 8#50 0:55 1:75 A:205092929;C:134351479;G:140981680;T:282458912;N:2060 55 75     205092929 134351479 140981680 282458912 2060 ERX1468340 ERS1023487 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.29975 0.85617 0.14999 0.11598 0.97023 0.8981 0.81631 0.69434 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3710 3710 ERR1397080 ERX1468339 ERS1023486 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 186 1 1 SAMEA3716337 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 9 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716337|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:41Z|INSDC status:public|Submitter Id:2322d9f0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 9 mpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TGTCTATC is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph186|sample name:2322d9f0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#49 15566389 Illumina sequencing of library 15566389 constructed from sample accession ERS1023486 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TGTCTATC. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#49.cram cram 654882020.0 5037554.0 SC RUN 18715 8#49 0:55 1:75 A:176142868;C:110275594;G:118303230;T:250156724;N:3604 55 75     176142868 110275594 118303230 250156724 3604 ERX1468339 ERS1023486 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.33949 0.8483 0.176 0.09714 0.97542 0.90749 0.84111 0.67388 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3711 3711 ERR1397079 ERX1468338 ERS1023485 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 24 SAMEA3716336 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716336|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:40Z|INSDC status:public|Submitter Id:2319d940 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TTCAGCTC is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:2319d940 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#48 15566388 Illumina sequencing of library 15566388 constructed from sample accession ERS1023485 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TTCAGCTC. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#48.cram cram 677343030.0 5210331.0 SC RUN 18715 8#48 0:55 1:75 A:177744951;C:121003073;G:129268553;T:249323382;N:3071 55 75     177744951 121003073 129268553 249323382 3071 ERX1468338 ERS1023485 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.27162 0.86035 0.10137 0.08341 0.97573 0.91376 0.82856 0.62728 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3712 3712 ERR1397078 ERX1468337 ERS1023484 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 23 SAMEA3716335 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716335|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:40Z|INSDC status:public|Submitter Id:2310b180 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TACTAGTC is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:2310b180 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#47 15566387 Illumina sequencing of library 15566387 constructed from sample accession ERS1023484 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TACTAGTC. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#47.cram cram 756384720.0 5818344.0 SC RUN 18715 8#47 0:55 1:75 A:204421756;C:131322874;G:139056982;T:281579686;N:3422 55 75     204421756 131322874 139056982 281579686 3422 ERX1468337 ERS1023484 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.31847 0.85466 0.13579 0.08314 0.97559 0.91484 0.85907 0.69484 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3713 3713 ERR1397077 ERX1468336 ERS1023483 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 22 SAMEA3716334 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716334|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:39Z|INSDC status:public|Submitter Id:2307b0d0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TCAGATTC is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:2307b0d0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#46 15566386 Illumina sequencing of library 15566386 constructed from sample accession ERS1023483 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TCAGATTC. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#46.cram cram 736276970.0 5663669.0 SC RUN 18715 8#46 0:55 1:75 A:195907677;C:131386929;G:137210683;T:271768338;N:3343 55 75     195907677 131386929 137210683 271768338 3343 ERX1468336 ERS1023483 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.25731 0.83896 0.10708 0.0752 0.97725 0.91829 0.82893 0.68981 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3714 3714 ERR1397076 ERX1468335 ERS1023482 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 21 SAMEA3716333 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716333|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:39Z|INSDC status:public|Submitter Id:22feb020 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TATGCCAG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:22feb020 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#45 15566385 Illumina sequencing of library 15566385 constructed from sample accession ERS1023482 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TATGCCAG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#45.cram cram 666434860.0 5126422.0 SC RUN 18715 8#45 0:55 1:75 A:175545494;C:119084096;G:124317188;T:247486133;N:1949 55 75     175545494 119084096 124317188 247486133 1949 ERX1468335 ERS1023482 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.28297 0.85288 0.13833 0.10107 0.97534 0.90991 0.80466 0.52355 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3715 3715 ERR1397075 ERX1468334 ERS1023481 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 20 SAMEA3716332 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716332|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:38Z|INSDC status:public|Submitter Id:22f5af70 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TGGCTCAG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:22f5af70 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#44 15566384 Illumina sequencing of library 15566384 constructed from sample accession ERS1023481 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TGGCTCAG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#44.cram cram 695152510.0 5347327.0 SC RUN 18715 8#44 0:55 1:75 A:184288447;C:123186272;G:129742627;T:257932830;N:2334 55 75     184288447 123186272 129742627 257932830 2334 ERX1468334 ERS1023481 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.31006 0.8513 0.12966 0.09655 0.97461 0.91423 0.8429 0.69582 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3716 3716 ERR1397074 ERX1468333 ERS1023480 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 19 SAMEA3716331 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716331|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:38Z|INSDC status:public|Submitter Id:22ecaec0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TCATTGAG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:22ecaec0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#43 15566383 Illumina sequencing of library 15566383 constructed from sample accession ERS1023480 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TCATTGAG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#43.cram cram 533568230.0 4104371.0 SC RUN 18715 8#43 0:55 1:75 A:143539058;C:96004871;G:98641156;T:195381631;N:1514 55 75     143539058 96004871 98641156 195381631 1514 ERX1468333 ERS1023480 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.2816 0.83134 0.10829 0.09548 0.97463 0.91463 0.82774 0.63791 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3717 3717 ERR1397073 ERX1468332 ERS1023479 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 18 SAMEA3716330 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716330|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:37Z|INSDC status:public|Submitter Id:22e3ae10 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TGTATGCG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:22e3ae10 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#42 15566382 Illumina sequencing of library 15566382 constructed from sample accession ERS1023479 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TGTATGCG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#42.cram cram 661945700.0 5091890.0 SC RUN 18715 8#42 0:55 1:75 A:179311956;C:118843676;G:120891014;T:242897159;N:1895 55 75     179311956 118843676 120891014 242897159 1895 ERX1468332 ERS1023479 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.29346 0.84765 0.13347 0.11035 0.97303 0.91295 0.80889 0.64077 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3718 3718 ERR1397072 ERX1468331 ERS1023478 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 17 SAMEA3716329 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716329|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:37Z|INSDC status:public|Submitter Id:22daad60 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TCCAGTCG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:22daad60 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#41 15566381 Illumina sequencing of library 15566381 constructed from sample accession ERS1023478 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TCCAGTCG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#41.cram cram 665846740.0 5121898.0 SC RUN 18715 8#41 0:55 1:75 A:176220973;C:118768091;G:124615863;T:246239820;N:1993 55 75     176220973 118768091 124615863 246239820 1993 ERX1468331 ERS1023478 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.28802 0.86238 0.12173 0.09559 0.97262 0.90765 0.80726 0.66136 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3719 3719 ERR1397071 ERX1468330 ERS1023477 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 16 SAMEA3716328 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716328|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:36Z|INSDC status:public|Submitter Id:22d1acb0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TAAGTTCG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:22d1acb0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#40 15566380 Illumina sequencing of library 15566380 constructed from sample accession ERS1023477 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TAAGTTCG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#40.cram cram 619781760.0 4767552.0 SC RUN 18715 8#40 0:55 1:75 A:166468116;C:111775459;G:114959803;T:226576853;N:1529 55 75     166468116 111775459 114959803 226576853 1529 ERX1468330 ERS1023477 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.27098 0.83733 0.10627 0.08837 0.97457 0.90989 0.82134 0.55638 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3720 3720 ERR1397070 ERX1468329 ERS1023476 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 15 SAMEA3716327 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716327|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:36Z|INSDC status:public|Submitter Id:22c884f0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TCAGGAGG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:22c884f0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#39 15566379 Illumina sequencing of library 15566379 constructed from sample accession ERS1023476 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TCAGGAGG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#39.cram cram 651681420.0 5012934.0 SC RUN 18715 8#39 0:55 1:75 A:177714223;C:117422574;G:117918287;T:238624462;N:1874 55 75     177714223 117422574 117918287 238624462 1874 ERX1468329 ERS1023476 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.30203 0.82354 0.13321 0.08477 0.97595 0.91587 0.83389 0.66905 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3721 3721 ERR1397069 ERX1468328 ERS1023475 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 14 SAMEA3716326 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716326|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:36Z|INSDC status:public|Submitter Id:22bf8440 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TCTCACGG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:22bf8440 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#38 15566378 Illumina sequencing of library 15566378 constructed from sample accession ERS1023475 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TCTCACGG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#38.cram cram 662342720.0 5094944.0 SC RUN 18715 8#38 0:55 1:75 A:178580497;C:115417983;G:120453380;T:247888799;N:2061 55 75     178580497 115417983 120453380 247888799 2061 ERX1468328 ERS1023475 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.30376 0.86314 0.16369 0.09566 0.97739 0.91557 0.82256 0.68053 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3722 3722 ERR1397068 ERX1468327 ERS1023474 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 13 SAMEA3716325 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716325|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:35Z|INSDC status:public|Submitter Id:22b68390 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf tert wild type sibling adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The wild type adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter wild type fish from the clutch. A 8 base indexing sequence TACTTCGG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:22b68390 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#37 15566377 Illumina sequencing of library 15566377 constructed from sample accession ERS1023474 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TACTTCGG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#37.cram cram 696072520.0 5354404.0 SC RUN 18715 8#37 0:55 1:75 A:186700497;C:125763963;G:128699401;T:254906770;N:1889 55 75     186700497 125763963 128699401 254906770 1889 ERX1468327 ERS1023474 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.27617 0.85667 0.1301 0.08773 0.97684 0.91514 0.79798 0.64081 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3723 3723 ERR1397067 ERX1468326 ERS1023473 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 12 SAMEA3716324 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716324|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:35Z|INSDC status:public|Submitter Id:22ad82e0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TGAACTGG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:22ad82e0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#36 15566376 Illumina sequencing of library 15566376 constructed from sample accession ERS1023473 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TGAACTGG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#36.cram cram 731306420.0 5625434.0 SC RUN 18715 8#36 0:55 1:75 A:193958125;C:134273924;G:136394750;T:266677546;N:2075 55 75     193958125 134273924 136394750 266677546 2075 ERX1468326 ERS1023473 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.24621 0.84195 0.08689 0.07535 0.97638 0.91851 0.80524 0.61404 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3724 3724 ERR1397066 ERX1468325 ERS1023472 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 11 SAMEA3716323 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716323|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:34Z|INSDC status:public|Submitter Id:22a45b20 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TTGGTATG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:22a45b20 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#35 15566375 Illumina sequencing of library 15566375 constructed from sample accession ERS1023472 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TTGGTATG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#35.cram cram 665997670.0 5123059.0 SC RUN 18715 8#35 0:55 1:75 A:181566480;C:120809592;G:121644240;T:241975360;N:1998 55 75     181566480 120809592 121644240 241975360 1998 ERX1468325 ERS1023472 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.26496 0.82274 0.10057 0.07626 0.97441 0.91595 0.81657 0.64747 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3725 3725 ERR1397065 ERX1468324 ERS1023471 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 10 SAMEA3716322 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716322|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:34Z|INSDC status:public|Submitter Id:229b8180 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TAACGCTG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:229b8180 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#34 15566374 Illumina sequencing of library 15566374 constructed from sample accession ERS1023471 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TAACGCTG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#34.cram cram 694634590.0 5343343.0 SC RUN 18715 8#34 0:55 1:75 A:186244179;C:125715272;G:128699352;T:253973213;N:2574 55 75     186244179 125715272 128699352 253973213 2574 ERX1468324 ERS1023471 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.26311 0.82812 0.10775 0.09376 0.97313 0.90983 0.80442 0.5326 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3726 3726 ERR1397064 ERX1468323 ERS1023470 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 9 SAMEA3716321 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716321|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:33Z|INSDC status:public|Submitter Id:228fe8c0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TCGAAGTG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:228fe8c0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#33 15566373 Illumina sequencing of library 15566373 constructed from sample accession ERS1023470 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TCGAAGTG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#33.cram cram 694711290.0 5343933.0 SC RUN 18715 8#33 0:55 1:75 A:188079963;C:126858196;G:128818574;T:250952301;N:2256 55 75     188079963 126858196 128818574 250952301 2256 ERX1468323 ERS1023470 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.25746 0.83173 0.07713 0.08005 0.97437 0.91431 0.83094 0.63526 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3727 3727 ERR1397063 ERX1468322 ERS1023469 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 8 SAMEA3716320 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716320|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:33Z|INSDC status:public|Submitter Id:2286e810 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TTCCATTG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:2286e810 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#32 15566372 Illumina sequencing of library 15566372 constructed from sample accession ERS1023469 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TTCCATTG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#32.cram cram 655146440.0 5039588.0 SC RUN 18715 8#32 0:55 1:75 A:178645019;C:116883757;G:120893841;T:238720622;N:3201 55 75     178645019 116883757 120893841 238720622 3201 ERX1468322 ERS1023469 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.24055 0.83244 0.1125 0.10225 0.97291 0.90928 0.77504 0.6656 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3728 3728 ERR1397062 ERX1468321 ERS1023468 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 7 SAMEA3716319 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716319|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:32Z|INSDC status:public|Submitter Id:227caee0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TAGTCTTG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:227caee0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#31 15566371 Illumina sequencing of library 15566371 constructed from sample accession ERS1023468 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TAGTCTTG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#31.cram cram 730891590.0 5622243.0 SC RUN 18715 8#31 0:55 1:75 A:198514053;C:130409691;G:134606848;T:267358664;N:2334 55 75     198514053 130409691 134606848 267358664 2334 ERX1468321 ERS1023468 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.28597 0.85275 0.12917 0.11083 0.97504 0.9165 0.79987 0.6128 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3729 3729 ERR1397061 ERX1468320 ERS1023467 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 6 SAMEA3716318 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716318|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:32Z|INSDC status:public|Submitter Id:2271b260 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TGTGGTTG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:2271b260 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#30 15566370 Illumina sequencing of library 15566370 constructed from sample accession ERS1023467 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TGTGGTTG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#30.cram cram 660668580.0 5082066.0 SC RUN 18715 8#30 0:55 1:75 A:179797750;C:120562968;G:120663983;T:239642031;N:1848 55 75     179797750 120562968 120663983 239642031 1848 ERX1468320 ERS1023467 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.24637 0.83519 0.11648 0.10047 0.97112 0.90806 0.75586 0.63304 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3730 3730 ERR1397060 ERX1468319 ERS1023466 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 5 SAMEA3716317 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716317|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:31Z|INSDC status:public|Submitter Id:2266b5e0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TCCTCAAT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:2266b5e0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#29 15566369 Illumina sequencing of library 15566369 constructed from sample accession ERS1023466 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TCCTCAAT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#29.cram cram 641844320.0 4937264.0 SC RUN 18715 8#29 0:55 1:75 A:170784947;C:114236819;G:119506285;T:237313307;N:2962 55 75     170784947 114236819 119506285 237313307 2962 ERX1468319 ERS1023466 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.24614 0.83823 0.11448 0.08337 0.97356 0.90593 0.76773 0.64034 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3731 3731 ERR1397059 ERX1468318 ERS1023465 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 4 SAMEA3716316 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716316|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:31Z|INSDC status:public|Submitter Id:225be070 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TACAGGAT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:225be070 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#28 15566368 Illumina sequencing of library 15566368 constructed from sample accession ERS1023465 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TACAGGAT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#28.cram cram 587079870.0 4515999.0 SC RUN 18715 8#28                       ERX1468318 ERS1023465 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.14143 0.59868 0.09232 0.09907 0.97648 0.91616 0.55833 0.54275 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3732 3732 ERR1397058 ERX1468317 ERS1023464 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 3 SAMEA3716315 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716315|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:30Z|INSDC status:public|Submitter Id:22506ec0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TAGTGACT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:22506ec0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#27 15566367 Illumina sequencing of library 15566367 constructed from sample accession ERS1023464 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TAGTGACT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#27.cram cram 656951230.0 5053471.0 SC RUN 18715 8#27 0:55 1:75 A:176154435;C:112733310;G:125269118;T:242792191;N:2176 55 75     176154435 112733310 125269118 242792191 2176 ERX1468317 ERS1023464 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.30886 0.85046 0.11844 0.0971 0.97658 0.91583 0.89951 0.76866 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3733 3733 ERR1397057 ERX1468316 ERS1023463 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 2 SAMEA3716314 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716314|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:30Z|INSDC status:public|Submitter Id:22452420 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TTCCTGCT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:22452420 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#26 15566366 Illumina sequencing of library 15566366 constructed from sample accession ERS1023463 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TTCCTGCT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#26.cram cram 637042380.0 4900326.0 SC RUN 18715 8#26 0:55 1:75 A:169999761;C:113778382;G:122043906;T:231217073;N:3258 55 75     169999761 113778382 122043906 231217073 3258 ERX1468316 ERS1023463 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.31489 0.85017 0.11073 0.08344 0.97366 0.91528 0.83569 0.68063 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3734 3734 ERR1397056 ERX1468315 ERS1023462 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 110 1 1 SAMEA3716313 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716313|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:29Z|INSDC status:public|Submitter Id:2239d980 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 month and 1 wpf homozygous tert adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. The homozygous adults were obtained by crossing parents heterozygous for tert sa6541 and growing the quarter homozygous fish from the clutch. A 8 base indexing sequence TGCGATCT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph110|sample name:2239d980 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#25 15566365 Illumina sequencing of library 15566365 constructed from sample accession ERS1023462 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TGCGATCT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#25.cram cram 567513050.0 4365485.0 SC RUN 18715 8#25 0:55 1:75 A:150769806;C:98997671;G:107141083;T:210602580;N:1910 55 75     150769806 98997671 107141083 210602580 1910 ERX1468315 ERS1023462 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.31513 0.8639 0.11016 0.07449 0.9752 0.90985 0.88328 0.70792 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3735 3735 ERR1397055 ERX1468314 ERS1023461 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 113 1 12 SAMEA3716312 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 26 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716312|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:29Z|INSDC status:public|Submitter Id:22303c90 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 26 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TTGACTCT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph113|sample name:22303c90 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#24 15566364 Illumina sequencing of library 15566364 constructed from sample accession ERS1023461 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TTGACTCT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#24.cram cram 541389290.0 4164533.0 SC RUN 18715 8#24 0:55 1:75 A:149630682;C:93128764;G:102059718;T:196567547;N:2579 55 75     149630682 93128764 102059718 196567547 2579 ERX1468314 ERS1023461 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.31938 0.80432 0.16112 0.16984 0.97183 0.90893 0.82211 0.73255 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3736 3736 ERR1397054 ERX1468313 ERS1023460 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 113 1 11 SAMEA3716311 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 26 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716311|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:28Z|INSDC status:public|Submitter Id:22265180 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 26 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TGCATAGT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph113|sample name:22265180 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#23 15566363 Illumina sequencing of library 15566363 constructed from sample accession ERS1023460 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TGCATAGT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#23.cram cram 571818000.0 4398600.0 SC RUN 18715 8#23 0:55 1:75 A:158875843;C:99417127;G:106799809;T:206723059;N:2162 55 75     158875843 99417127 106799809 206723059 2162 ERX1468313 ERS1023460 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.30236 0.79208 0.15953 0.16714 0.9693 0.90343 0.81603 0.53838 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3737 3737 ERR1397053 ERX1468312 ERS1023459 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 113 1 10 SAMEA3716310 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 26 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716310|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:28Z|INSDC status:public|Submitter Id:221bf140 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 26 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TGATACGT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph113|sample name:221bf140 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#22 15566362 Illumina sequencing of library 15566362 constructed from sample accession ERS1023459 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TGATACGT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#22.cram cram 486876910.0 3745207.0 SC RUN 18715 8#22 0:55 1:75 A:129941384;C:87127302;G:90702777;T:179103590;N:1857 55 75     129941384 87127302 90702777 179103590 1857 ERX1468312 ERS1023459 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.27884 0.83381 0.12097 0.11714 0.97039 0.8983 0.81908 0.64542 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3738 3738 ERR1397052 ERX1468311 ERS1023458 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 113 1 9 SAMEA3716309 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 26 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716309|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:27Z|INSDC status:public|Submitter Id:22119100 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 26 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TCGAGCGT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph113|sample name:22119100 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#21 15566361 Illumina sequencing of library 15566361 constructed from sample accession ERS1023458 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TCGAGCGT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#21.cram cram 321968660.0 2476682.0 SC RUN 18715 8#21 0:55 1:75 A:85611967;C:56953379;G:60212796;T:119189501;N:1017 55 75     85611967 56953379 60212796 119189501 1017 ERX1468311 ERS1023458 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.2616 0.85744 0.09546 0.10386 0.97341 0.89327 0.84115 0.52093 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3739 3739 ERR1397051 ERX1468310 ERS1023457 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 113 1 8 SAMEA3716308 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 26 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716308|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:27Z|INSDC status:public|Submitter Id:220730c0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 26 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TTGGAGGT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph113|sample name:220730c0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#20 15566360 Illumina sequencing of library 15566360 constructed from sample accession ERS1023457 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TTGGAGGT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#20.cram cram 472624360.0 3635572.0 SC RUN 18715 8#20 0:55 1:75 A:126831392;C:83556709;G:88455943;T:173779093;N:1223 55 75     126831392 83556709 88455943 173779093 1223 ERX1468310 ERS1023457 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.30388 0.84241 0.11508 0.11573 0.97116 0.90003 0.39774 0.70203 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3740 3740 ERR1397050 ERX1468309 ERS1023456 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 113 1 7 SAMEA3716307 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 26 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716307|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:26Z|INSDC status:public|Submitter Id:21fc5b50 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 26 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TCTGCTGT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph113|sample name:21fc5b50 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#19 15566359 Illumina sequencing of library 15566359 constructed from sample accession ERS1023456 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TCTGCTGT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#19.cram cram 602614090.0 4635493.0 SC RUN 18715 8#19 0:55 1:75 A:163499230;C:104602930;G:113213757;T:221296100;N:2073 55 75     163499230 104602930 113213757 221296100 2073 ERX1468309 ERS1023456 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.35019 0.84609 0.13232 0.13362 0.96822 0.89412 0.8825 0.74339 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3741 3741 ERR1397049 ERX1468308 ERS1023455 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 113 1 6 SAMEA3716306 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 26 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716306|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:26Z|INSDC status:public|Submitter Id:21f22220 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 26 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TTCTGTGT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph113|sample name:21f22220 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#18 15566358 Illumina sequencing of library 15566358 constructed from sample accession ERS1023455 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TTCTGTGT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#18.cram cram 620771320.0 4775164.0 SC RUN 18715 8#18 0:55 1:75 A:170120424;C:109984137;G:117603882;T:223060767;N:2110 55 75     170120424 109984137 117603882 223060767 2110 ERX1468308 ERS1023455 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.29675 0.83916 0.12868 0.14148 0.96613 0.8984 0.79183 0.65344 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3742 3742 ERR1397048 ERX1468307 ERS1023454 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 113 1 5 SAMEA3716305 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 26 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716305|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:25Z|INSDC status:public|Submitter Id:21e81000 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 26 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TGTACCTT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph113|sample name:21e81000 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#17 15566357 Illumina sequencing of library 15566357 constructed from sample accession ERS1023454 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TGTACCTT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#17.cram cram 620956960.0 4776592.0 SC RUN 18715 8#17 0:55 1:75 A:167465723;C:108421495;G:117858045;T:227208072;N:3625 55 75     167465723 108421495 117858045 227208072 3625 ERX1468307 ERS1023454 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.28111 0.84477 0.11758 0.12272 0.97137 0.89832 0.849 0.70528 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3743 3743 ERR1397047 ERX1468306 ERS1023453 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 113 1 4 SAMEA3716304 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 26 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716304|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:25Z|INSDC status:public|Submitter Id:21dc9e50 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 26 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TCCGTCTT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph113|sample name:21dc9e50 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#16 15566356 Illumina sequencing of library 15566356 constructed from sample accession ERS1023453 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TCCGTCTT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#16.cram cram 647011300.0 4977010.0 SC RUN 18715 8#16 0:55 1:75 A:170845029;C:117050187;G:126808386;T:232304633;N:3065 55 75     170845029 117050187 126808386 232304633 3065 ERX1468306 ERS1023453 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.26816 0.85786 0.09644 0.09888 0.9694 0.90751 0.79908 0.6443 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3744 3744 ERR1397046 ERX1468305 ERS1023452 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 113 1 3 SAMEA3716303 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 26 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716303|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:24Z|INSDC status:public|Submitter Id:21d34f80 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 26 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TAAGCGTT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph113|sample name:21d34f80 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#15 15566355 Illumina sequencing of library 15566355 constructed from sample accession ERS1023452 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TAAGCGTT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#15.cram cram 457286700.0 3517590.0 SC RUN 18715 8#15 0:55 1:75 A:118667898;C:84631347;G:85673386;T:168312768;N:1301 55 75     118667898 84631347 85673386 168312768 1301 ERX1468305 ERS1023452 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.23276 0.86209 0.10575 0.09847 0.97358 0.9052 0.78944 0.62306 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3745 3745 ERR1397045 ERX1468304 ERS1023451 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 113 1 2 SAMEA3716302 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 26 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716302|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:24Z|INSDC status:public|Submitter Id:21c8a120 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 26 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TCTCGGTT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph113|sample name:21c8a120 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#14 15566354 Illumina sequencing of library 15566354 constructed from sample accession ERS1023451 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TCTCGGTT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#14.cram cram 653102060.0 5023862.0 SC RUN 18715 8#14 0:55 1:75 A:174751774;C:115388239;G:124463430;T:238496439;N:2178 55 75     174751774 115388239 124463430 238496439 2178 ERX1468304 ERS1023451 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.2967 0.86134 0.12119 0.11716 0.97072 0.9011 0.84585 0.56695 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3746 3746 ERR1397044 ERX1468303 ERS1023450 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 113 1 1 SAMEA3716301 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 26 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716301|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:23Z|INSDC status:public|Submitter Id:21beb610 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 26 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TGGTTGTT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph113|sample name:21beb610 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#13 15566353 Illumina sequencing of library 15566353 constructed from sample accession ERS1023450 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TGGTTGTT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#13.cram cram 551198960.0 4239992.0 SC RUN 18715 8#13 0:55 1:75 A:148509015;C:97254852;G:104086449;T:201346621;N:2023 55 75     148509015 97254852 104086449 201346621 2023 ERX1468303 ERS1023450 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.28017 0.87069 0.11381 0.11448 0.97133 0.90106 0.84612 0.68133 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3747 3747 ERR1397043 ERX1468302 ERS1023449 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 112 1 12 SAMEA3716300 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716300|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:23Z|INSDC status:public|Submitter Id:21b4cb00 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence CTTGTACT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph112|sample name:21b4cb00 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#12 15566352 Illumina sequencing of library 15566352 constructed from sample accession ERS1023449 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence CTTGTACT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#12.cram cram 683965360.0 5261272.0 SC RUN 18715 8#12 0:55 1:75 A:181490420;C:124392573;G:129140040;T:248939248;N:3079 55 75     181490420 124392573 129140040 248939248 3079 ERX1468302 ERS1023449 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.25401 0.85131 0.10056 0.08236 0.97431 0.91419 0.81852 0.53153 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3748 3748 ERR1397042 ERX1468301 ERS1023448 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 112 1 11 SAMEA3716299 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716299|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:22Z|INSDC status:public|Submitter Id:21a98060 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence GGCTACAG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph112|sample name:21a98060 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#11 15566351 Illumina sequencing of library 15566351 constructed from sample accession ERS1023448 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence GGCTACAG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#11.cram cram 678711150.0 5220855.0 SC RUN 18715 8#11 0:55 1:75 A:179239904;C:124839850;G:129344689;T:245284425;N:2282 55 75     179239904 124839850 129344689 245284425 2282 ERX1468301 ERS1023448 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.25995 0.85813 0.08951 0.08509 0.97362 0.91532 0.84938 0.5878 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3749 3749 ERR1397041 ERX1468300 ERS1023447 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 112 1 10 SAMEA3716298 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716298|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:22Z|INSDC status:public|Submitter Id:219e5cd0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TAGCTTGT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph112|sample name:219e5cd0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#10 15566350 Illumina sequencing of library 15566350 constructed from sample accession ERS1023447 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TAGCTTGT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#10.cram cram 512021380.0 3938626.0 SC RUN 18715 8#10 0:55 1:75 A:134633141;C:95267180;G:96292177;T:185827489;N:1393 55 75     134633141 95267180 96292177 185827489 1393 ERX1468300 ERS1023447 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.27511 0.8473 0.08789 0.07504 0.97484 0.91932 0.83725 0.53104 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3750 3750 ERR1397040 ERX1468299 ERS1023446 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 112 1 9 SAMEA3716297 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716297|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:21Z|INSDC status:public|Submitter Id:219423a0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence GATCAGCG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph112|sample name:219423a0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#9 15566349 Illumina sequencing of library 15566349 constructed from sample accession ERS1023446 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence GATCAGCG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#9.cram cram 606955700.0 4668890.0 SC RUN 18715 8#9 0:55 1:75 A:161328190;C:111573232;G:113967253;T:220085334;N:1691 55 75     161328190 111573232 113967253 220085334 1691 ERX1468299 ERS1023446 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.27581 0.81211 0.10852 0.0992 0.97311 0.91023 0.84113 0.65956 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3751 3751 ERR1397039 ERX1468298 ERS1023445 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 112 1 8 SAMEA3716296 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716296|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:21Z|INSDC status:public|Submitter Id:218a3890 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence ACTTGATG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph112|sample name:218a3890 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#8 15566348 Illumina sequencing of library 15566348 constructed from sample accession ERS1023445 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence ACTTGATG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#8.cram cram 631737210.0 4859517.0 SC RUN 18715 8#8 0:55 1:75 A:168090778;C:115132937;G:119109490;T:229402219;N:1786 55 75     168090778 115132937 119109490 229402219 1786 ERX1468298 ERS1023445 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.28735 0.86714 0.09468 0.08742 0.97266 0.91165 0.82804 0.43981 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3752 3752 ERR1397038 ERX1468297 ERS1023444 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 112 1 7 SAMEA3716295 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716295|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:20Z|INSDC status:public|Submitter Id:217fd850 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence CAGATCTG is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph112|sample name:217fd850 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#7 15566347 Illumina sequencing of library 15566347 constructed from sample accession ERS1023444 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence CAGATCTG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#7.cram cram 629907200.0 4845440.0 SC RUN 18715 8#7 0:55 1:75 A:167238249;C:113933791;G:119656035;T:229077206;N:1919 55 75     167238249 113933791 119656035 229077206 1919 ERX1468297 ERS1023444 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.28015 0.85121 0.09694 0.0866 0.97579 0.91873 0.49517 0.67663 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3753 3753 ERR1397037 ERX1468296 ERS1023443 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 112 1 6 SAMEA3716294 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716294|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:20Z|INSDC status:public|Submitter Id:21757810 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence GCCAATGT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph112|sample name:21757810 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#6 15566346 Illumina sequencing of library 15566346 constructed from sample accession ERS1023443 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence GCCAATGT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#6.cram cram 549775980.0 4229046.0 SC RUN 18715 8#6 0:55 1:75 A:145007963;C:100751331;G:102099529;T:201915350;N:1807 55 75     145007963 100751331 102099529 201915350 1807 ERX1468296 ERS1023443 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.2874 0.85663 0.08661 0.0687 0.97788 0.91705 0.84995 0.44346 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3754 3754 ERR1397036 ERX1468295 ERS1023442 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 112 1 5 SAMEA3716293 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716293|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:19Z|INSDC status:public|Submitter Id:216b17d0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence ACAGTGGT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph112|sample name:216b17d0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#5 15566345 Illumina sequencing of library 15566345 constructed from sample accession ERS1023442 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence ACAGTGGT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#5.cram cram 609585470.0 4689119.0 SC RUN 18715 8#5 0:55 1:75 A:160001548;C:112004296;G:114635311;T:222942641;N:1674 55 75     160001548 112004296 114635311 222942641 1674 ERX1468295 ERS1023442 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.24791 0.87348 0.09277 0.0825 0.97536 0.91543 0.83597 0.65901 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3755 3755 ERR1397035 ERX1468294 ERS1023441 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 112 1 4 SAMEA3716292 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716292|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:19Z|INSDC status:public|Submitter Id:2160b790 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TGACCACT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph112|sample name:2160b790 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#4 15566344 Illumina sequencing of library 15566344 constructed from sample accession ERS1023441 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TGACCACT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#4.cram cram 678764840.0 5221268.0 SC RUN 18715 8#4 0:55 1:75 A:178838072;C:124911287;G:130189123;T:244823100;N:3258 55 75     178838072 124911287 130189123 244823100 3258 ERX1468294 ERS1023441 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.25304 0.81978 0.09241 0.08656 0.97676 0.91747 0.84034 0.65122 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3756 3756 ERR1397034 ERX1468293 ERS1023440 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 112 1 3 SAMEA3716291 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716291|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:18Z|INSDC status:public|Submitter Id:21556cf0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TTAGGCAT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph112|sample name:21556cf0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#3 15566343 Illumina sequencing of library 15566343 constructed from sample accession ERS1023440 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence TTAGGCAT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#3.cram cram 681501470.0 5242319.0 SC RUN 18715 8#3 0:55 1:75 A:181660061;C:124276603;G:127126649;T:248435294;N:2863 55 75     181660061 124276603 127126649 248435294 2863 ERX1468293 ERS1023440 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.27754 0.81927 0.08779 0.07376 0.97717 0.92334 0.85395 0.62252 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3757 3757 ERR1397033 ERX1468292 ERS1023439 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 112 1 2 SAMEA3716290 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716290|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:18Z|INSDC status:public|Submitter Id:21498610 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence CGATGTTT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph112|sample name:21498610 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#2 15566342 Illumina sequencing of library 15566342 constructed from sample accession ERS1023439 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence CGATGTTT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#2.cram cram 696821970.0 5360169.0 SC RUN 18715 8#2 0:55 1:75 A:186653953;C:128161902;G:131712165;T:250291266;N:2684 55 75     186653953 128161902 131712165 250291266 2684 ERX1468292 ERS1023439 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.24475 0.81186 0.08713 0.06706 0.97798 0.92281 0.83555 0.55607 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
3758 3758 ERR1397032 ERX1468291 ERS1023438 ERP013838 PRJEB12367 Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults Transcriptome_profiling_of_zebrafish_muscle_from_wild_type_and_tert_knockout_adults-sc-4036 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of dissected muscle from wildtype and tert homozygous adult zebrafish for transcriptional profiling ArrayExpress:E ERAD 456     ZMP phentoype 112 1 1 SAMEA3716289 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Adult ZFS:0000044 3 month|ArrayExpress OrganismPart:Adult muscle|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2015 12 17|External Id:SAMEA3716289|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:23:28Z|INSDC last update:2015 12 17T16:32:17Z|INSDC status:public|Submitter Id:2134eca0 a400 11e5 8adb 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a 3 mpf wild type adult zebrafish muscle tissue dissected from the region between the anal fin and the caudal fin plus ERCC spike mix 2 Ambion. A 8 base indexing sequence ATCACGTT is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph112|sample name:2134eca0 a400 11e5 8adb 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18715 8#1 15566341 Illumina sequencing of library 15566341 constructed from sample accession ERS1023438 for study accession ERP013838. This is part of an Illumina multiplexed sequencing run 18715 8. This submission includes reads tagged with the sequence ATCACGTT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013838 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18715_8#1.cram cram 637072930.0 4900561.0 SC RUN 18715 8#1 0:55 1:75 A:169596079;C:116706958;G:122297212;T:228469365;N:3316 55 75     169596079 116706958 122297212 228469365 3316 ERX1468291 ERS1023438 ERA612387 European Nucleotide Archive Wellcome Sanger Institute 2 0.2369 0.84014 0.08404 0.07279 0.9764 0.92289 0.81134 0.63042 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-17 Adult Adult Multi-tissue Multi-system
9343 9343 ERR2935792 ERX2938586 ERS2922622 ERP112367 PRJEB30004 RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E-MTAB-7464 Transcriptome Analysis Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples. ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24   Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Cnt mRNA ML 4 SAMEA5138255 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138255|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:Cnt mRNA ML 4|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:Cnt mRNA ML 4|scientific name:Danio rerio|sex:male|strain:AB                 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E MTAB 7464:Cnt mRNA ML 4 p Cnt mRNA ML 4 p RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:0|Experimental Factor: organism part:caudal fin ssRNA-seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112367 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24 Cnt-mRNA-ML-4_2.fastq.gz Cnt-mRNA-ML-4_1.fastq.gz fastq fastq 12134105440.0 75838159.0 E MTAB 7464:Cnt mRNA ML 4 0:80 1:80 A:3262023701;C:2677095735;G:2964643096;T:3227367048;N:2975860 80 80     3262023701 2677095735 2964643096 3227367048 2975860 ERX2938586 ERS2922622 ERA1667271 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.91144 0.90945 0.31692 0.30691 0.75203 0.75722 0.51882 0.5197 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2018-11-28 Adult Adult Multi-tissue Multi-system
9344 9344 ERR2935791 ERX2938585 ERS2922621 ERP112367 PRJEB30004 RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E-MTAB-7464 Transcriptome Analysis Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples. ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24   Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Cnt mRNA ML 3 SAMEA5138254 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138254|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:Cnt mRNA ML 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:Cnt mRNA ML 3|scientific name:Danio rerio|sex:male|strain:AB                 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E MTAB 7464:Cnt mRNA ML 3 p Cnt mRNA ML 3 p RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:0|Experimental Factor: organism part:caudal fin ssRNA-seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112367 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24 Cnt-mRNA-ML-3_1.fastq.gz Cnt-mRNA-ML-3_2.fastq.gz fastq fastq 10198941920.0 63743387.0 E MTAB 7464:Cnt mRNA ML 3 0:80 1:80 A:2707258482;C:2295053882;G:2521099885;T:2673029444;N:2500227 80 80     2707258482 2295053882 2521099885 2673029444 2500227 ERX2938585 ERS2922621 ERA1667271 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.88029 0.87951 0.30611 0.30513 0.76189 0.7685 0.52656 0.52076 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2018-11-28 Adult Adult Multi-tissue Multi-system
9345 9345 ERR2935790 ERX2938584 ERS2922620 ERP112367 PRJEB30004 RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E-MTAB-7464 Transcriptome Analysis Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples. ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24   Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Cnt mRNA ML 2 SAMEA5138253 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138253|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:Cnt mRNA ML 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:Cnt mRNA ML 2|scientific name:Danio rerio|sex:female|strain:AB                 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E MTAB 7464:Cnt mRNA ML 2 p Cnt mRNA ML 2 p RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:0|Experimental Factor: organism part:caudal fin ssRNA-seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112367 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24 Cnt-mRNA-ML-2_1.fastq.gz Cnt-mRNA-ML-2_2.fastq.gz fastq fastq 13001272960.0 81257956.0 E MTAB 7464:Cnt mRNA ML 2 0:80 1:80 A:3429977204;C:2902807573;G:3288394622;T:3376870832;N:3222729 80 80     3429977204 2902807573 3288394622 3376870832 3222729 ERX2938584 ERS2922620 ERA1667271 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.89439 0.89378 0.3049 0.30551 0.75771 0.76761 0.52718 0.52248 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2018-11-28 Adult Adult Multi-tissue Multi-system
9346 9346 ERR2935789 ERX2938583 ERS2922619 ERP112367 PRJEB30004 RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E-MTAB-7464 Transcriptome Analysis Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples. ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24   Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Cnt mRNA ML 1 SAMEA5138252 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138252|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:Cnt mRNA ML 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:Cnt mRNA ML 1|scientific name:Danio rerio|sex:female|strain:AB                 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E MTAB 7464:Cnt mRNA ML 1 p Cnt mRNA ML 1 p RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:0|Experimental Factor: organism part:caudal fin ssRNA-seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112367 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24 Cnt-mRNA-ML-1_2.fastq.gz Cnt-mRNA-ML-1_1.fastq.gz fastq fastq 10689399040.0 66808744.0 E MTAB 7464:Cnt mRNA ML 1 0:80 1:80 A:2897858681;C:2320332197;G:2613694217;T:2854881563;N:2632382 80 80     2897858681 2320332197 2613694217 2854881563 2632382 ERX2938583 ERS2922619 ERA1667271 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.87118 0.87075 0.30823 0.30776 0.74673 0.75692 0.49822 0.50666 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2018-11-28 Adult Adult Multi-tissue Multi-system
9347 9347 ERR2935788 ERX2938582 ERS2922618 ERP112367 PRJEB30004 RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E-MTAB-7464 Transcriptome Analysis Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples. ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24   Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina 7dpa mRNA ML 4 SAMEA5138251 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138251|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:7dpa mRNA ML 4|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:7dpa mRNA ML 4|scientific name:Danio rerio|sex:male|strain:AB                 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E MTAB 7464:7dpa mRNA ML 4 p 7dpa mRNA ML 4 p RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:7|Experimental Factor: organism part:caudal fin ssRNA-seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112367 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24 7dpa-mRNA-ML-4_1.fastq.gz 7dpa-mRNA-ML-4_2.fastq.gz fastq fastq 11636085120.0 72725532.0 E MTAB 7464:7dpa mRNA ML 4 0:80 1:80 A:3154141550;C:2591688923;G:2792349992;T:3095216690;N:2687965 80 80     3154141550 2591688923 2792349992 3095216690 2687965 ERX2938582 ERS2922618 ERA1667271 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.8808 0.88291 0.28917 0.2893 0.73377 0.74097 0.50493 0.4989 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2018-11-28 Adult Adult Multi-tissue Multi-system
9348 9348 ERR2935787 ERX2938581 ERS2922617 ERP112367 PRJEB30004 RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E-MTAB-7464 Transcriptome Analysis Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples. ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24   Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina 7dpa mRNA ML 3 SAMEA5138250 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138250|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:7dpa mRNA ML 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:7dpa mRNA ML 3|scientific name:Danio rerio|sex:male|strain:AB                 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E MTAB 7464:7dpa mRNA ML 3 p 7dpa mRNA ML 3 p RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:7|Experimental Factor: organism part:caudal fin ssRNA-seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112367 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24 7dpa-mRNA-ML-3_1.fastq.gz 7dpa-mRNA-ML-3_2.fastq.gz fastq fastq 9873881440.0 61711759.0 E MTAB 7464:7dpa mRNA ML 3 0:80 1:80 A:2682240945;C:2177286149;G:2380282226;T:2631847017;N:2225103 80 80     2682240945 2177286149 2380282226 2631847017 2225103 ERX2938581 ERS2922617 ERA1667271 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.83715 0.84278 0.34243 0.34676 0.73764 0.75041 0.50878 0.49819 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2018-11-28 Adult Adult Multi-tissue Multi-system
9349 9349 ERR2935786 ERX2938580 ERS2922616 ERP112367 PRJEB30004 RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E-MTAB-7464 Transcriptome Analysis Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples. ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24   Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina 7dpa mRNA ML 2 SAMEA5138249 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138249|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:7dpa mRNA ML 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:7dpa mRNA ML 2|scientific name:Danio rerio|sex:female|strain:AB                 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E MTAB 7464:7dpa mRNA ML 2 p 7dpa mRNA ML 2 p RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:7|Experimental Factor: organism part:caudal fin ssRNA-seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112367 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24 7dpa-mRNA-ML-2_2.fastq.gz 7dpa-mRNA-ML-2_1.fastq.gz fastq fastq 12193073280.0 76206708.0 E MTAB 7464:7dpa mRNA ML 2 0:80 1:80 A:3333326821;C:2692186511;G:2887657057;T:3277111703;N:2791188 80 80     3333326821 2692186511 2887657057 3277111703 2791188 ERX2938580 ERS2922616 ERA1667271 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.8495 0.851 0.36393 0.36549 0.72466 0.73582 0.50377 0.4964 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2018-11-28 Adult Adult Multi-tissue Multi-system
9350 9350 ERR2935785 ERX2938579 ERS2922615 ERP112367 PRJEB30004 RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E-MTAB-7464 Transcriptome Analysis Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples. ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24   Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina 7dpa mRNA ML 1 SAMEA5138248 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138248|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:7dpa mRNA ML 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:7dpa mRNA ML 1|scientific name:Danio rerio|sex:female|strain:AB                 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E MTAB 7464:7dpa mRNA ML 1 p 7dpa mRNA ML 1 p RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:7|Experimental Factor: organism part:caudal fin ssRNA-seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112367 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24 7dpa-mRNA-ML-1_1.fastq.gz 7dpa-mRNA-ML-1_2.fastq.gz fastq fastq 11533139040.0 72082119.0 E MTAB 7464:7dpa mRNA ML 1 0:80 1:80 A:3069170319;C:2575356466;G:2889466424;T:2996503729;N:2642102 80 80     3069170319 2575356466 2889466424 2996503729 2642102 ERX2938579 ERS2922615 ERA1667271 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.86529 0.86845 0.33913 0.34252 0.72928 0.74194 0.50425 0.50214 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2018-11-28 Adult Adult Multi-tissue Multi-system
9351 9351 ERR2935784 ERX2938578 ERS2922614 ERP112367 PRJEB30004 RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E-MTAB-7464 Transcriptome Analysis Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples. ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24   Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina 1dpa mRNA ML 4 SAMEA5138247 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138247|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:1dpa mRNA ML 4|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:1dpa mRNA ML 4|scientific name:Danio rerio|sex:male|strain:AB                 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E MTAB 7464:1dpa mRNA ML 4 p 1dpa mRNA ML 4 p RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:1|Experimental Factor: organism part:caudal fin ssRNA-seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112367 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24 1dpa-mRNA-ML-4_1.fastq.gz 1dpa-mRNA-ML-4_2.fastq.gz fastq fastq 13728291840.0 85801824.0 E MTAB 7464:1dpa mRNA ML 4 0:80 1:80 A:3747242594;C:3041779368;G:3248651209;T:3687437813;N:3180856 80 80     3747242594 3041779368 3248651209 3687437813 3180856 ERX2938578 ERS2922614 ERA1667271 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.90774 0.91111 0.34968 0.34939 0.72809 0.73472 0.50073 0.49547 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2018-11-28 Adult Adult Multi-tissue Multi-system
9352 9352 ERR2935783 ERX2938577 ERS2922613 ERP112367 PRJEB30004 RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E-MTAB-7464 Transcriptome Analysis Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples. ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24   Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina 1dpa mRNA ML 3 SAMEA5138246 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138246|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:1dpa mRNA ML 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:1dpa mRNA ML 3|scientific name:Danio rerio|sex:male|strain:AB                 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E MTAB 7464:1dpa mRNA ML 3 p 1dpa mRNA ML 3 p RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:1|Experimental Factor: organism part:caudal fin ssRNA-seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112367 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24 1dpa-mRNA-ML-3_2.fastq.gz 1dpa-mRNA-ML-3_1.fastq.gz fastq fastq 12524780320.0 78279877.0 E MTAB 7464:1dpa mRNA ML 3 0:80 1:80 A:3452368285;C:2754592593;G:2905324477;T:3409605329;N:2889636 80 80     3452368285 2754592593 2905324477 3409605329 2889636 ERX2938577 ERS2922613 ERA1667271 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.90778 0.91013 0.32736 0.3259 0.73724 0.74251 0.51117 0.51031 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2018-11-28 Adult Adult Multi-tissue Multi-system
9353 9353 ERR2935782 ERX2938576 ERS2922612 ERP112367 PRJEB30004 RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E-MTAB-7464 Transcriptome Analysis Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples. ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24   Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina 1dpa mRNA ML 2 SAMEA5138245 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138245|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:1dpa mRNA ML 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:1dpa mRNA ML 2|scientific name:Danio rerio|sex:female|strain:AB                 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E MTAB 7464:1dpa mRNA ML 2 p 1dpa mRNA ML 2 p RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:1|Experimental Factor: organism part:caudal fin ssRNA-seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112367 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24 1dpa-mRNA-ML-2_1.fastq.gz 1dpa-mRNA-ML-2_2.fastq.gz fastq fastq 15395445120.0 96221532.0 E MTAB 7464:1dpa mRNA ML 2 0:80 1:80 A:4187891415;C:3447519966;G:3632085998;T:4124408897;N:3538844 80 80     4187891415 3447519966 3632085998 4124408897 3538844 ERX2938576 ERS2922612 ERA1667271 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.90197 0.90707 0.33526 0.33624 0.7371 0.74479 0.51163 0.50652 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2018-11-28 Adult Adult Multi-tissue Multi-system
9354 9354 ERR2935781 ERX2938575 ERS2922611 ERP112367 PRJEB30004 RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E-MTAB-7464 Transcriptome Analysis Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples. ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24   Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina 1dpa mRNA ML 1 SAMEA5138244 Izmir Biomedicine and Genome Center / Turkey ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138244|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:1dpa mRNA ML 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:1dpa mRNA ML 1|scientific name:Danio rerio|sex:female|strain:AB                 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model E MTAB 7464:1dpa mRNA ML 1 p 1dpa mRNA ML 1 p RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:1|Experimental Factor: organism part:caudal fin ssRNA-seq TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112367 NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24 1dpa-mRNA-ML-1_2.fastq.gz 1dpa-mRNA-ML-1_1.fastq.gz fastq fastq 9835056000.0 61469100.0 E MTAB 7464:1dpa mRNA ML 1 0:80 1:80 A:2673004774;C:2192168640;G:2335585327;T:2632030261;N:2266998 80 80     2673004774 2192168640 2335585327 2632030261 2266998 ERX2938575 ERS2922611 ERA1667271 Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive 2 0.89673 0.89924 0.33937 0.33954 0.72342 0.73032 0.49857 0.48103 80 80 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   Turkey 2018-11-28 Adult Adult Multi-tissue Multi-system
9831 9831 ERR4029236 ERX4030552 ERS4513990 ERP121186 PRJEB37848 RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E-MTAB-8959 Transcriptome Analysis The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss. Tissue types included liver skin muscle heart gut gill eye brain for all three species with additionally pyloric caeca kidney head kidney and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts FPKM or TPM were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation. ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16   Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. ZF Sk 1 SAMEA6786310 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786310|INSDC center name:CIGENE Faculty of Biosciences The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF Sk 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:skin|sample name:E MTAB 8959:ZF Sk 1|scientific name:Danio rerio|sex:male                 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E MTAB 8959:ZF Sk 1 p ZF Sk 1 p RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. Experimental Factor: organism part:skin|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP121186 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16 ZF-Sk-1_ATTACTCG-AGGCGAAG_R1_001.fastq.gz ZF-Sk-1_ATTACTCG-AGGCGAAG_R2_001.fastq.gz fastq fastq 4614183504.0 18310252.0 E MTAB 8959:ZF Sk 1 ATTACTCG AGGCGAAG R 0:126 1:126 A:1263161349;C:1046676688;G:1038530310;T:1265433988;N:381169 126 126     1263161349 1046676688 1038530310 1265433988 381169 ERX4030552 ERS4513990 ERA2508028 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive 2 0.93462 0.93416 0.10434 0.10373 0.71254 0.7162 0.4722 0.46786 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Norway 2020-04-16 Adult Adult Multi-tissue Multi-system
9832 9832 ERR4029235 ERX4030551 ERS4513989 ERP121186 PRJEB37848 RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E-MTAB-8959 Transcriptome Analysis The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss. Tissue types included liver skin muscle heart gut gill eye brain for all three species with additionally pyloric caeca kidney head kidney and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts FPKM or TPM were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation. ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16   Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. ZF M 2 SAMEA6786309 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786309|INSDC center name:CIGENE Faculty of Biosciences The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF M 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:muscle|sample name:E MTAB 8959:ZF M 2|scientific name:Danio rerio|sex:male                 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E MTAB 8959:ZF M 2 p ZF M 2 p RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. Experimental Factor: organism part:muscle|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP121186 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16 ZF-M-2_ATTACTCG-TAATCTTA_R2_001.fastq.gz ZF-M-2_ATTACTCG-TAATCTTA_R1_001.fastq.gz fastq fastq 4318736184.0 17137842.0 E MTAB 8959:ZF M 2 ATTACTCG TAATCTTA R 0:126 1:126 A:1127118469;C:1038158146;G:1022013812;T:1130979521;N:466236 126 126     1127118469 1038158146 1022013812 1130979521 466236 ERX4030551 ERS4513989 ERA2508028 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive 2 0.97246 0.97334 0.03723 0.03642 0.8061 0.8058 0.55712 0.55957 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Norway 2020-04-16 Adult Adult Multi-tissue Multi-system
9834 9834 ERR4029233 ERX4030549 ERS4513987 ERP121186 PRJEB37848 RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E-MTAB-8959 Transcriptome Analysis The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss. Tissue types included liver skin muscle heart gut gill eye brain for all three species with additionally pyloric caeca kidney head kidney and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts FPKM or TPM were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation. ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16   Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. ZF H 1 SAMEA6786307 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786307|INSDC center name:CIGENE Faculty of Biosciences The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF H 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:heart|sample name:E MTAB 8959:ZF H 1|scientific name:Danio rerio|sex:male                 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E MTAB 8959:ZF H 1 p ZF H 1 p RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. Experimental Factor: organism part:heart|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP121186 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16 ZF-H-1_ATTACTCG-CAGGACGT_R2_001.fastq.gz ZF-H-1_ATTACTCG-CAGGACGT_R1_001.fastq.gz fastq fastq 4423848660.0 17554955.0 E MTAB 8959:ZF H 1 ATTACTCG CAGGACGT R 0:126 1:126 A:1218639096;C:1001394110;G:990248385;T:1213102170;N:464899 126 126     1218639096 1001394110 990248385 1213102170 464899 ERX4030549 ERS4513987 ERA2508028 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive 2 0.95192 0.95388 0.08243 0.07997 0.75678 0.75915 0.50881 0.49325 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Norway 2020-04-16 Adult Adult Multi-tissue Multi-system
9835 9835 ERR4029232 ERX4030548 ERS4513986 ERP121186 PRJEB37848 RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E-MTAB-8959 Transcriptome Analysis The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss. Tissue types included liver skin muscle heart gut gill eye brain for all three species with additionally pyloric caeca kidney head kidney and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts FPKM or TPM were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation. ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16   Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. ZF Gi 2 SAMEA6786306 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786306|INSDC center name:CIGENE Faculty of Biosciences The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF Gi 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:gill|sample name:E MTAB 8959:ZF Gi 2|scientific name:Danio rerio|sex:male                 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E MTAB 8959:ZF Gi 2 p ZF Gi 2 p RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. Experimental Factor: organism part:gill|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP121186 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16 ZF-Gi-2_TCCGGAGA-TATAGCCT_R2_001.fastq.gz ZF-Gi-2_TCCGGAGA-TATAGCCT_R1_001.fastq.gz fastq fastq 5144739264.0 20415632.0 E MTAB 8959:ZF Gi 2 TCCGGAGA TATAGCCT R 0:126 1:126 A:1417436878;C:1153901826;G:1150711944;T:1422099770;N:588846 126 126     1417436878 1153901826 1150711944 1422099770 588846 ERX4030548 ERS4513986 ERA2508028 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive 2 0.9241 0.92549 0.09819 0.09689 0.69282 0.69441 0.50621 0.50455 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Norway 2020-04-16 Adult Adult Multi-tissue Multi-system
9837 9837 ERR4029230 ERX4030546 ERS4513984 ERP121186 PRJEB37848 RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E-MTAB-8959 Transcriptome Analysis The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss. Tissue types included liver skin muscle heart gut gill eye brain for all three species with additionally pyloric caeca kidney head kidney and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts FPKM or TPM were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation. ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16   Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. ZF E 2 SAMEA6786304 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786304|INSDC center name:CIGENE Faculty of Biosciences The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF E 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:eye|sample name:E MTAB 8959:ZF E 2|scientific name:Danio rerio|sex:male                 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E MTAB 8959:ZF E 2 p ZF E 2 p RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. Experimental Factor: organism part:eye|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP121186 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16 ZF-E-2_TCCGGAGA-ATAGAGGC_R2_001.fastq.gz ZF-E-2_TCCGGAGA-ATAGAGGC_R1_001.fastq.gz fastq fastq 5023188324.0 19933287.0 E MTAB 8959:ZF E 2 TCCGGAGA ATAGAGGC R 0:126 1:126 A:1387107663;C:1131488657;G:1116622956;T:1387461813;N:507235 126 126     1387107663 1131488657 1116622956 1387461813 507235 ERX4030546 ERS4513984 ERA2508028 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive 2 0.94348 0.94343 0.12065 0.11931 0.68509 0.68848 0.51004 0.51626 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Norway 2020-04-16 Adult Adult Multi-tissue Multi-system
9838 9838 ERR4029229 ERX4030545 ERS4513983 ERP121186 PRJEB37848 RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E-MTAB-8959 Transcriptome Analysis The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss. Tissue types included liver skin muscle heart gut gill eye brain for all three species with additionally pyloric caeca kidney head kidney and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts FPKM or TPM were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation. ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16   Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. ZF B 1 SAMEA6786303 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786303|INSDC center name:CIGENE Faculty of Biosciences The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF B 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:brain|sample name:E MTAB 8959:ZF B 1|scientific name:Danio rerio|sex:male                 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E MTAB 8959:ZF B 1 p ZF B 1 p RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. Experimental Factor: organism part:brain|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP121186 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16 ZF-B-1_TCCGGAGA-CCTATCCT_R1_001.fastq.gz ZF-B-1_TCCGGAGA-CCTATCCT_R2_001.fastq.gz fastq fastq 4581319932.0 18179841.0 E MTAB 8959:ZF B 1 TCCGGAGA CCTATCCT R 0:126 1:126 A:1290565823;C:1002821741;G:990971158;T:1296339062;N:622148 126 126     1290565823 1002821741 990971158 1296339062 622148 ERX4030545 ERS4513983 ERA2508028 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive 2 0.94092 0.94175 0.16309 0.16239 0.69351 0.69597 0.50407 0.5013 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Norway 2020-04-16 Adult Adult Multi-tissue Multi-system
9982 9982 ERR4568390 ERX4504063 ERS5050806 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Proximal Rep3 SAMEA7292236 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292236|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Proximal Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Proximal Rep3|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Proximal Rep3 p HypoTH Proximal Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HP3_CRRA200004859-1a_HV532DSXX_L4_1.fq.gz HP3_CRRA200004859-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7117020000.0 23723400.0 E MTAB 9528:HP3 CRRA200004859 1a HV532DSXX L4 0:150 1:150 A:1864896771;C:1704008842;G:1704487221;T:1843451594;N:175572 150 150     1864896771 1704008842 1704487221 1843451594 175572 ERX4504063 ERS5050806 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.94335 0.9433 0.08657 0.08625 0.72498 0.72636 0.48274 0.4859 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9983 9983 ERR4568389 ERX4504062 ERS5050805 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Proximal Rep2 SAMEA7292235 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292235|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Proximal Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Proximal Rep2|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Proximal Rep2 p HypoTH Proximal Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HP2_CRRA200004858-1a_HV532DSXX_L4_1.fq.gz HP2_CRRA200004858-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7810736700.0 26035789.0 E MTAB 9528:HP2 CRRA200004858 1a HV532DSXX L4 0:150 1:150 A:2064202307;C:1840783570;G:1863746983;T:2041812726;N:191114 150 150     2064202307 1840783570 1863746983 2041812726 191114 ERX4504062 ERS5050805 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93642 0.93627 0.08781 0.08757 0.72841 0.72872 0.48431 0.48311 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9984 9984 ERR4568388 ERX4504061 ERS5050804 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Proximal Rep1 SAMEA7292234 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292234|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Proximal Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Proximal Rep1|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Proximal Rep1 p HypoTH Proximal Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HP1_CRRA200004857-1a_HV532DSXX_L4_1.fq.gz HP1_CRRA200004857-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7143318600.0 23811062.0 E MTAB 9528:HP1 CRRA200004857 1a HV532DSXX L4 0:150 1:150 A:1883244963;C:1695388732;G:1697412462;T:1867096015;N:176428 150 150     1883244963 1695388732 1697412462 1867096015 176428 ERX4504061 ERS5050804 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.9408 0.94186 0.08491 0.08465 0.73129 0.73099 0.47185 0.47442 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9985 9985 ERR4568387 ERX4504060 ERS5050803 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Proximal Rep3 SAMEA7292233 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292233|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Proximal Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Proximal Rep3|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Proximal Rep3 p EuTH Proximal Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EP3_CRRA200004850-1a_HV532DSXX_L4_1.fq.gz EP3_CRRA200004850-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7860809700.0 26202699.0 E MTAB 9528:EP3 CRRA200004850 1a HV532DSXX L4 0:150 1:150 A:2068735854;C:1871645002;G:1876330645;T:2043901317;N:196882 150 150     2068735854 1871645002 1876330645 2043901317 196882 ERX4504060 ERS5050803 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93854 0.93903 0.09256 0.09314 0.74014 0.74059 0.47935 0.47779 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9986 9986 ERR4568386 ERX4504059 ERS5050802 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Proximal Rep2 SAMEA7292232 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292232|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Proximal Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Proximal Rep2|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Proximal Rep2 p EuTH Proximal Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EP2_CRRA200004849-1a_HV532DSXX_L4_1.fq.gz EP2_CRRA200004849-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7168033200.0 23893444.0 E MTAB 9528:EP2 CRRA200004849 1a HV532DSXX L4 0:150 1:150 A:1903193161;C:1689671926;G:1689805787;T:1885183061;N:179265 150 150     1903193161 1689671926 1689805787 1885183061 179265 ERX4504059 ERS5050802 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93988 0.93957 0.08429 0.08448 0.74399 0.74375 0.4672 0.47077 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9987 9987 ERR4568385 ERX4504058 ERS5050801 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Proximal Rep1 SAMEA7292231 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292231|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Proximal Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Proximal Rep1|sampling site:proximal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Proximal Rep1 p EuTH Proximal Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:proximal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EP1_CRRA200004848-1a_HV532DSXX_L4_1.fq.gz EP1_CRRA200004848-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7993254600.0 26644182.0 E MTAB 9528:EP1 CRRA200004848 1a HV532DSXX L4 0:150 1:150 A:2055964917;C:1952736981;G:1951688671;T:2032664860;N:199171 150 150     2055964917 1952736981 1951688671 2032664860 199171 ERX4504058 ERS5050801 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.94523 0.94513 0.09369 0.09348 0.74511 0.74525 0.48633 0.48842 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9988 9988 ERR4568384 ERX4504057 ERS5050800 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Middle Rep3 SAMEA7292230 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292230|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Middle Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Middle Rep3|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Middle Rep3 p HypoTH Middle Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HM3_CRRA200004862-1a_HV532DSXX_L4_1.fq.gz HM3_CRRA200004862-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7418093400.0 24726978.0 E MTAB 9528:HM3 CRRA200004862 1a HV532DSXX L4 0:150 1:150 A:1979368375;C:1736175227;G:1747418895;T:1954949103;N:181800 150 150     1979368375 1736175227 1747418895 1954949103 181800 ERX4504057 ERS5050800 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93389 0.93398 0.0839 0.08406 0.72147 0.72115 0.47407 0.47898 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9989 9989 ERR4568383 ERX4504056 ERS5050799 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Middle Rep2 SAMEA7292229 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292229|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Middle Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Middle Rep2|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Middle Rep2 p HypoTH Middle Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HM2_CRRA200004861-1a_HV532DSXX_L4_1.fq.gz HM2_CRRA200004861-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7047855300.0 23492851.0 E MTAB 9528:HM2 CRRA200004861 1a HV532DSXX L4 0:150 1:150 A:1909885369;C:1626900113;G:1623501695;T:1887391464;N:176659 150 150     1909885369 1626900113 1623501695 1887391464 176659 ERX4504056 ERS5050799 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93212 0.93173 0.08713 0.08625 0.7136 0.71411 0.47182 0.46635 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9990 9990 ERR4568382 ERX4504055 ERS5050798 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Middle Rep1 SAMEA7292228 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292228|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Middle Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Middle Rep1|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Middle Rep1 p HypoTH Middle Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HM1_CRRA200004860-1a_HV532DSXX_L4_1.fq.gz HM1_CRRA200004860-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7368139500.0 24560465.0 E MTAB 9528:HM1 CRRA200004860 1a HV532DSXX L4 0:150 1:150 A:1979116696;C:1681144383;G:1748755925;T:1958940264;N:182232 150 150     1979116696 1681144383 1748755925 1958940264 182232 ERX4504055 ERS5050798 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.90037 0.90035 0.07933 0.07951 0.72547 0.72512 0.46313 0.45076 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9991 9991 ERR4568381 ERX4504054 ERS5050797 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Middle Rep3 SAMEA7292227 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292227|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Middle Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Middle Rep3|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Middle Rep3 p EuTH Middle Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EM3_CRRA200004853-1a_HV532DSXX_L4_1.fq.gz EM3_CRRA200004853-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8203926600.0 27346422.0 E MTAB 9528:EM3 CRRA200004853 1a HV532DSXX L4 0:150 1:150 A:2145970242;C:1969430575;G:1966154582;T:2122170071;N:201130 150 150     2145970242 1969430575 1966154582 2122170071 201130 ERX4504054 ERS5050797 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.9358 0.93551 0.11154 0.11215 0.73908 0.73813 0.50711 0.50991 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9992 9992 ERR4568380 ERX4504053 ERS5050796 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Middle Rep2 SAMEA7292226 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292226|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Middle Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Middle Rep2|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Middle Rep2 p EuTH Middle Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EM2_CRRA200004852-1a_HV532DSXX_L4_1.fq.gz EM2_CRRA200004852-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8189085300.0 27296951.0 E MTAB 9528:EM2 CRRA200004852 1a HV532DSXX L4 0:150 1:150 A:2190135788;C:1917852780;G:1910200259;T:2170694756;N:201717 150 150     2190135788 1917852780 1910200259 2170694756 201717 ERX4504053 ERS5050796 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93471 0.93387 0.0982 0.0981 0.73357 0.73401 0.47523 0.47764 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9993 9993 ERR4568379 ERX4504052 ERS5050795 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Middle Rep1 SAMEA7292225 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292225|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Middle Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Middle Rep1|sampling site:middle portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Middle Rep1 p EuTH Middle Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:middle portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 EM1_CRRA200004851-1a_HV532DSXX_L4_1.fq.gz EM1_CRRA200004851-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7099416900.0 23664723.0 E MTAB 9528:EM1 CRRA200004851 1a HV532DSXX L4 0:150 1:150 A:1906046714;C:1656677333;G:1651795527;T:1884722014;N:175312 150 150     1906046714 1656677333 1651795527 1884722014 175312 ERX4504052 ERS5050795 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93383 0.93423 0.08879 0.08881 0.73699 0.73669 0.47814 0.47895 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9994 9994 ERR4568378 ERX4504051 ERS5050794 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Distal Rep3 SAMEA7292224 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292224|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Distal Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Distal Rep3|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Distal Rep3 p HypoTH Distal Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HD3_CRRA200004865-1a_HV532DSXX_L4_1.fq.gz HD3_CRRA200004865-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8040672900.0 26802243.0 E MTAB 9528:HD3 CRRA200004865 1a HV532DSXX L4 0:150 1:150 A:2167099154;C:1865357004;G:1864002622;T:2144021108;N:193012 150 150     2167099154 1865357004 1864002622 2144021108 193012 ERX4504051 ERS5050794 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.92854 0.92899 0.09996 0.09934 0.71902 0.71881 0.4815 0.47867 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9995 9995 ERR4568377 ERX4504050 ERS5050793 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Distal Rep2 SAMEA7292223 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292223|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Distal Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Distal Rep2|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Distal Rep2 p HypoTH Distal Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HD2_CRRA200004864-1a_HV532DSXX_L4_1.fq.gz HD2_CRRA200004864-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8313797700.0 27712659.0 E MTAB 9528:HD2 CRRA200004864 1a HV532DSXX L4 0:150 1:150 A:2273004120;C:1900982980;G:1898877384;T:2240725057;N:208159 150 150     2273004120 1900982980 1898877384 2240725057 208159 ERX4504050 ERS5050793 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.92628 0.92613 0.09471 0.09395 0.72003 0.72054 0.47995 0.47659 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9996 9996 ERR4568376 ERX4504049 ERS5050792 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Distal Rep1 SAMEA7292222 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292222|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Distal Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Distal Rep1|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Distal Rep1 p HypoTH Distal Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HD1_CRRA200004863-1a_HV532DSXX_L4_1.fq.gz HD1_CRRA200004863-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7169598300.0 23898661.0 E MTAB 9528:HD1 CRRA200004863 1a HV532DSXX L4 0:150 1:150 A:1941925699;C:1655391745;G:1656382398;T:1915720427;N:178031 150 150     1941925699 1655391745 1656382398 1915720427 178031 ERX4504049 ERS5050792 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.92656 0.92587 0.09244 0.09155 0.72537 0.72577 0.483 0.48459 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9997 9997 ERR4568375 ERX4504048 ERS5050791 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Distal Rep3 SAMEA7292221 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292221|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Distal Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Distal Rep3|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Distal Rep3 p EuTH Distal Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 ED3_CRRA200004856-1a_HV532DSXX_L4_1.fq.gz ED3_CRRA200004856-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8216298900.0 27387663.0 E MTAB 9528:ED3 CRRA200004856 1a HV532DSXX L4 0:150 1:150 A:2202070307;C:1915188230;G:1918164478;T:2180672072;N:203813 150 150     2202070307 1915188230 1918164478 2180672072 203813 ERX4504048 ERS5050791 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93043 0.92995 0.07828 0.07796 0.73799 0.73912 0.46784 0.47067 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9998 9998 ERR4568374 ERX4504047 ERS5050790 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Distal Rep2 SAMEA7292220 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292220|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Distal Rep2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Distal Rep2|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Distal Rep2 p EuTH Distal Rep2 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 ED2_CRRA200004855-1a_HV532DSXX_L4_1.fq.gz ED2_CRRA200004855-1a_HV532DSXX_L4_2.fq.gz fastq fastq 6629601000.0 22098670.0 E MTAB 9528:ED2 CRRA200004855 1a HV532DSXX L4 0:150 1:150 A:1741036830;C:1583210201;G:1581636803;T:1723551874;N:165292 150 150     1741036830 1583210201 1581636803 1723551874 165292 ERX4504047 ERS5050790 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.93472 0.93506 0.0948 0.09463 0.75235 0.75235 0.49522 0.49267 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
9999 9999 ERR4568373 ERX4504046 ERS5050789 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit EuTH Distal Rep1 SAMEA7292219 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292219|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:EuTH Distal Rep1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:euthyroid fish|sample name:E MTAB 9528:EuTH Distal Rep1|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:EuTH Distal Rep1 p EuTH Distal Rep1 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:euthyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 ED1_CRRA200004854-1a_HV532DSXX_L4_1.fq.gz ED1_CRRA200004854-1a_HV532DSXX_L4_2.fq.gz fastq fastq 7261648200.0 24205494.0 E MTAB 9528:ED1 CRRA200004854 1a HV532DSXX L4 0:150 1:150 A:1943655774;C:1694798398;G:1699834504;T:1923179081;N:180443 150 150     1943655774 1694798398 1699834504 1923179081 180443 ERX4504046 ERS5050789 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.92967 0.92953 0.08728 0.08781 0.73819 0.73797 0.49368 0.49233 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system
10147 10147 ERR5005147 ERX4814430 ERS5474667 ERP125923 PRJEB42059 RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E-MTAB-9924 Other DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17   Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. 6wpf rep2 RNA SAMEA7727294 Genomics and Epigenetics Division, Garvan Institute of Medical Research, ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727294|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:6wpf rep2 RNA|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:6wpf rep2 RNA|sex:mixed|strain:Mixed AB and Tubingen                 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E MTAB 9924:6wpf rep2 RNA p 6wpf rep2 RNA p RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. Experimental Factor: age:6|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP125923 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17 6wpf_rep2_RNA_R1.fastq.gz 6wpf_rep2_RNA_R2.fastq.gz fastq fastq 11929324428.0 40157012.0 E MTAB 9924:6wpf rep2 RNA R 0:148.72 1:148.34 A:3237937670;C:2713313024;G:2724528618;T:3251908184;N:1636932 148 148     3237937670 2713313024 2724528618 3251908184 1636932 ERX4814430 ERS5474667 ERA3199751 Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive 2 0.93069 0.93326 0.13891 0.13708 0.69779 0.71701 0.49797 0.49993 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Australia 2020-12-17 Larval Larval Multi-tissue Multi-system
10148 10148 ERR5005146 ERX4814429 ERS5474666 ERP125923 PRJEB42059 RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E-MTAB-9924 Other DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17   Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. 6wpf rep1 RNA SAMEA7727293 Genomics and Epigenetics Division, Garvan Institute of Medical Research, ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727293|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:6wpf rep1 RNA|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:6wpf rep1 RNA|sex:mixed|strain:Mixed AB and Tubingen                 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain E MTAB 9924:6wpf rep1 RNA p 6wpf rep1 RNA p RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions. Experimental Factor: age:6|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP125923 HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17 6wpf_rep1_RNA_R1.fastq.gz 6wpf_rep1_RNA_R2.fastq.gz fastq fastq 19633084666.0 66362913.0 E MTAB 9924:6wpf rep1 RNA R 0:148.10 1:147.74 A:5348913370;C:4443593237;G:4456508875;T:5380825384;N:3243800 148 147     5348913370 4443593237 4456508875 5380825384 3243800 ERX4814429 ERS5474666 ERA3199751 Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive 2 0.92182 0.92338 0.12138 0.11866 0.68499 0.70236 0.50638 0.51742 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Australia 2020-12-17 Larval Larval Multi-tissue Multi-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");;