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,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,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,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,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
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
10188,ERR600685,ERX557514,ERS460539,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2537630,SC,ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:42:28Z|External Id:SAMEA2537630|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:42:28Z|INSDC status:public|Submitter Id:stI oocytes TC9 WT F sc 1951842|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TCGAAGTGAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC9 WT F sc 1951842|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 13129 8#9,10325318,Illumina sequencing of library 10325318  constructed from sample accession ERS460539 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TCGAAGTG.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003932,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16,13129_8#9.cram,cram,2109545984.0,16480828.0,SC RUN 13129 8#9,0:53 1:75,A:539694535;C:346663352;G:388843341;T:829045236;N:5299520,53,75,,,539694535,346663352,388843341,829045236,5299520,ERX557514,ERS460539,ERA358077,SC,Wellcome Sanger Institute,2,0.39712,0.80906,0.2298,0.0288,0.97575,0.82292,0.20258,0.50014,53,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-16,Zygote,Embryo,Multi-tissue,Multi-system
10189,ERR600684,ERX557513,ERS460538,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2537629,SC,ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:41:18Z|External Id:SAMEA2537629|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:41:18Z|INSDC status:public|Submitter Id:stI oocytes TC8 buc 4 sc 1951841|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TTCCATTGAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC8 buc 4 sc 1951841|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 13129 8#8,10325317,Illumina sequencing of library 10325317  constructed from sample accession ERS460538 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TTCCATTG.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003932,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16,13129_8#8.cram,cram,1995224064.0,15587688.0,SC RUN 13129 8#8,0:53 1:75,A:508909383;C:332355977;G:373835062;T:775089830;N:5033812,53,75,,,508909383,332355977,373835062,775089830,5033812,ERX557513,ERS460538,ERA358077,SC,Wellcome Sanger Institute,2,0.31242,0.8426,0.16835,0.02824,0.96921,0.81606,0.27677,0.49882,53,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-16,Zygote,Embryo,Multi-tissue,Multi-system
10190,ERR600683,ERX557512,ERS460537,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2537628,SC,ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:57:23Z|External Id:SAMEA2537628|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:57:23Z|INSDC status:public|Submitter Id:stI oocytes TC7 buc 3 sc 1951840|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TAGTCTTGAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC7 buc 3 sc 1951840|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 13129 8#7,10325316,Illumina sequencing of library 10325316  constructed from sample accession ERS460537 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TAGTCTTG.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003932,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16,13129_8#7.cram,cram,1335316864.0,10432163.0,SC RUN 13129 8#7,0:53 1:75,A:318582120;C:238156133;G:258642941;T:516548945;N:3386725,53,75,,,318582120,238156133,258642941,516548945,3386725,ERX557512,ERS460537,ERA358077,SC,Wellcome Sanger Institute,2,0.32517,0.89235,0.16229,0.04485,0.97634,0.90057,0.32073,0.47925,53,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-16,Zygote,Embryo,Multi-tissue,Multi-system
10191,ERR600682,ERX557511,ERS460536,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2537627,SC,ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:42:28Z|External Id:SAMEA2537627|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:42:28Z|INSDC status:public|Submitter Id:stI oocytes TC6 buc 2 sc 1951839|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TGTGGTTGAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC6 buc 2 sc 1951839|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 13129 8#6,10325315,Illumina sequencing of library 10325315  constructed from sample accession ERS460536 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TGTGGTTG.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003932,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16,13129_8#6.cram,cram,2044001792.0,15968764.0,SC RUN 13129 8#6,0:53 1:75,A:525134102;C:334554692;G:372135205;T:806953076;N:5224717,53,75,,,525134102,334554692,372135205,806953076,5224717,ERX557511,ERS460536,ERA358077,SC,Wellcome Sanger Institute,2,0.32466,0.83888,0.17696,0.03057,0.97451,0.82938,0.2392,0.48605,53,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-16,Zygote,Embryo,Multi-tissue,Multi-system
10192,ERR600681,ERX557510,ERS460535,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2537626,SC,ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:41:18Z|External Id:SAMEA2537626|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:41:18Z|INSDC status:public|Submitter Id:stI oocytes TC5 buc 1 sc 1951838|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TCCTCAATAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC5 buc 1 sc 1951838|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 13129 8#5,10325314,Illumina sequencing of library 10325314  constructed from sample accession ERS460535 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TCCTCAAT.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003932,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16,13129_8#5.cram,cram,2936817024.0,22943883.0,SC RUN 13129 8#5,0:53 1:75,A:708314449;C:473731341;G:531306146;T:1215982569;N:7482519,53,75,,,708314449,473731341,531306146,1215982569,7482519,ERX557510,ERS460535,ERA358077,SC,Wellcome Sanger Institute,2,0.38759,0.88578,0.22255,0.03034,0.9707,0.80984,0.2075,0.47267,53,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-16,Zygote,Embryo,Multi-tissue,Multi-system
10193,ERR600680,ERX557509,ERS460534,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2537625,SC,ArrayExpress Genotype:Tgbuc:del80|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:57:23Z|External Id:SAMEA2537625|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:57:23Z|INSDC status:public|Submitter Id:stI oocytes TC4 Tg 1 sc 1951837|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TACAGGATAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC4 Tg 1 sc 1951837|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 13129 8#4,10325313,Illumina sequencing of library 10325313  constructed from sample accession ERS460534 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TACAGGAT.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003932,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16,13129_8#4.cram,cram,2384869248.0,18631791.0,SC RUN 13129 8#4,0:53 1:75,A:579389373;C:378753292;G:429075103;T:991563565;N:6087915,53,75,,,579389373,378753292,429075103,991563565,6087915,ERX557509,ERS460534,ERA358077,SC,Wellcome Sanger Institute,2,0.48038,0.84929,0.28951,0.03671,0.97788,0.81249,0.13153,0.4899,53,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-16,Zygote,Embryo,Multi-tissue,Multi-system
10194,ERR600679,ERX557508,ERS460533,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2537624,SC,ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:42:28Z|External Id:SAMEA2537624|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:42:28Z|INSDC status:public|Submitter Id:stI oocytes TC3 WT 3 sc 1951836|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TAGTGACTAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC3 WT 3 sc 1951836|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 13129 8#3,10325312,Illumina sequencing of library 10325312  constructed from sample accession ERS460533 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TAGTGACT.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003932,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16,13129_8#3.cram,cram,2105031424.0,16445558.0,SC RUN 13129 8#3,0:53 1:75,A:508334707;C:332423893;G:374815782;T:884154321;N:5302721,53,75,,,508334707,332423893,374815782,884154321,5302721,ERX557508,ERS460533,ERA358077,SC,Wellcome Sanger Institute,2,0.50684,0.84751,0.30664,0.04222,0.97853,0.81343,0.11336,0.49639,53,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-16,Zygote,Embryo,Multi-tissue,Multi-system
10195,ERR600678,ERX557507,ERS460532,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2537623,SC,ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:41:18Z|External Id:SAMEA2537623|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:41:18Z|INSDC status:public|Submitter Id:stI oocytes TC2 WT 2 sc 1951835|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TTCCTGCTAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC2 WT 2 sc 1951835|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 13129 8#2,10325311,Illumina sequencing of library 10325311  constructed from sample accession ERS460532 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TTCCTGCT.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003932,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16,13129_8#2.cram,cram,1616469504.0,12628668.0,SC RUN 13129 8#2,0:53 1:75,A:415492342;C:254209235;G:288719848;T:653979238;N:4068841,53,75,,,415492342,254209235,288719848,653979238,4068841,ERX557507,ERS460532,ERA358077,SC,Wellcome Sanger Institute,2,0.44661,0.81908,0.25181,0.0449,0.96469,0.80306,0.22578,0.49499,53,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-16,Zygote,Embryo,Multi-tissue,Multi-system
10196,ERR600677,ERX557506,ERS460531,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2537622,SC,ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 16T09:23:11Z|ENA LAST UPDATE:2018 03 08T17:57:22Z|External Id:SAMEA2537622|INSDC center name:SC|INSDC first public:2014 09 16T09:23:11Z|INSDC last update:2018 03 08T17:57:22Z|INSDC status:public|Submitter Id:stI oocytes TC1 WT 1 sc 1951834|common name:zebrafish|sample description:3 prime end enriched mRNA from oocytes. A 10 base indexing sequence TGCGATCTAT is bases 13 to 22 of read 1 followed by polyT.|sample name:stI oocytes TC1 WT 1 sc 1951834|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 13129 8#1,10325310,Illumina sequencing of library 10325310  constructed from sample accession ERS460531 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13129 8.  This submission includes reads tagged with the sequence TGCGATCT.,qPCR only,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP003932,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2014 09 16|ENA LAST UPDATE:2018 11 16,13129_8#1.cram,cram,1741512832.0,13605569.0,SC RUN 13129 8#1,0:53 1:75,A:460247357;C:265029516;G:295203994;T:716636989;N:4394976,53,75,,,460247357,265029516,295203994,716636989,4394976,ERX557506,ERS460531,ERA358077,SC,Wellcome Sanger Institute,2,0.36591,0.79177,0.21838,0.03785,0.97569,0.81095,0.16098,0.49496,53,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-16,Zygote,Embryo,Multi-tissue,Multi-system
10197,ERR596433,ERX553396,ERS462797,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2547987,SC,ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:41:51Z|External Id:SAMEA2547987|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:41:51Z|INSDC status:public|Submitter Id:stI oocytes Fraction9 WT F sc 1971686|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction9 WT F sc 1971686|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina MiSeq paired end sequencing,SC EXP 13147 1#9,10347698,Illumina sequencing of library 10347698  constructed from sample accession ERS462797 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence GATCAG.,RNA seq dUTP,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,ERP003932,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16,13147_1#9.cram,cram,552103200.0,1840344.0,SC RUN 13147 1#9,0:150 1:150,A:124691243;C:154385942;G:155440122;T:117585893;N:0,150,150,,,124691243,154385942,155440122,117585893,0,ERX553396,ERS462797,ERA356861,SC,Wellcome Sanger Institute,2,0.97349,0.97184,0.25562,0.26367,0.73754,0.76534,0.68526,0.65497,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-09,Zygote,Embryo,Multi-tissue,Multi-system
10198,ERR596432,ERX553395,ERS462796,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2547986,SC,ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:58:35Z|External Id:SAMEA2547986|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:58:35Z|INSDC status:public|Submitter Id:stI oocytes Fraction8 buc 4 sc 1971685|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction8 buc 4 sc 1971685|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina MiSeq paired end sequencing,SC EXP 13147 1#8,10347697,Illumina sequencing of library 10347697  constructed from sample accession ERS462796 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence ACTTGA.,RNA seq dUTP,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,ERP003932,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16,13147_1#8.cram,cram,625194300.0,2083981.0,SC RUN 13147 1#8,0:150 1:150,A:145587865;C:170554648;G:171453968;T:137597813;N:6,150,150,,,145587865,170554648,171453968,137597813,6,ERX553395,ERS462796,ERA356861,SC,Wellcome Sanger Institute,2,0.97066,0.96788,0.23219,0.23823,0.7205,0.75623,0.61734,0.60233,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-09,Zygote,Embryo,Multi-tissue,Multi-system
10199,ERR596431,ERX553394,ERS462795,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2547985,SC,ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:42:18Z|External Id:SAMEA2547985|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:42:18Z|INSDC status:public|Submitter Id:stI oocytes Fraction7 buc 3 sc 1971684|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction7 buc 3 sc 1971684|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina MiSeq paired end sequencing,SC EXP 13147 1#7,10347696,Illumina sequencing of library 10347696  constructed from sample accession ERS462795 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence CAGATC.,RNA seq dUTP,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,ERP003932,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16,13147_1#7.cram,cram,498083400.0,1660278.0,SC RUN 13147 1#7,0:150 1:150,A:127449944;C:127409242;G:133869886;T:109354327;N:1,150,150,,,127449944,127409242,133869886,109354327,1,ERX553394,ERS462795,ERA356861,SC,Wellcome Sanger Institute,2,0.94952,0.95502,0.14913,0.14846,0.73807,0.74572,0.54621,0.54335,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-09,Zygote,Embryo,Multi-tissue,Multi-system
10200,ERR596430,ERX553393,ERS462794,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2547984,SC,ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:41:51Z|External Id:SAMEA2547984|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:41:51Z|INSDC status:public|Submitter Id:stI oocytes Fraction6 buc 2 sc 1971683|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction6 buc 2 sc 1971683|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina MiSeq paired end sequencing,SC EXP 13147 1#6,10347695,Illumina sequencing of library 10347695  constructed from sample accession ERS462794 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence GCCAAT.,RNA seq dUTP,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,ERP003932,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16,13147_1#6.cram,cram,433626600.0,1445422.0,SC RUN 13147 1#6,0:150 1:150,A:113030099;C:110060861;G:116695113;T:93840526;N:1,150,150,,,113030099,110060861,116695113,93840526,1,ERX553393,ERS462794,ERA356861,SC,Wellcome Sanger Institute,2,0.94512,0.95418,0.13754,0.13509,0.76274,0.77542,0.54752,0.54127,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-09,Zygote,Embryo,Multi-tissue,Multi-system
10201,ERR596429,ERX553392,ERS462793,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2547983,SC,ArrayExpress Genotype:buc|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:58:34Z|External Id:SAMEA2547983|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:58:34Z|INSDC status:public|Submitter Id:stI oocytes Fraction5 buc 1 sc 1971682|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction5 buc 1 sc 1971682|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina MiSeq paired end sequencing,SC EXP 13147 1#5,10347694,Illumina sequencing of library 10347694  constructed from sample accession ERS462793 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence ACAGTG.,RNA seq dUTP,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,ERP003932,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16,13147_1#5.cram,cram,670533600.0,2235112.0,SC RUN 13147 1#5,0:150 1:150,A:152057213;C:184952145;G:191337018;T:142187224;N:0,150,150,,,152057213,184952145,191337018,142187224,0,ERX553392,ERS462793,ERA356861,SC,Wellcome Sanger Institute,2,0.95987,0.95954,0.20495,0.20606,0.73726,0.7529,0.61328,0.61986,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-09,Zygote,Embryo,Multi-tissue,Multi-system
10202,ERR596428,ERX553391,ERS462792,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2547982,SC,ArrayExpress Genotype:Tgbuc:del80|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:42:18Z|External Id:SAMEA2547982|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:42:18Z|INSDC status:public|Submitter Id:stI oocytes Fraction4 Tg 1 sc 1971681|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction4 Tg 1 sc 1971681|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina MiSeq paired end sequencing,SC EXP 13147 1#4,10347693,Illumina sequencing of library 10347693  constructed from sample accession ERS462792 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence TGACCA.,RNA seq dUTP,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,ERP003932,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16,13147_1#4.cram,cram,524202300.0,1747341.0,SC RUN 13147 1#4,0:150 1:150,A:117529161;C:147865152;G:153007969;T:105800018;N:0,150,150,,,117529161,147865152,153007969,105800018,0,ERX553391,ERS462792,ERA356861,SC,Wellcome Sanger Institute,2,0.95955,0.96175,0.21001,0.20834,0.76445,0.78281,0.70435,0.68975,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-09,Zygote,Embryo,Multi-tissue,Multi-system
10203,ERR596427,ERX553390,ERS462791,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2547981,SC,ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:41:51Z|External Id:SAMEA2547981|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:41:51Z|INSDC status:public|Submitter Id:stI oocytes Fraction3 WT 3 sc 1971680|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction3 WT 3 sc 1971680|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina MiSeq paired end sequencing,SC EXP 13147 1#3,10347692,Illumina sequencing of library 10347692  constructed from sample accession ERS462791 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence TTAGGC.,RNA seq dUTP,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,ERP003932,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16,13147_1#3.cram,cram,1142124300.0,3807081.0,SC RUN 13147 1#3,0:150 1:150,A:239327535;C:334933829;G:339423780;T:228439155;N:1,150,150,,,239327535,334933829,339423780,228439155,1,ERX553390,ERS462791,ERA356861,SC,Wellcome Sanger Institute,2,0.98041,0.98099,0.28225,0.28585,0.80273,0.81012,0.81256,0.81436,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-09,Zygote,Embryo,Multi-tissue,Multi-system
10204,ERR596426,ERX553389,ERS462790,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2547980,SC,ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:58:34Z|External Id:SAMEA2547980|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:58:34Z|INSDC status:public|Submitter Id:stI oocytes Fraction2 WT 2 sc 1971679|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction2 WT 2 sc 1971679|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina MiSeq paired end sequencing,SC EXP 13147 1#2,10347691,Illumina sequencing of library 10347691  constructed from sample accession ERS462790 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence CGATGT.,RNA seq dUTP,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,ERP003932,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16,13147_1#2.cram,cram,714969600.0,2383232.0,SC RUN 13147 1#2,0:150 1:150,A:151578902;C:207835645;G:217545196;T:138009856;N:1,150,150,,,151578902,207835645,217545196,138009856,1,ERX553389,ERS462790,ERA356861,SC,Wellcome Sanger Institute,2,0.97925,0.981,0.2548,0.25496,0.77447,0.78462,0.77035,0.76498,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-09,Zygote,Embryo,Multi-tissue,Multi-system
10205,ERR596425,ERX553388,ERS462789,ERP003932,PRJEB4632,Zebrafish oocyte maturation,Zebrafish_oocyte_maturation-sc-2013-09-24T12:03:04Z-2777,Transcriptome Analysis,The data within this study has been generated to study zebrafish oocyte maturation.,,,,,SAMEA2547979,SC,ArrayExpress Genotype:WT|ArrayExpress OrganismPart:ovaries|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 09 09T09:35:46Z|ENA LAST UPDATE:2018 03 08T17:42:18Z|External Id:SAMEA2547979|INSDC center name:SC|INSDC first public:2014 09 09T09:35:46Z|INSDC last update:2018 03 08T17:42:18Z|INSDC status:public|Submitter Id:stI oocytes Fraction1 WT 1 sc 1971678|common name:zebrafish|sample description:Oocyte RNA fraction.|sample name:stI oocytes Fraction1 WT 1 sc 1971678|scientific name:Danio rerio|strain:AB,,,,,,,,,Illumina MiSeq paired end sequencing,SC EXP 13147 1#1,10347690,Illumina sequencing of library 10347690  constructed from sample accession ERS462789 for study accession ERP003932.  This is part of an Illumina multiplexed sequencing run 13147 1.  This submission includes reads tagged with the sequence ATCACG.,RNA seq dUTP,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiSeq,,ERP003932,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2014 09 09|ENA LAST UPDATE:2018 11 16,13147_1#1.cram,cram,567682800.0,1892276.0,SC RUN 13147 1#1,0:150 1:150,A:133087363;C:153887726;G:158264603;T:122443107;N:1,150,150,,,133087363,153887726,158264603,122443107,1,ERX553388,ERS462789,ERA356861,SC,Wellcome Sanger Institute,2,0.94832,0.94927,0.19305,0.19445,0.72421,0.73551,0.59172,0.60783,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2014-09-09,Zygote,Embryo,Multi-tissue,Multi-system
33696,SRR30599775,SRX26022476,SRS22594195,SRP531514,PRJNA1158727,CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30,GSE276705,Transcriptome Analysis,Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.,,,,ebf3a wt  5 dpf  rep 2,GSM8504328,,source name:head with eyes  10 12 embryos pooled|tissue:head with eyes|age:5 dpf|genotype:ebf3a wild types|geo loc name:missing|collection date:missing,ebf3a wt  5 dpf  rep 2,Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  10 12 embryos pooled,,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,tissue:head with eyes|age:5 dpf|genotype:ebf3a wild types,GSM8504328,GSM8504328: ebf3a wt  5 dpf  rep 2; Danio rerio; RNA Seq,GSM8504328 r1,GSM8504328,1,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP531514,,,Ebf-WT-2-5dpf_R1_001.fastq.gz Ebf-WT-2-5dpf_R2_001.fastq.gz,fastq fastq,17620546500.0,58735155.0,GSM8504328 r1,0:150 1:150,A:4442356407;C:4365499245;G:4407165860;T:4405169272;N:355716,150,150,,,4442356407,4365499245,4407165860,4405169272,355716,SRX26022476,SRS22594195,SRA1966071,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-09-09,Larval,Larval,Multi-tissue,Multi-system
33697,SRR30599776,SRX26022475,SRS22594194,SRP531514,PRJNA1158727,CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30,GSE276705,Transcriptome Analysis,Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.,,,,ebf3a wt  5 dpf  rep 1,GSM8504327,,source name:head with eyes  10 12 embryos pooled|tissue:head with eyes|age:5 dpf|genotype:ebf3a wild types|geo loc name:missing|collection date:missing,ebf3a wt  5 dpf  rep 1,Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  10 12 embryos pooled,,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,tissue:head with eyes|age:5 dpf|genotype:ebf3a wild types,GSM8504327,GSM8504327: ebf3a wt  5 dpf  rep 1; Danio rerio; RNA Seq,GSM8504327 r1,GSM8504327,1,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP531514,,,Ebf-WT-1-5dpf_R1_001.fastq.gz Ebf-WT-1-5dpf_R2_001.fastq.gz,fastq fastq,14881331700.0,49604439.0,GSM8504327 r1,0:150 1:150,A:3819750403;C:3611501542;G:3658667991;T:3791111572;N:300192,150,150,,,3819750403,3611501542,3658667991,3791111572,300192,SRX26022475,SRS22594194,SRA1966071,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-09-09,Larval,Larval,Multi-tissue,Multi-system
33698,SRR30599777,SRX26022474,SRS22594193,SRP531514,PRJNA1158727,CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30,GSE276705,Transcriptome Analysis,Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.,,,,ebf3a hom  5 dpf  rep 2,GSM8504326,,source name:head with eyes  10 12 embryos pooled|tissue:head with eyes|age:5 dpf|genotype:ebf3a homozygous|geo loc name:missing|collection date:missing,ebf3a hom  5 dpf  rep 2,Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  10 12 embryos pooled,,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,tissue:head with eyes|age:5 dpf|genotype:ebf3a homozygous,GSM8504326,GSM8504326: ebf3a hom  5 dpf  rep 2; Danio rerio; RNA Seq,GSM8504326 r1,GSM8504326,1,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP531514,,,Ebf-Homo-2-5dpf_R1_001.fastq.gz Ebf-Homo-2-5dpf_R2_001.fastq.gz,fastq fastq,13980599100.0,46601997.0,GSM8504326 r1,0:150 1:150,A:3559157122;C:3432017726;G:3462680948;T:3526461889;N:281415,150,150,,,3559157122,3432017726,3462680948,3526461889,281415,SRX26022474,SRS22594193,SRA1966071,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-09-09,Larval,Larval,Multi-tissue,Multi-system
33699,SRR30599778,SRX26022473,SRS22594192,SRP531514,PRJNA1158727,CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30,GSE276705,Transcriptome Analysis,Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.,,,,ebf3a hom  5 dpf  rep 1,GSM8504325,,source name:head with eyes  10 12 embryos pooled|tissue:head with eyes|age:5 dpf|genotype:ebf3a homozygous|geo loc name:missing|collection date:missing,ebf3a hom  5 dpf  rep 1,Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,head with eyes  10 12 embryos pooled,,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,tissue:head with eyes|age:5 dpf|genotype:ebf3a homozygous,GSM8504325,GSM8504325: ebf3a hom  5 dpf  rep 1; Danio rerio; RNA Seq,GSM8504325 r1,GSM8504325,1,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP531514,,,Ebf-Homo-1-5dpf_R1_001.fastq.gz Ebf-Homo-1-5dpf_R2_001.fastq.gz,fastq fastq,16257229800.0,54190766.0,GSM8504325 r1,0:150 1:150,A:4127739980;C:3994508761;G:4048290353;T:4086361510;N:329196,150,150,,,4127739980,3994508761,4048290353,4086361510,329196,SRX26022473,SRS22594192,SRA1966071,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-09-09,Larval,Larval,Multi-tissue,Multi-system
33700,SRR30599779,SRX26022472,SRS22594191,SRP531514,PRJNA1158727,CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30,GSE276705,Transcriptome Analysis,Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.,,,,ebf3a wt  2 dpf  rep 2,GSM8504324,,source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types|geo loc name:missing|collection date:missing,ebf3a wt  2 dpf  rep 2,Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,upper body with eyes  15 20 embryos pooled,,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types,GSM8504324,GSM8504324: ebf3a wt  2 dpf  rep 2; Danio rerio; RNA Seq,GSM8504324 r1,GSM8504324,1,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP531514,,,Ebf-WT-2-2dpf_R1_001.fastq.gz Ebf-WT-2-2dpf_R2_001.fastq.gz,fastq fastq,22635570600.0,75451902.0,GSM8504324 r1,0:150 1:150,A:6279354286;C:5013138453;G:5250498169;T:6092284847;N:294845,150,150,,,6279354286,5013138453,5250498169,6092284847,294845,SRX26022472,SRS22594191,SRA1966071,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-09-09,Hatching,Embryo,Multi-tissue,Multi-system
33701,SRR30599780,SRX26022471,SRS22594190,SRP531514,PRJNA1158727,CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30,GSE276705,Transcriptome Analysis,Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.,,,,ebf3a wt  2 dpf  rep 1,GSM8504323,,source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types|geo loc name:missing|collection date:missing,ebf3a wt  2 dpf  rep 1,Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,upper body with eyes  15 20 embryos pooled,,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types,GSM8504323,GSM8504323: ebf3a wt  2 dpf  rep 1; Danio rerio; RNA Seq,GSM8504323 r1,GSM8504323,1,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP531514,,,Ebf-WT-1-2dpf_R1_001.fastq.gz Ebf-WT-1-2dpf_R2_001.fastq.gz,fastq fastq,19711425600.0,65704752.0,GSM8504323 r1,0:150 1:150,A:5541464229;C:4291380685;G:4497372769;T:5380954703;N:253214,150,150,,,5541464229,4291380685,4497372769,5380954703,253214,SRX26022471,SRS22594190,SRA1966071,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-09-09,Hatching,Embryo,Multi-tissue,Multi-system
33702,SRR30599781,SRX26022470,SRS22594189,SRP531514,PRJNA1158727,CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30,GSE276705,Transcriptome Analysis,Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.,,,,ebf3a het  2 dpf  rep 2,GSM8504322,,source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous|geo loc name:missing|collection date:missing,ebf3a het  2 dpf  rep 2,Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,upper body with eyes  15 20 embryos pooled,,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous,GSM8504322,GSM8504322: ebf3a het  2 dpf  rep 2; Danio rerio; RNA Seq,GSM8504322 r1,GSM8504322,1,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP531514,,,Ebf-HET-2-2dpf_R1_001.fastq.gz Ebf-HET-2-2dpf_R2_001.fastq.gz,fastq fastq,15108144300.0,50360481.0,GSM8504322 r1,0:150 1:150,A:4240605272;C:3297282748;G:3449975456;T:4120084716;N:196108,150,150,,,4240605272,3297282748,3449975456,4120084716,196108,SRX26022470,SRS22594189,SRA1966071,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-09-09,Hatching,Embryo,Multi-tissue,Multi-system
33703,SRR30599782,SRX26022469,SRS22594188,SRP531514,PRJNA1158727,CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30,GSE276705,Transcriptome Analysis,Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.,,,,ebf3a het  2 dpf  rep 1,GSM8504321,,source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous|geo loc name:missing|collection date:missing,ebf3a het  2 dpf  rep 1,Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,upper body with eyes  15 20 embryos pooled,,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous,GSM8504321,GSM8504321: ebf3a het  2 dpf  rep 1; Danio rerio; RNA Seq,GSM8504321 r1,GSM8504321,1,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP531514,,,Ebf-HET-1-2dpf_R1_001.fastq.gz Ebf-HET-1-2dpf_R2_001.fastq.gz,fastq fastq,16538340600.0,55127802.0,GSM8504321 r1,0:150 1:150,A:4633062848;C:3617047326;G:3792365071;T:4495647394;N:217961,150,150,,,4633062848,3617047326,3792365071,4495647394,217961,SRX26022469,SRS22594188,SRA1966071,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-09-09,Hatching,Embryo,Multi-tissue,Multi-system
33704,SRR30599783,SRX26022468,SRS22594186,SRP531514,PRJNA1158727,CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30,GSE276705,Transcriptome Analysis,Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.,,,,ebf3a hom  2 dpf  rep 2,GSM8504320,,source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous|geo loc name:missing|collection date:missing,ebf3a hom  2 dpf  rep 2,Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,upper body with eyes  15 20 embryos pooled,,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous,GSM8504320,GSM8504320: ebf3a hom  2 dpf  rep 2; Danio rerio; RNA Seq,GSM8504320 r1,GSM8504320,1,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP531514,,,Ebf-HOMO-2-2dpf_R1_001.fastq.gz Ebf-HOMO-2-2dpf_R2_001.fastq.gz,fastq fastq,14586421200.0,48621404.0,GSM8504320 r1,0:150 1:150,A:4099529019;C:3162437766;G:3348146726;T:3976118566;N:189123,150,150,,,4099529019,3162437766,3348146726,3976118566,189123,SRX26022468,SRS22594186,SRA1966071,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-09-09,Hatching,Embryo,Multi-tissue,Multi-system
33705,SRR30599784,SRX26022467,SRS22594187,SRP531514,PRJNA1158727,CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30,GSE276705,Transcriptome Analysis,Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.,,,,ebf3a hom  2 dpf  rep 1,GSM8504319,,source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous|geo loc name:missing|collection date:missing,ebf3a hom  2 dpf  rep 1,Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,upper body with eyes  15 20 embryos pooled,,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous,GSM8504319,GSM8504319: ebf3a hom  2 dpf  rep 1; Danio rerio; RNA Seq,GSM8504319 r1,GSM8504319,1,Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP531514,,,Ebf-HOMO-1-2dpf_R1_001.fastq.gz Ebf-HOMO-1-2dpf_R2_001.fastq.gz,fastq fastq,14235405000.0,47451350.0,GSM8504319 r1,0:150 1:150,A:3937137116;C:3134793115;G:3336004625;T:3827286589;N:183555,150,150,,,3937137116,3134793115,3336004625,3827286589,183555,SRX26022467,SRS22594187,SRA1966071,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-09-09,Hatching,Embryo,Multi-tissue,Multi-system
36707,SRR835172,SRX271968,SRS416264,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,il 97h 42 440,GSM1129630,,tissue:iridophores|hpf,il 97h 42 440,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,iridophores,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129630,GSM1129630: il 97h 42 440; Danio rerio; RNA Seq,GSM1129630 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129630,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,il_97h_42_440.fq.bz2,fastq,113120952.0,2693356.0,GSM1129630 r1,0:42,A:26578283;C:27647612;G:26417805;T:32470133;N:7119,42,,,,26578283,27647612,26417805,32470133,7119,SRX271968,SRS416264,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",1,0.85151,,0.08761,,0.85766,,0.53122,,42,,B,,usable mapping rate,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Multi-tissue,Multi-system
36708,SRR835171,SRX271967,SRS416263,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,il 77h 49 440,GSM1129629,,tissue:iridophores|hpf,il 77h 49 440,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,iridophores,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129629,GSM1129629: il 77h 49 440; Danio rerio; RNA Seq,GSM1129629 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129629,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,il_77h_49_440.fq.bz2,fastq,119102886.0,2835783.0,GSM1129629 r1,0:42,A:27449590;C:27743213;G:26605006;T:37297547;N:7530,42,,,,27449590,27743213,26605006,37297547,7530,SRX271967,SRS416263,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",1,0.85274,,0.12109,,0.86239,,0.52589,,42,,B,,usable mapping rate,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Multi-tissue,Multi-system
36709,SRR835170,SRX271966,SRS416261,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,il 77h 44 440,GSM1129628,,tissue:iridophores|hpf,il 77h 44 440,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,iridophores,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129628,GSM1129628: il 77h 44 440; Danio rerio; RNA Seq,GSM1129628 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129628,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,il_77h_44_440.fq.bz2,fastq,319536210.0,7608005.0,GSM1129628 r1,0:42,A:72602262;C:81003831;G:76662728;T:89248984;N:18405,42,,,,72602262,81003831,76662728,89248984,18405,SRX271966,SRS416261,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",1,0.88506,,0.08161,,0.85756,,0.50585,,42,,B,,usable mapping rate,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Multi-tissue,Multi-system
36710,SRR835169,SRX271965,SRS416262,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,il 77h 38 351,GSM1129627,,tissue:iridophores|hpf,il 77h 38 351,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,iridophores,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129627,GSM1129627: il 77h 38 351; Danio rerio; RNA Seq,GSM1129627 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129627,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,il_77h_38_351_AGTGT.fq.bz2,fastq,105470208.0,2929728.0,GSM1129627 r1,0:36,A:23660397;C:24772356;G:27192539;T:29844080;N:836,36,,,,23660397,24772356,27192539,29844080,836,SRX271965,SRS416262,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",1,0.76356,,0.07685,,0.86634,,0.51592,,36,,B,,usable mapping rate,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Multi-tissue,Multi-system
36711,SRR835168,SRX271964,SRS416260,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,il 58h 50 440,GSM1129626,,tissue:iridophores|hpf,il 58h 50 440,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,iridophores,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129626,GSM1129626: il 58h 50 440; Danio rerio; RNA Seq,GSM1129626 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129626,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,il_58h_50_440.fq.bz2,fastq,158731692.0,3779326.0,GSM1129626 r1,0:42,A:35358330;C:37377423;G:36834086;T:49152866;N:8987,42,,,,35358330,37377423,36834086,49152866,8987,SRX271964,SRS416260,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",1,0.78748,,0.04211,,0.88183,,0.51498,,42,,B,,usable mapping rate,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Multi-tissue,Multi-system
40439,SRR3144620,SRX1560771,SRS1275344,SRP069287,PRJNA310829,Danio rerio strain:AB Raw sequence reads,PRJNA310829,Other,transcriptional profile of both macrophages M and endothelial end cells EC between three different lesion stages uninjured control con  upon macrophage arrival arr  and during macrophage traction tra.,,,,,macrophage and endothelial cells,,strain:AB|age:Day3|sex:not determined|tissue:macrophage and endothelial cells|BioSampleModel:Model organism or animal,,,,,,,,,Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction,macrophage and endothelial cells,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>,SRP069287,,,EC-con-2-27_1.fq.gz,fastq,2627841170.0,26309124.0,macrophages and endothelial cells,0:99.88 1:0,A:787503280;C:537314192;G:533698336;T:769265722;N:59640,99,0,,,787503280,537314192,533698336,769265722,59640,SRX1560771,SRS1275344,SRA347117,SouthWest university Of China|Laboratory of Molecular Developmental Biology,Southwest University of China,1,0.87616,,0.42753,,0.88477,,0.63864,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2016-02-23,Larval,Larval,Multi-tissue,Multi-system
40947,SRR3465556,SRX1735458,SRS1416510,SRP074122,PRJNA319956,Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.,GSE80768,Transcriptome Analysis,Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.,,pubmed:27783941,,9267X14 tumor,GSM2136824,,source name:brain tumor|tissue:brain tumor,9267X14 tumor,USeq’s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values,brain tumor,Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.,tissue:brain tumor,GSM2136824,GSM2136824: 9267X14 tumor; Danio rerio; RNA Seq,GSM2136824,,1,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,GEO Accession:GSM2136824,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP074122,,,9267X14_120613_SN141_0510_AC0TF4ACXX_8.txt.gz,fastq,1403474100.0,28069482.0,GSM2136824 r1,0:50,A:379029580;C:327462448;G:316163138;T:380761095;N:57839,50,,,,379029580,327462448,316163138,380761095,57839,SRX1735458,SRS1416510,SRA421168,GEO,"Oncological Sciences, University of Utah",1,0.91779,,0.10471,,0.68018,,0.46831,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-28,Undetermined,Undetermined,Multi-tissue,Multi-system
40948,SRR3465555,SRX1735457,SRS1416511,SRP074122,PRJNA319956,Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.,GSE80768,Transcriptome Analysis,Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.,,pubmed:27783941,,9267X13 tumor,GSM2136823,,source name:brain tumor|tissue:brain tumor,9267X13 tumor,USeq’s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values,brain tumor,Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.,tissue:brain tumor,GSM2136823,GSM2136823: 9267X13 tumor; Danio rerio; RNA Seq,GSM2136823,,1,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,GEO Accession:GSM2136823,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP074122,,,9267X13_120613_SN141_0510_AC0TF4ACXX_8.txt.gz,fastq,1055273100.0,21105462.0,GSM2136823 r1,0:50,A:284702255;C:246805964;G:238397873;T:285323357;N:43651,50,,,,284702255,246805964,238397873,285323357,43651,SRX1735457,SRS1416511,SRA421168,GEO,"Oncological Sciences, University of Utah",1,0.92157,,0.09143,,0.73494,,0.47743,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-28,Undetermined,Undetermined,Multi-tissue,Multi-system
40949,SRR3465554,SRX1735456,SRS1416509,SRP074122,PRJNA319956,Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.,GSE80768,Transcriptome Analysis,Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.,,pubmed:27783941,,9267X12 tumor,GSM2136822,,source name:brain tumor|tissue:brain tumor,9267X12 tumor,USeq’s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values,brain tumor,Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.,tissue:brain tumor,GSM2136822,GSM2136822: 9267X12 tumor; Danio rerio; RNA Seq,GSM2136822,,1,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,GEO Accession:GSM2136822,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP074122,,,9267X12_120613_SN141_0510_AC0TF4ACXX_8.txt.gz,fastq,1235405300.0,24708106.0,GSM2136822 r1,0:50,A:334940379;C:286734309;G:278305987;T:335374199;N:50426,50,,,,334940379,286734309,278305987,335374199,50426,SRX1735456,SRS1416509,SRA421168,GEO,"Oncological Sciences, University of Utah",1,0.91587,,0.10088,,0.68107,,0.48664,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-28,Undetermined,Undetermined,Multi-tissue,Multi-system
40950,SRR3465553,SRX1735455,SRS1416508,SRP074122,PRJNA319956,Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.,GSE80768,Transcriptome Analysis,Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.,,pubmed:27783941,,9267X8 tumor,GSM2136821,,source name:brain tumor|tissue:brain tumor,9267X8 tumor,USeq’s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values,brain tumor,Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.,tissue:brain tumor,GSM2136821,GSM2136821: 9267X8 tumor; Danio rerio; RNA Seq,GSM2136821,,1,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,GEO Accession:GSM2136821,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP074122,,,9267X8_120613_SN141_0510_AC0TF4ACXX_7.txt.gz,fastq,1049619800.0,20992396.0,GSM2136821 r1,0:50,A:284508112;C:243447832;G:236471909;T:285153684;N:38263,50,,,,284508112,243447832,236471909,285153684,38263,SRX1735455,SRS1416508,SRA421168,GEO,"Oncological Sciences, University of Utah",1,0.92111,,0.10635,,0.68061,,0.48665,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-28,Undetermined,Undetermined,Multi-tissue,Multi-system
40951,SRR3465552,SRX1735454,SRS1416507,SRP074122,PRJNA319956,Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.,GSE80768,Transcriptome Analysis,Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.,,pubmed:27783941,,9267X7 tumor,GSM2136820,,source name:brain tumor|tissue:brain tumor,9267X7 tumor,USeq’s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values,brain tumor,Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.,tissue:brain tumor,GSM2136820,GSM2136820: 9267X7 tumor; Danio rerio; RNA Seq,GSM2136820,,1,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,GEO Accession:GSM2136820,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP074122,,,9267X7_120613_SN141_0510_AC0TF4ACXX_7.txt.gz,fastq,1050373350.0,21007467.0,GSM2136820 r1,0:50,A:283795799;C:244445968;G:237807604;T:284286043;N:37936,50,,,,283795799,244445968,237807604,284286043,37936,SRX1735454,SRS1416507,SRA421168,GEO,"Oncological Sciences, University of Utah",1,0.91684,,0.09541,,0.70808,,0.4782,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-28,Undetermined,Undetermined,Multi-tissue,Multi-system
40952,SRR3465551,SRX1735453,SRS1416506,SRP074122,PRJNA319956,Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.,GSE80768,Transcriptome Analysis,Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.,,pubmed:27783941,,9267X6 tumor,GSM2136819,,source name:brain tumor|tissue:brain tumor,9267X6 tumor,USeq’s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values,brain tumor,Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.,tissue:brain tumor,GSM2136819,GSM2136819: 9267X6 tumor; Danio rerio; RNA Seq,GSM2136819,,1,Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.,GEO Accession:GSM2136819,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP074122,,,9267X6_120613_SN141_0510_AC0TF4ACXX_7.txt.gz,fastq,909187300.0,18183746.0,GSM2136819 r1,0:50,A:246296969;C:211315305;G:203857359;T:247684298;N:33369,50,,,,246296969,211315305,203857359,247684298,33369,SRX1735453,SRS1416506,SRA421168,GEO,"Oncological Sciences, University of Utah",1,0.92029,,0.11221,,0.68578,,0.47422,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-28,Undetermined,Undetermined,Multi-tissue,Multi-system