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
186,DRR162555,DRX153174,DRS083235,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 39 mpf zebrafish replicate5,SAMD00152503,,sample name:m39 5|age:39 month|biological replicate:5|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152503,DRX153174,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152503,,,,1721110400.0,8605552.0,DRR162555,0:100 1:100,A:449613689;C:409864831;G:412050483;T:447085797;N:2495600,100,100,,,449613689,409864831,412050483,447085797,2495600,DRX153174,DRS083235,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96635,0.94149,0.03182,0.03006,0.81631,0.82449,0.53424,0.53879,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
187,DRR162554,DRX153173,DRS083234,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 39 mpf zebrafish replicate4,SAMD00152502,,sample name:m39 4|age:39 month|biological replicate:4|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152502,DRX153173,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152502,,,,771888600.0,3859443.0,DRR162554,0:100 1:100,A:209886275;C:175458903;G:177995758;T:207451261;N:1096403,100,100,,,209886275,175458903,177995758,207451261,1096403,DRX153173,DRS083234,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.95789,0.92781,0.03714,0.03527,0.80075,0.80917,0.5336,0.53957,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
188,DRR162553,DRX153172,DRS083233,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 39 mpf zebrafish replicate3,SAMD00152501,,sample name:m39 3|age:39 month|biological replicate:3|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152501,DRX153172,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152501,,,,1750331200.0,8751656.0,DRR162553,0:100 1:100,A:470950871;C:402540953;G:405453019;T:468920181;N:2466176,100,100,,,470950871,402540953,405453019,468920181,2466176,DRX153172,DRS083233,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96458,0.93283,0.03644,0.03456,0.82169,0.82858,0.5481,0.54735,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
189,DRR162552,DRX153171,DRS083232,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 39 mpf zebrafish replicate2,SAMD00152500,,sample name:m39 2|age:39 month|biological replicate:2|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152500,DRX153171,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152500,,,,1067838800.0,5339194.0,DRR162552,0:100 1:100,A:298532843;C:233982076;G:237439824;T:296396354;N:1487703,100,100,,,298532843,233982076,237439824,296396354,1487703,DRX153171,DRS083232,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.95828,0.92985,0.04771,0.04523,0.79488,0.80294,0.49034,0.56243,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
190,DRR162551,DRX153170,DRS083231,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 39 mpf zebrafish replicate1,SAMD00152499,,sample name:m39 1|age:39 month|biological replicate:1|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152499,DRX153170,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152499,,,,1067002000.0,5335010.0,DRR162551,0:100 1:100,A:278427675;C:254036661;G:255175092;T:277557906;N:1804666,100,100,,,278427675,254036661,255175092,277557906,1804666,DRX153170,DRS083231,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.95438,0.92802,0.05748,0.05502,0.79192,0.79819,0.52464,0.52682,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
191,DRR162550,DRX153169,DRS083230,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 16 mpf zebrafish replicate5,SAMD00152498,,sample name:m16 5|age:16 month|biological replicate:5|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152498,DRX153169,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152498,,,,930106600.0,4650533.0,DRR162550,0:100 1:100,A:242979975;C:221639069;G:223234689;T:240720049;N:1532818,100,100,,,242979975,221639069,223234689,240720049,1532818,DRX153169,DRS083230,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96995,0.94193,0.02755,0.02642,0.84816,0.85549,0.57425,0.52005,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
192,DRR162549,DRX153168,DRS083229,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 16 mpf zebrafish replicate4,SAMD00152497,,sample name:m16 4|age:16 month|biological replicate:4|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152497,DRX153168,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152497,,,,785247000.0,3926235.0,DRR162549,0:100 1:100,A:201565472;C:190838604;G:191695270;T:199849282;N:1298372,100,100,,,201565472,190838604,191695270,199849282,1298372,DRX153168,DRS083229,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96925,0.95032,0.02522,0.02431,0.83528,0.84135,0.45946,0.52823,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
193,DRR162548,DRX153167,DRS083228,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 16 mpf zebrafish replicate3,SAMD00152496,,sample name:m16 3|age:16 month|biological replicate:3|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152496,DRX153167,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152496,,,,712659400.0,3563297.0,DRR162548,0:100 1:100,A:184163345;C:171746662;G:173153688;T:182436940;N:1158765,100,100,,,184163345,171746662,173153688,182436940,1158765,DRX153167,DRS083228,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.97092,0.94516,0.02464,0.02354,0.82925,0.83721,0.55084,0.55847,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
194,DRR162547,DRX153166,DRS083227,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 16 mpf zebrafish replicate2,SAMD00152495,,sample name:m16 2|age:16 month|biological replicate:2|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152495,DRX153166,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152495,,,,795706600.0,3978533.0,DRR162547,0:100 1:100,A:205087113;C:192675977;G:193703665;T:203054171;N:1185674,100,100,,,205087113,192675977,193703665,203054171,1185674,DRX153166,DRS083227,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.9693,0.94476,0.03018,0.02924,0.81615,0.82564,0.52874,0.52813,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
195,DRR162546,DRX153165,DRS083226,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 16 mpf zebrafish replicate1,SAMD00152494,,sample name:m16 1|age:16 month|biological replicate:1|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152494,DRX153165,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152494,,,,851036600.0,4255183.0,DRR162546,0:100 1:100,A:224583615;C:200474581;G:201849331;T:222664124;N:1464949,100,100,,,224583615,200474581,201849331,222664124,1464949,DRX153165,DRS083226,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96969,0.95023,0.02693,0.02563,0.84567,0.85218,0.58468,0.58831,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
196,DRR162545,DRX153164,DRS083225,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 7 mpf zebrafish replicate5,SAMD00152493,,sample name:m07 5|age:7 month|biological replicate:5|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152493,DRX153164,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152493,,,,1024543600.0,5122718.0,DRR162545,0:100 1:100,A:255646947;C:257072899;G:256778094;T:253384531;N:1661129,100,100,,,255646947,257072899,256778094,253384531,1661129,DRX153164,DRS083225,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.97634,0.95731,0.01486,0.01517,0.87592,0.89252,0.50702,0.50609,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
197,DRR162544,DRX153163,DRS083224,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 7 mpf zebrafish replicate4,SAMD00152492,,sample name:m07 4|age:7 month|biological replicate:4|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152492,DRX153163,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152492,,,,1039809600.0,5199048.0,DRR162544,0:100 1:100,A:260916983;C:258869102;G:260873844;T:257458225;N:1691446,100,100,,,260916983,258869102,260873844,257458225,1691446,DRX153163,DRS083224,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.97612,0.94137,0.01751,0.01634,0.85527,0.86367,0.50786,0.50679,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
198,DRR162543,DRX153162,DRS083223,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 7 mpf zebrafish replicate3,SAMD00152491,,sample name:m07 3|age:7 month|biological replicate:3|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152491,DRX153162,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152491,,,,1081187000.0,5405935.0,DRR162543,0:100 1:100,A:272702030;C:267625388;G:270437426;T:268730517;N:1691639,100,100,,,272702030,267625388,270437426,268730517,1691639,DRX153162,DRS083223,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.97471,0.93399,0.02247,0.02056,0.86876,0.87519,0.54092,0.53031,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
199,DRR162542,DRX153161,DRS083222,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 7 mpf zebrafish replicate2,SAMD00152490,,sample name:m07 2|age:7 month|biological replicate:2|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152490,DRX153161,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152490,,,,1375265200.0,6876326.0,DRR162542,0:100 1:100,A:352606827;C:334370724;G:335176090;T:350910646;N:2200913,100,100,,,352606827,334370724,335176090,350910646,2200913,DRX153161,DRS083222,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96089,0.92859,0.02237,0.02125,0.76824,0.7777,0.51352,0.51124,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
200,DRR162541,DRX153160,DRS083221,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 7 mpf zebrafish replicate1,SAMD00152489,,sample name:m07 1|age:7 month|biological replicate:1|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152489,DRX153160,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152489,,,,1331668400.0,6658342.0,DRR162541,0:100 1:100,A:339618846;C:325463872;G:328670370;T:335855545;N:2059767,100,100,,,339618846,325463872,328670370,335855545,2059767,DRX153160,DRS083221,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.9743,0.93669,0.02259,0.02116,0.84676,0.85476,0.54434,0.53825,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Muscle,Muscular System
201,DRR162540,DRX153159,DRS083220,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 2 mpf zebrafish replicate5,SAMD00152488,,sample name:m02 5|age:2 month|biological replicate:5|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152488,DRX153159,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152488,,,,1063436200.0,5317181.0,DRR162540,0:100 1:100,A:275438061;C:255805442;G:257091950;T:273487067;N:1613680,100,100,,,275438061,255805442,257091950,273487067,1613680,DRX153159,DRS083220,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96295,0.92896,0.04409,0.0427,0.75355,0.76499,0.49339,0.50418,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System
202,DRR162539,DRX153158,DRS083219,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 2 mpf zebrafish replicate4,SAMD00152487,,sample name:m02 4|age:2 month|biological replicate:4|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152487,DRX153158,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152487,,,,1233640200.0,6168201.0,DRR162539,0:100 1:100,A:318959646;C:297211942;G:300002324;T:315647570;N:1818718,100,100,,,318959646,297211942,300002324,315647570,1818718,DRX153158,DRS083219,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96511,0.92512,0.04175,0.04058,0.77607,0.78835,0.48689,0.50535,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System
203,DRR162538,DRX153157,DRS083218,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 2 mpf zebrafish replicate3,SAMD00152486,,sample name:m02 3|age:2 month|biological replicate:3|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152486,DRX153157,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152486,,,,675957200.0,3379786.0,DRR162538,0:100 1:100,A:173033870;C:164578076;G:165481544;T:171780353;N:1083357,100,100,,,173033870,164578076,165481544,171780353,1083357,DRX153157,DRS083218,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.97251,0.94405,0.03347,0.03256,0.82432,0.83159,0.55228,0.47905,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System
204,DRR162537,DRX153156,DRS083217,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 2 mpf zebrafish replicate2,SAMD00152485,,sample name:m02 2|age:2 month|biological replicate:2|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152485,DRX153156,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152485,,,,1260768000.0,6303840.0,DRR162537,0:100 1:100,A:319433176;C:310903964;G:312279388;T:316219239;N:1932233,100,100,,,319433176,310903964,312279388,316219239,1932233,DRX153156,DRS083217,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96774,0.93275,0.04099,0.04003,0.76919,0.79626,0.51687,0.50638,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System
205,DRR162536,DRX153155,DRS083216,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,muscle sample from 2 mpf zebrafish replicate1,SAMD00152484,,sample name:m02 1|age:2 month|biological replicate:1|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152484,DRX153155,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152484,,,,1318898400.0,6594492.0,DRR162536,0:100 1:100,A:337402722;C:321381897;G:323422706;T:334658718;N:2032357,100,100,,,337402722,321381897,323422706,334658718,2032357,DRX153155,DRS083216,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.9692,0.93768,0.02944,0.02852,0.79431,0.80359,0.50636,0.51065,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System
10000,ERR6806877,ERX6430470,ERS5060067,ERP123913,PRJEB40292,Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers,ena-STUDY-I3S-10-09-2020-08:12:35:299-4,Other,The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA  suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However  the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges  including lack of sequence conservation. In this work  we performed a combined analysis of ATAC seq  ChIP seq  4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements  regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas  we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences  we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis  demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall  we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements  contributing to the prediction of new disease causative enhancers and their role in human disease.,ChIP seq  ATAC seq  HiChIP seq  4C seq  RNA seq|chromatin accessibility|cis regulatory mutations|pancreas and pancreatic diseases|transcriptional enhancers|ENA FIRST PUBLIC:2020 09 11|ENA LAST UPDATE:2021 09 22,,Adult zebrafish muscle RNA seq replicate2 raw reads,Zebrafish Muscle RNA seq replicate2,SAMEA7301508,I3S,ENA first public:2021 09 23|ENA last update:2021 09 23|External Id:SAMEA7301508|INSDC center alias:I3S|INSDC center name:I3S|INSDC first public:2021 09 23T20:37:00Z|INSDC last update:2021 09 23T20:37:00Z|INSDC status:public|Submitter Id:Zebrafish Muscle RNA seq replicate2|common name:zebrafish|sample name:Zebrafish Muscle RNA seq replicate2|tissue type:muscle,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT I3S 23 09 2021 16:43:09:330 8,Muscle2,1,Total RNA extracted with TRIZOL from zebrafish muscle and preprared for sequencing with the TruSeq kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP123913,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2021 09 23|ENA LAST UPDATE:2021 09 23,Muscle_Old_1.fastq.gz,fastq,1886870950.0,37737419.0,ena RUN I3S 23 09 2021 16:43:09:330 8,0:50 1:0,A:479832533;C:470338808;G:443061655;T:493513324;N:124630,50,0,,,479832533,470338808,443061655,493513324,124630,ERX6430470,ERS5060067,ERA6385885,I3S|European Nucleotide Archive,I3S,1,0.95119,,0.04224,,0.79251,,0.52332,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Portugal,2020-09-11,Adult,Adult,Muscle,Muscular System
10001,ERR6806876,ERX6430469,ERS5060066,ERP123913,PRJEB40292,Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers,ena-STUDY-I3S-10-09-2020-08:12:35:299-4,Other,The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA  suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However  the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges  including lack of sequence conservation. In this work  we performed a combined analysis of ATAC seq  ChIP seq  4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements  regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas  we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences  we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis  demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall  we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements  contributing to the prediction of new disease causative enhancers and their role in human disease.,ChIP seq  ATAC seq  HiChIP seq  4C seq  RNA seq|chromatin accessibility|cis regulatory mutations|pancreas and pancreatic diseases|transcriptional enhancers|ENA FIRST PUBLIC:2020 09 11|ENA LAST UPDATE:2021 09 22,,Adult zebrafish muscle RNA seq replicate1 raw reads,Zebrafish Muscle RNA seq replicate1,SAMEA7301507,I3S,ENA first public:2021 09 23|ENA last update:2021 09 23|External Id:SAMEA7301507|INSDC center alias:I3S|INSDC center name:I3S|INSDC first public:2021 09 23T20:37:00Z|INSDC last update:2021 09 23T20:37:00Z|INSDC status:public|Submitter Id:Zebrafish Muscle RNA seq replicate1|common name:zebrafish|sample name:Zebrafish Muscle RNA seq replicate1|tissue type:muscle,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT I3S 23 09 2021 16:43:09:330 7,Muscle1,1,Total RNA extracted with TRIZOL from zebrafish muscle and preprared for sequencing with the TruSeq kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP123913,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2021 09 23|ENA LAST UPDATE:2021 09 23,Muscle_Young_1.fastq.gz,fastq,1795352850.0,35907057.0,ena RUN I3S 23 09 2021 16:43:09:330 7,0:50 1:0,A:451489686;C:453210606;G:425250111;T:465282474;N:119973,50,0,,,451489686,453210606,425250111,465282474,119973,ERX6430469,ERS5060066,ERA6385885,I3S|European Nucleotide Archive,I3S,1,0.95698,,0.02942,,0.82126,,0.56075,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Portugal,2020-09-11,Adult,Adult,Muscle,Muscular System
25351,SRR25868024,SRX21589429,SRS18767002,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m des EOM group 3,GSM7749535,,source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,20m des EOM group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ,GSM7749535,GSM7749535: 20m des EOM group 3; Danio rerio; RNA Seq,GSM7749535 r1,GSM7749535,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_106_S17_L003_R1_001.fastq.gz P25101_106_S17_L003_R2_001.fastq.gz,fastq fastq,20778069912.0,68801556.0,GSM7749535 r1,0:151 1:151,A:5758676496;C:4631979297;G:4821571380;T:5565739517;N:103222,151,151,,,5758676496,4631979297,4821571380,5565739517,103222,SRX21589429,SRS18767002,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.9548,0.94562,0.05971,0.06026,0.75939,0.764,0.52511,0.52644,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25352,SRR25868025,SRX21589428,SRS18767001,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m des EOM group 2,GSM7749534,,source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,20m des EOM group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ,GSM7749534,GSM7749534: 20m des EOM group 2; Danio rerio; RNA Seq,GSM7749534 r1,GSM7749534,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_105_S16_L003_R1_001.fastq.gz P25101_105_S16_L003_R2_001.fastq.gz,fastq fastq,24114490412.0,79849306.0,GSM7749534 r1,0:151 1:151,A:6709705839;C:5352296650;G:5629660538;T:6422707312;N:120073,151,151,,,6709705839,5352296650,5629660538,6422707312,120073,SRX21589428,SRS18767001,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95523,0.9459,0.05709,0.05736,0.76047,0.76392,0.53211,0.53919,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25353,SRR25868026,SRX21589427,SRS18767000,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m des EOM group 1,GSM7749533,,source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,20m des EOM group 1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ,GSM7749533,GSM7749533: 20m des EOM group 1; Danio rerio; RNA Seq,GSM7749533 r1,GSM7749533,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_104_S15_L003_R1_001.fastq.gz P25101_104_S15_L003_R2_001.fastq.gz,fastq fastq,25533595358.0,84548329.0,GSM7749533 r1,0:151 1:151,A:7048075605;C:5727768890;G:5996832455;T:6760791489;N:126919,151,151,,,7048075605,5727768890,5996832455,6760791489,126919,SRX21589427,SRS18767000,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95578,0.94764,0.05575,0.05642,0.76449,0.76656,0.49924,0.52213,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25354,SRR25868027,SRX21589426,SRS18766999,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m wt EOM group 3,GSM7749532,,source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing,20m wt EOM group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT,GSM7749532,GSM7749532: 20m wt EOM group 3; Danio rerio; RNA Seq,GSM7749532 r1,GSM7749532,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_103_S14_L003_R1_001.fastq.gz P25101_103_S14_L003_R2_001.fastq.gz,fastq fastq,20926207254.0,69292077.0,GSM7749532 r1,0:151 1:151,A:5774697444;C:4697440497;G:4906711794;T:5547254173;N:103346,151,151,,,5774697444,4697440497,4906711794,5547254173,103346,SRX21589426,SRS18766999,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95486,0.94747,0.05329,0.05381,0.76457,0.76725,0.53365,0.54294,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25355,SRR25868028,SRX21589425,SRS18766998,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m wt EOM group 2,GSM7749531,,source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing,20m wt EOM group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT,GSM7749531,GSM7749531: 20m wt EOM group 2; Danio rerio; RNA Seq,GSM7749531 r1,GSM7749531,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_102_S13_L003_R2_001.fastq.gz P25101_102_S13_L003_R1_001.fastq.gz,fastq fastq,28078830218.0,92976259.0,GSM7749531 r1,0:151 1:151,A:7806960381;C:6272379496;G:6608688265;T:7390663010;N:139066,151,151,,,7806960381,6272379496,6608688265,7390663010,139066,SRX21589425,SRS18766998,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95324,0.94585,0.05086,0.05134,0.77315,0.77739,0.52072,0.52824,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25356,SRR25868029,SRX21589424,SRS18766997,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m wt EOM group 1,GSM7749530,,source name:20 mpf extraocular muscle|age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing,20m wt EOM group 1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:extraocular muscle|strain:AB|cell type:extraocular myofibers|genotype:WT,GSM7749530,GSM7749530: 20m wt EOM group 1; Danio rerio; RNA Seq,GSM7749530 r1,GSM7749530,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_101_S12_L003_R1_001.fastq.gz P25101_101_S12_L003_R2_001.fastq.gz,fastq fastq,20239673372.0,67018786.0,GSM7749530 r1,0:151 1:151,A:5648333279;C:4484295706;G:4758753699;T:5348189630;N:101058,151,151,,,5648333279,4484295706,4758753699,5348189630,101058,SRX21589424,SRS18766997,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95478,0.94612,0.05456,0.05574,0.76098,0.76668,0.50391,0.54818,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25363,SRR25868065,SRX21589470,SRS18767043,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,des EOM group 3,GSM7749563,,source name:extraocular muscle|tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,des EOM group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ,GSM7749563,GSM7749563: des EOM group 3; Danio rerio; RNA Seq,GSM7749563 r1,GSM7749563,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_106_S10_L001_R1_001.fastq.gz P17251_106_S10_L001_R2_001.fastq.gz,fastq fastq,30795037848.0,101970324.0,GSM7749563 r1,0:151 1:151,A:8369479918;C:7035512003;G:7341959696;T:8047708763;N:377468,151,151,,,8369479918,7035512003,7341959696,8047708763,377468,SRX21589470,SRS18767043,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.95744,0.94806,0.06123,0.06213,0.75911,0.76382,0.53005,0.53206,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25364,SRR25868066,SRX21589469,SRS18767042,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,des EOM group 2,GSM7749562,,source name:extraocular muscle|tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,des EOM group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ,GSM7749562,GSM7749562: des EOM group 2; Danio rerio; RNA Seq,GSM7749562 r1,GSM7749562,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_105_S9_L001_R1_001.fastq.gz P17251_105_S9_L001_R2_001.fastq.gz,fastq fastq,24388992708.0,80758254.0,GSM7749562 r1,0:151 1:151,A:6579219632;C:5651892239;G:6170251564;T:5987329579;N:299694,151,151,,,6579219632,5651892239,6170251564,5987329579,299694,SRX21589469,SRS18767042,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.96142,0.94783,0.02509,0.02601,0.81036,0.81913,0.52284,0.51505,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25365,SRR25868067,SRX21589468,SRS18767041,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,des EOM group 1,GSM7749561,,source name:extraocular muscle|tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,des EOM group 1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:desma / ;desmb / ,GSM7749561,GSM7749561: des EOM group 1; Danio rerio; RNA Seq,GSM7749561 r1,GSM7749561,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_104_S8_L001_R1_001.fastq.gz P17251_104_S8_L001_R2_001.fastq.gz,fastq fastq,29806211630.0,98696065.0,GSM7749561 r1,0:151 1:151,A:8054341813;C:6852446548;G:7265656917;T:7633398634;N:367718,151,151,,,8054341813,6852446548,7265656917,7633398634,367718,SRX21589468,SRS18767041,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.96453,0.95482,0.03012,0.03029,0.81387,0.8172,0.58568,0.59213,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25366,SRR25868068,SRX21589467,SRS18767040,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,wt EOM group 3,GSM7749560,,source name:extraocular muscle|tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing,wt EOM group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:WT,GSM7749560,GSM7749560: wt EOM group 3; Danio rerio; RNA Seq,GSM7749560 r1,GSM7749560,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_103_S7_L001_R1_001.fastq.gz P17251_103_S7_L001_R2_001.fastq.gz,fastq fastq,26137673878.0,86548589.0,GSM7749560 r1,0:151 1:151,A:7187162255;C:5876920613;G:6131493954;T:6941780771;N:316285,151,151,,,7187162255,5876920613,6131493954,6941780771,316285,SRX21589467,SRS18767040,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.95152,0.94053,0.05757,0.05838,0.76039,0.76617,0.53014,0.53234,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25367,SRR25868069,SRX21589466,SRS18767039,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,wt EOM group 2,GSM7749559,,source name:extraocular muscle|tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing,wt EOM group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:WT,GSM7749559,GSM7749559: wt EOM group 2; Danio rerio; RNA Seq,GSM7749559 r1,GSM7749559,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_102_S6_L001_R1_001.fastq.gz P17251_102_S6_L001_R2_001.fastq.gz,fastq fastq,34491293764.0,114209582.0,GSM7749559 r1,0:151 1:151,A:8992817747;C:8219342517;G:8708492755;T:8570219055;N:421690,151,151,,,8992817747,8219342517,8708492755,8570219055,421690,SRX21589466,SRS18767039,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.9625,0.95296,0.02853,0.02942,0.78871,0.79198,0.52313,0.52622,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
25368,SRR25868070,SRX21589465,SRS18767038,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,wt EOM group 1,GSM7749558,,source name:extraocular muscle|tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:WT|geo loc name:missing|collection date:missing,wt EOM group 1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,extraocular muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:extraocular muscle|age:5 mpf|strain:AB|cell type:extraocular myofibers|genotype:WT,GSM7749558,GSM7749558: wt EOM group 1; Danio rerio; RNA Seq,GSM7749558 r1,GSM7749558,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_101_S5_L001_R1_001.fastq.gz P17251_101_S5_L001_R2_001.fastq.gz,fastq fastq,30105044858.0,99685579.0,GSM7749558 r1,0:151 1:151,A:7737199705;C:7317149958;G:7543227439;T:7507099789;N:367967,151,151,,,7737199705,7317149958,7543227439,7507099789,367967,SRX21589465,SRS18767038,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.96635,0.95927,0.02631,0.02749,0.80659,0.81203,0.5009,0.49931,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Muscle,Muscular System
26375,SRR25897903,SRX21618264,SRS18790609,SRP458313,PRJNA1012699,Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish,GSE242251,Transcriptome Analysis,LMNA mutations cause laminopathies  a group of rare genetic diseases with no known cure  only symptomatic treatment and supportive care. In this study  we characterized five LMNA mutations LMNAL35P  LMNAA539V  LMNAW520G  LMNAE358K  and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior  muscle endurance  and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.,,pubmed:38834813,,RNA seq  LMNA R453W 3,GSM7757086,,source name:muscle|tissue:muscle|genotype:LMNA R453W|treatment:N1|geo loc name:missing|collection date:missing,RNA seq  LMNA R453W 3,Raw data qulity contol by fastQC Trimmomatic  those that meet the following conditions will be deleted: 1 Base quality <3 from either 3’ or 5’ end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample,muscle,,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC  which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 °C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.,tissue:muscle|genotype:LMNA R453W|treatment:N1,GSM7757086,GSM7757086: RNA seq  LMNA R453W 3; Danio rerio; RNA Seq,GSM7757086 r1,GSM7757086,1,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP458313,,loader:fastq load.py,T9M_R_3_2_paired.fq T9M_R_3_1_paired.fq,fastq fastq,4869616993.0,16355391.0,GSM7757086 r1,0:148.93 1:148.81,A:1252653780;C:1163645903;G:1169939131;T:1283327663;N:50516,148,148,,,1252653780,1163645903,1169939131,1283327663,50516,SRX21618264,SRS18790609,SRA1704662,"Institute of Molecular and Genomic Medicine, National Health Research Institutes","Institute of Molecular and Genomic Medicine, National Health Research Institutes",2,0.91878,0.92144,0.02287,0.02202,0.7457,0.74499,0.47719,0.47439,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2023-09-04,Adult,Adult,Muscle,Muscular System
26376,SRR25897904,SRX21618263,SRS18790608,SRP458313,PRJNA1012699,Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish,GSE242251,Transcriptome Analysis,LMNA mutations cause laminopathies  a group of rare genetic diseases with no known cure  only symptomatic treatment and supportive care. In this study  we characterized five LMNA mutations LMNAL35P  LMNAA539V  LMNAW520G  LMNAE358K  and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior  muscle endurance  and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.,,pubmed:38834813,,RNA seq  LMNA R453W 2,GSM7757085,,source name:muscle|tissue:muscle|genotype:LMNA R453W|treatment:N1|geo loc name:missing|collection date:missing,RNA seq  LMNA R453W 2,Raw data qulity contol by fastQC Trimmomatic  those that meet the following conditions will be deleted: 1 Base quality <3 from either 3’ or 5’ end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample,muscle,,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC  which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 °C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.,tissue:muscle|genotype:LMNA R453W|treatment:N1,GSM7757085,GSM7757085: RNA seq  LMNA R453W 2; Danio rerio; RNA Seq,GSM7757085 r1,GSM7757085,1,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP458313,,loader:fastq load.py,T9M_R_2_1_paired.fq T9M_R_2_2_paired.fq,fastq fastq,5609014914.0,18915448.0,GSM7757085 r1,0:148.41 1:148.12,A:1288527357;C:1501761141;G:1493621898;T:1325044624;N:59894,148,148,,,1288527357,1501761141,1493621898,1325044624,59894,SRX21618263,SRS18790608,SRA1704662,"Institute of Molecular and Genomic Medicine, National Health Research Institutes","Institute of Molecular and Genomic Medicine, National Health Research Institutes",2,0.95814,0.96074,0.11463,0.11555,0.77713,0.7767,0.62814,0.63117,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2023-09-04,Adult,Adult,Muscle,Muscular System
26377,SRR25897905,SRX21618262,SRS18790607,SRP458313,PRJNA1012699,Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish,GSE242251,Transcriptome Analysis,LMNA mutations cause laminopathies  a group of rare genetic diseases with no known cure  only symptomatic treatment and supportive care. In this study  we characterized five LMNA mutations LMNAL35P  LMNAA539V  LMNAW520G  LMNAE358K  and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior  muscle endurance  and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.,,pubmed:38834813,,RNA seq  LMNA L35P 3,GSM7757084,,source name:muscle|tissue:muscle|genotype:LMNA L35P|treatment:N1|geo loc name:missing|collection date:missing,RNA seq  LMNA L35P 3,Raw data qulity contol by fastQC Trimmomatic  those that meet the following conditions will be deleted: 1 Base quality <3 from either 3’ or 5’ end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample,muscle,,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC  which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 °C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.,tissue:muscle|genotype:LMNA L35P|treatment:N1,GSM7757084,GSM7757084: RNA seq  LMNA L35P 3; Danio rerio; RNA Seq,GSM7757084 r1,GSM7757084,1,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP458313,,loader:fastq load.py,T9M_L_3_1_paired.fq T9M_L_3_2_paired.fq,fastq fastq,4769512473.0,16048426.0,GSM7757084 r1,0:148.44 1:148.76,A:1232520200;C:1137981187;G:1146811734;T:1252148485;N:50867,148,148,,,1232520200,1137981187,1146811734,1252148485,50867,SRX21618262,SRS18790607,SRA1704662,"Institute of Molecular and Genomic Medicine, National Health Research Institutes","Institute of Molecular and Genomic Medicine, National Health Research Institutes",2,0.95126,0.95371,0.04556,0.04517,0.75205,0.75083,0.49205,0.49278,54,112,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2023-09-04,Adult,Adult,Muscle,Muscular System
26378,SRR25897906,SRX21618261,SRS18790606,SRP458313,PRJNA1012699,Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish,GSE242251,Transcriptome Analysis,LMNA mutations cause laminopathies  a group of rare genetic diseases with no known cure  only symptomatic treatment and supportive care. In this study  we characterized five LMNA mutations LMNAL35P  LMNAA539V  LMNAW520G  LMNAE358K  and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior  muscle endurance  and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.,,pubmed:38834813,,RNA seq  LMNA L35P 2,GSM7757083,,source name:muscle|tissue:muscle|genotype:LMNA L35P|treatment:N1|geo loc name:missing|collection date:missing,RNA seq  LMNA L35P 2,Raw data qulity contol by fastQC Trimmomatic  those that meet the following conditions will be deleted: 1 Base quality <3 from either 3’ or 5’ end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample,muscle,,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC  which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 °C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.,tissue:muscle|genotype:LMNA L35P|treatment:N1,GSM7757083,GSM7757083: RNA seq  LMNA L35P 2; Danio rerio; RNA Seq,GSM7757083 r1,GSM7757083,1,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP458313,,loader:fastq load.py,T9M_L_2_1_paired.fq T9M_L_2_2_paired.fq,fastq fastq,3918432824.0,13209622.0,GSM7757083 r1,0:148.33 1:148.31,A:1055586946;C:892801402;G:895757042;T:1074245534;N:41900,148,148,,,1055586946,892801402,895757042,1074245534,41900,SRX21618261,SRS18790606,SRA1704662,"Institute of Molecular and Genomic Medicine, National Health Research Institutes","Institute of Molecular and Genomic Medicine, National Health Research Institutes",2,0.93802,0.93862,0.13654,0.13491,0.70609,0.70483,0.50253,0.50539,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2023-09-04,Adult,Adult,Muscle,Muscular System
26379,SRR25897907,SRX21618260,SRS18790604,SRP458313,PRJNA1012699,Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish,GSE242251,Transcriptome Analysis,LMNA mutations cause laminopathies  a group of rare genetic diseases with no known cure  only symptomatic treatment and supportive care. In this study  we characterized five LMNA mutations LMNAL35P  LMNAA539V  LMNAW520G  LMNAE358K  and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior  muscle endurance  and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.,,pubmed:38834813,,RNA seq  LMNA E358K 3,GSM7757082,,source name:muscle|tissue:muscle|genotype:LMNA E358K|treatment:N1|geo loc name:missing|collection date:missing,RNA seq  LMNA E358K 3,Raw data qulity contol by fastQC Trimmomatic  those that meet the following conditions will be deleted: 1 Base quality <3 from either 3’ or 5’ end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample,muscle,,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC  which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 °C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.,tissue:muscle|genotype:LMNA E358K|treatment:N1,GSM7757082,GSM7757082: RNA seq  LMNA E358K 3; Danio rerio; RNA Seq,GSM7757082 r1,GSM7757082,1,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP458313,,loader:fastq load.py,T9M_E_3_1_paired.fq T9M_E_3_2_paired.fq,fastq fastq,2965977779.0,9986265.0,GSM7757082 r1,0:148.42 1:148.59,A:778091521;C:696132224;G:696171619;T:795550067;N:32348,148,148,,,778091521,696132224,696171619,795550067,32348,SRX21618260,SRS18790604,SRA1704662,"Institute of Molecular and Genomic Medicine, National Health Research Institutes","Institute of Molecular and Genomic Medicine, National Health Research Institutes",2,0.93505,0.94207,0.03691,0.03615,0.76165,0.76067,0.52238,0.51874,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2023-09-04,Adult,Adult,Muscle,Muscular System
26380,SRR25897908,SRX21618259,SRS18790605,SRP458313,PRJNA1012699,Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish,GSE242251,Transcriptome Analysis,LMNA mutations cause laminopathies  a group of rare genetic diseases with no known cure  only symptomatic treatment and supportive care. In this study  we characterized five LMNA mutations LMNAL35P  LMNAA539V  LMNAW520G  LMNAE358K  and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior  muscle endurance  and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.,,pubmed:38834813,,RNA seq  LMNA A539V 3,GSM7757081,,source name:muscle|tissue:muscle|genotype:LMNA A539V|treatment:N1|geo loc name:missing|collection date:missing,RNA seq  LMNA A539V 3,Raw data qulity contol by fastQC Trimmomatic  those that meet the following conditions will be deleted: 1 Base quality <3 from either 3’ or 5’ end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample,muscle,,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC  which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 °C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.,tissue:muscle|genotype:LMNA A539V|treatment:N1,GSM7757081,GSM7757081: RNA seq  LMNA A539V 3; Danio rerio; RNA Seq,GSM7757081 r1,GSM7757081,1,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP458313,,loader:fastq load.py,T9M_A_3_1_paired.fq T9M_A_3_2_paired.fq,fastq fastq,6072897265.0,20397882.0,GSM7757081 r1,0:148.52 1:149.20,A:1542358988;C:1476134606;G:1476481844;T:1577859108;N:62719,148,149,,,1542358988,1476134606,1476481844,1577859108,62719,SRX21618259,SRS18790605,SRA1704662,"Institute of Molecular and Genomic Medicine, National Health Research Institutes","Institute of Molecular and Genomic Medicine, National Health Research Institutes",2,0.94916,0.95378,0.03578,0.03486,0.75868,0.75836,0.51302,0.51448,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2023-09-04,Adult,Adult,Muscle,Muscular System
26381,SRR25897909,SRX21618258,SRS18790603,SRP458313,PRJNA1012699,Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish,GSE242251,Transcriptome Analysis,LMNA mutations cause laminopathies  a group of rare genetic diseases with no known cure  only symptomatic treatment and supportive care. In this study  we characterized five LMNA mutations LMNAL35P  LMNAA539V  LMNAW520G  LMNAE358K  and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior  muscle endurance  and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.,,pubmed:38834813,,RNA seq  LMNA A539V 2,GSM7757080,,source name:muscle|tissue:muscle|genotype:LMNA A539V|treatment:N1|geo loc name:missing|collection date:missing,RNA seq  LMNA A539V 2,Raw data qulity contol by fastQC Trimmomatic  those that meet the following conditions will be deleted: 1 Base quality <3 from either 3’ or 5’ end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample,muscle,,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC  which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 °C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.,tissue:muscle|genotype:LMNA A539V|treatment:N1,GSM7757080,GSM7757080: RNA seq  LMNA A539V 2; Danio rerio; RNA Seq,GSM7757080 r1,GSM7757080,1,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP458313,,loader:fastq load.py,T9M_A_2_1_paired.fq T9M_A_2_2_paired.fq,fastq fastq,4391246410.0,14783214.0,GSM7757080 r1,0:148.32 1:148.72,A:1147509995;C:1034378687;G:1036117282;T:1173191690;N:48756,148,148,,,1147509995,1034378687,1036117282,1173191690,48756,SRX21618258,SRS18790603,SRA1704662,"Institute of Molecular and Genomic Medicine, National Health Research Institutes","Institute of Molecular and Genomic Medicine, National Health Research Institutes",2,0.92837,0.93449,0.03905,0.03824,0.76901,0.76869,0.52767,0.51995,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2023-09-04,Adult,Adult,Muscle,Muscular System
26382,SRR25897910,SRX21618257,SRS18790602,SRP458313,PRJNA1012699,Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish,GSE242251,Transcriptome Analysis,LMNA mutations cause laminopathies  a group of rare genetic diseases with no known cure  only symptomatic treatment and supportive care. In this study  we characterized five LMNA mutations LMNAL35P  LMNAA539V  LMNAW520G  LMNAE358K  and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior  muscle endurance  and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.,,pubmed:38834813,,RNA seq  LMNA A539V 1,GSM7757079,,source name:muscle|tissue:muscle|genotype:LMNA A539V|treatment:N1|geo loc name:missing|collection date:missing,RNA seq  LMNA A539V 1,Raw data qulity contol by fastQC Trimmomatic  those that meet the following conditions will be deleted: 1 Base quality <3 from either 3’ or 5’ end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample,muscle,,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC  which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 °C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.,tissue:muscle|genotype:LMNA A539V|treatment:N1,GSM7757079,GSM7757079: RNA seq  LMNA A539V 1; Danio rerio; RNA Seq,GSM7757079 r1,GSM7757079,1,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP458313,,loader:fastq load.py,T9M_A_1_1_paired.fq T9M_A_1_2_paired.fq,fastq fastq,5202925541.0,17505733.0,GSM7757079 r1,0:148.28 1:148.93,A:1362142748;C:1223349314;G:1225245385;T:1392131416;N:56678,148,148,,,1362142748,1223349314,1225245385,1392131416,56678,SRX21618257,SRS18790602,SRA1704662,"Institute of Molecular and Genomic Medicine, National Health Research Institutes","Institute of Molecular and Genomic Medicine, National Health Research Institutes",2,0.933,0.9394,0.02774,0.02708,0.76406,0.76232,0.52042,0.51106,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2023-09-04,Adult,Adult,Muscle,Muscular System
26383,SRR25897911,SRX21618256,SRS18790601,SRP458313,PRJNA1012699,Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish,GSE242251,Transcriptome Analysis,LMNA mutations cause laminopathies  a group of rare genetic diseases with no known cure  only symptomatic treatment and supportive care. In this study  we characterized five LMNA mutations LMNAL35P  LMNAA539V  LMNAW520G  LMNAE358K  and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior  muscle endurance  and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.,,pubmed:38834813,,RNA seq  LMNA WT 3,GSM7757078,,source name:muscle|tissue:muscle|genotype:LMNA WT|treatment:N1|geo loc name:missing|collection date:missing,RNA seq  LMNA WT 3,Raw data qulity contol by fastQC Trimmomatic  those that meet the following conditions will be deleted: 1 Base quality <3 from either 3’ or 5’ end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample,muscle,,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC  which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 °C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.,tissue:muscle|genotype:LMNA WT|treatment:N1,GSM7757078,GSM7757078: RNA seq  LMNA WT 3; Danio rerio; RNA Seq,GSM7757078 r1,GSM7757078,1,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP458313,,loader:fastq load.py,C9M_WT_3_1_paired.fq C9M_WT_3_2_paired.fq,fastq fastq,2628000986.0,8856042.0,GSM7757078 r1,0:148.09 1:148.66,A:662710830;C:644088161;G:643223497;T:677949643;N:28855,148,148,,,662710830,644088161,643223497,677949643,28855,SRX21618256,SRS18790601,SRA1704662,"Institute of Molecular and Genomic Medicine, National Health Research Institutes","Institute of Molecular and Genomic Medicine, National Health Research Institutes",2,0.9176,0.93277,0.04117,0.04045,0.78017,0.7792,0.55638,0.56128,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2023-09-04,Adult,Adult,Muscle,Muscular System
26384,SRR25897912,SRX21618255,SRS18790600,SRP458313,PRJNA1012699,Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish,GSE242251,Transcriptome Analysis,LMNA mutations cause laminopathies  a group of rare genetic diseases with no known cure  only symptomatic treatment and supportive care. In this study  we characterized five LMNA mutations LMNAL35P  LMNAA539V  LMNAW520G  LMNAE358K  and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior  muscle endurance  and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.,,pubmed:38834813,,RNA seq  LMNA WT 2,GSM7757077,,source name:muscle|tissue:muscle|genotype:LMNA WT|treatment:N1|geo loc name:missing|collection date:missing,RNA seq  LMNA WT 2,Raw data qulity contol by fastQC Trimmomatic  those that meet the following conditions will be deleted: 1 Base quality <3 from either 3’ or 5’ end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample,muscle,,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC  which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 °C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.,tissue:muscle|genotype:LMNA WT|treatment:N1,GSM7757077,GSM7757077: RNA seq  LMNA WT 2; Danio rerio; RNA Seq,GSM7757077 r1,GSM7757077,1,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP458313,,loader:fastq load.py,C9M_WT_2_1_paired.fq C9M_WT_2_2_paired.fq,fastq fastq,4059488026.0,13662720.0,GSM7757077 r1,0:148.27 1:148.85,A:1083849299;C:934373691;G:936737794;T:1104483688;N:43554,148,148,,,1083849299,934373691,936737794,1104483688,43554,SRX21618255,SRS18790600,SRA1704662,"Institute of Molecular and Genomic Medicine, National Health Research Institutes","Institute of Molecular and Genomic Medicine, National Health Research Institutes",2,0.90078,0.90963,0.03631,0.03544,0.77195,0.77086,0.5122,0.51745,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2023-09-04,Adult,Adult,Muscle,Muscular System
26385,SRR25897913,SRX21618254,SRS18790599,SRP458313,PRJNA1012699,Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish,GSE242251,Transcriptome Analysis,LMNA mutations cause laminopathies  a group of rare genetic diseases with no known cure  only symptomatic treatment and supportive care. In this study  we characterized five LMNA mutations LMNAL35P  LMNAA539V  LMNAW520G  LMNAE358K  and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior  muscle endurance  and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.,,pubmed:38834813,,RNA seq  LMNA WT 1,GSM7757076,,source name:muscle|tissue:muscle|genotype:LMNA WT|treatment:N1|geo loc name:missing|collection date:missing,RNA seq  LMNA WT 1,Raw data qulity contol by fastQC Trimmomatic  those that meet the following conditions will be deleted: 1 Base quality <3 from either 3’ or 5’ end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample,muscle,,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC  which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 °C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.,tissue:muscle|genotype:LMNA WT|treatment:N1,GSM7757076,GSM7757076: RNA seq  LMNA WT 1; Danio rerio; RNA Seq,GSM7757076 r1,GSM7757076,1,RNA was harvested using NucleoSpin® RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq® Stranded mRNA Library Prep,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP458313,,loader:fastq load.py,C9M_WT_1_1_paired.fq C9M_WT_1_2_paired.fq,fastq fastq,4489983125.0,15074997.0,GSM7757076 r1,0:148.39 1:149.46,A:1155122223;C:1073285000;G:1078875040;T:1182655637;N:45225,148,149,,,1155122223,1073285000,1078875040,1182655637,45225,SRX21618254,SRS18790599,SRA1704662,"Institute of Molecular and Genomic Medicine, National Health Research Institutes","Institute of Molecular and Genomic Medicine, National Health Research Institutes",2,0.91917,0.92221,0.02417,0.02377,0.75126,0.7489,0.48289,0.48398,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2023-09-04,Adult,Adult,Muscle,Muscular System
26511,SRR26050756,SRX21767126,SRS18873431,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 mutants  72hpf  biological replicate 4  cranial mylz2+ cells,GSM7778667,,source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1 / |geo loc name:missing|collection date:missing,psmb1 mutants  72hpf  biological replicate 4  cranial mylz2+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial mylz2+ cells muscle,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial mylz2+ cells muscle|genotype:psmb1 / ,GSM7778667,GSM7778667: psmb1 mutants  72hpf  biological replicate 4  cranial mylz2+ cells; Danio rerio; RNA Seq,GSM7778667 r1,GSM7778667,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP460207,,loader:fastq load.py,mylz2_M4_R2_001.fastq.gz mylz2_M4_R1_001.fastq.gz,fastq fastq,16253832000.0,54179440.0,GSM7778667 r1,0:150 1:150,A:4172321085;C:3956578712;G:3980023180;T:4144541347;N:367676,150,150,,,4172321085,3956578712,3980023180,4144541347,367676,SRX21767126,SRS18873431,SRA1711572,BWH,BWH,2,0.95935,0.95662,0.03769,0.03765,0.76556,0.76741,0.42151,0.41972,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Muscle,Muscular System
26512,SRR26050757,SRX21767125,SRS18873430,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 mutants  72hpf  biological replicate 3  cranial mylz2+ cells,GSM7778666,,source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1 / |geo loc name:missing|collection date:missing,psmb1 mutants  72hpf  biological replicate 3  cranial mylz2+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial mylz2+ cells muscle,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial mylz2+ cells muscle|genotype:psmb1 / ,GSM7778666,GSM7778666: psmb1 mutants  72hpf  biological replicate 3  cranial mylz2+ cells; Danio rerio; RNA Seq,GSM7778666 r1,GSM7778666,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP460207,,loader:fastq load.py,mylz2_M2_R1_001.fastq.gz mylz2_M2_R2_001.fastq.gz,fastq fastq,20441581200.0,68138604.0,GSM7778666 r1,0:150 1:150,A:5286416350;C:4932599128;G:4952935975;T:5269152687;N:477060,150,150,,,5286416350,4932599128,4952935975,5269152687,477060,SRX21767125,SRS18873430,SRA1711572,BWH,BWH,2,0.95599,0.95338,0.04497,0.04514,0.74811,0.74974,0.43348,0.43839,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Muscle,Muscular System
26513,SRR26050758,SRX21767124,SRS18873429,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 mutants  72hpf  biological replicate 1  cranial mylz2+ cells,GSM7778665,,source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1 / |geo loc name:missing|collection date:missing,psmb1 mutants  72hpf  biological replicate 1  cranial mylz2+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial mylz2+ cells muscle,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial mylz2+ cells muscle|genotype:psmb1 / ,GSM7778665,GSM7778665: psmb1 mutants  72hpf  biological replicate 1  cranial mylz2+ cells; Danio rerio; RNA Seq,GSM7778665 r1,GSM7778665,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP460207,,loader:fastq load.py,mylz2_M1_R2_001.fastq.gz mylz2_M1_R1_001.fastq.gz,fastq fastq,16429988100.0,54766627.0,GSM7778665 r1,0:150 1:150,A:4233929382;C:3979539796;G:4000710274;T:4215435332;N:373316,150,150,,,4233929382,3979539796,4000710274,4215435332,373316,SRX21767124,SRS18873429,SRA1711572,BWH,BWH,2,0.95781,0.95546,0.04249,0.04266,0.75359,0.7556,0.42698,0.43387,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Muscle,Muscular System
26514,SRR26050759,SRX21767123,SRS18873428,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 wild type/heterozygous 72hpf  biological replicate 4  cranial mylz2+ cells,GSM7778664,,source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 4  cranial mylz2+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial mylz2+ cells muscle,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ ,GSM7778664,GSM7778664: psmb1 wild type/heterozygous 72hpf  biological replicate 4  cranial mylz2+ cells; Danio rerio; RNA Seq,GSM7778664 r1,GSM7778664,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP460207,,loader:fastq load.py,mylz2_WH4_R1_001.fastq.gz mylz2_WH4_R2_001.fastq.gz,fastq fastq,14554941600.0,48516472.0,GSM7778664 r1,0:150 1:150,A:3762464429;C:3514503319;G:3535806865;T:3741838861;N:328126,150,150,,,3762464429,3514503319,3535806865,3741838861,328126,SRX21767123,SRS18873428,SRA1711572,BWH,BWH,2,0.96121,0.95881,0.04249,0.04242,0.77745,0.77999,0.43011,0.42743,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Muscle,Muscular System
26515,SRR26050760,SRX21767122,SRS18873427,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 wild type/heterozygous 72hpf  biological replicate 3  cranial mylz2+ cells,GSM7778663,,source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 3  cranial mylz2+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial mylz2+ cells muscle,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ ,GSM7778663,GSM7778663: psmb1 wild type/heterozygous 72hpf  biological replicate 3  cranial mylz2+ cells; Danio rerio; RNA Seq,GSM7778663 r1,GSM7778663,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP460207,,loader:fastq load.py,mylz2_WH3_R1_001.fastq.gz mylz2_WH3_R2_001.fastq.gz,fastq fastq,14286753900.0,47622513.0,GSM7778663 r1,0:150 1:150,A:3670719741;C:3471994517;G:3491814119;T:3651899112;N:326411,150,150,,,3670719741,3471994517,3491814119,3651899112,326411,SRX21767122,SRS18873427,SRA1711572,BWH,BWH,2,0.96159,0.96038,0.03967,0.04054,0.7749,0.77644,0.43006,0.42107,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Muscle,Muscular System
26516,SRR26050761,SRX21767121,SRS18873426,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 wild type/heterozygous 72hpf  biological replicate 2  cranial mylz2+ cells,GSM7778662,,source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 2  cranial mylz2+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial mylz2+ cells muscle,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ ,GSM7778662,GSM7778662: psmb1 wild type/heterozygous 72hpf  biological replicate 2  cranial mylz2+ cells; Danio rerio; RNA Seq,GSM7778662 r1,GSM7778662,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP460207,,loader:fastq load.py,mylz2_WH2_R1_001.fastq.gz mylz2_WH2_R2_001.fastq.gz,fastq fastq,13505114700.0,45017049.0,GSM7778662 r1,0:150 1:150,A:3494078647;C:3258926987;G:3282303631;T:3469494662;N:310773,150,150,,,3494078647,3258926987,3282303631,3469494662,310773,SRX21767121,SRS18873426,SRA1711572,BWH,BWH,2,0.95944,0.95769,0.04602,0.04619,0.78557,0.78748,0.43504,0.43352,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Muscle,Muscular System
26517,SRR26050762,SRX21767120,SRS18873425,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 wild type/heterozygous 72hpf  biological replicate 1  cranial mylz2+ cells,GSM7778661,,source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 1  cranial mylz2+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial mylz2+ cells muscle,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ ,GSM7778661,GSM7778661: psmb1 wild type/heterozygous 72hpf  biological replicate 1  cranial mylz2+ cells; Danio rerio; RNA Seq,GSM7778661 r1,GSM7778661,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP460207,,loader:fastq load.py,mylz2_WH1_R1_001.fastq.gz mylz2_WH1_R2_001.fastq.gz,fastq fastq,14988184200.0,49960614.0,GSM7778661 r1,0:150 1:150,A:3819900785;C:3673988527;G:3696333011;T:3797617860;N:344017,150,150,,,3819900785,3673988527,3696333011,3797617860,344017,SRX21767120,SRS18873425,SRA1711572,BWH,BWH,2,0.96471,0.96183,0.03703,0.03679,0.77167,0.7749,0.43436,0.43348,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Muscle,Muscular System
29641,SRR27397714,SRX23073965,SRS20033317,SRP480899,PRJNA1060279,EPIFISH,PRJNA1060279,Other,Epigenetic changes in fish during domestication,,,,RRBS library10,PG2,,strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 10|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of danio rerio,RRBS10,RRBS10,Library preparation kit used  Zymo Seq RRBS Library Kit,,,Bisulfite-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP480899,,,PG2_L7_1.fq.gz PG2_L7_2.fq.gz,fastq fastq,981695400.0,3272318.0,PG2 L7 1.fq.gz,0:150 1:150,A:253124715;C:152724975;G:341105704;T:234698202;N:41804,150,150,,,253124715,152724975,341105704,234698202,41804,SRX23073965,SRS20033317,SRA1777947,Nord University|Bioscience and Aquaculture,Nord University,2,0.0164,0.00047,0.01505,0.00036,0.9961,0.99965,0.58102,0.47058,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Norway,2024-01-02,Adult,Adult,Muscle,Muscular System
29642,SRR27397715,SRX23073964,SRS20033316,SRP480899,PRJNA1060279,EPIFISH,PRJNA1060279,Other,Epigenetic changes in fish during domestication,,,,RRBS library9,PG1,,strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 9|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of danio rerio,RRBS9,RRBS9,Library preparation kit used  Zymo Seq RRBS Library Kit,,,Bisulfite-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP480899,,,PG1_L7_1.fq.gz PG1_L7_2.fq.gz,fastq fastq,1157067600.0,3856892.0,PG1 L7 1.fq.gz,0:150 1:150,A:278308283;C:162228777;G:432676687;T:283803806;N:50047,150,150,,,278308283,162228777,432676687,283803806,50047,SRX23073964,SRS20033316,SRA1777947,Nord University|Bioscience and Aquaculture,Nord University,2,0.02347,0.02319,0.02188,0.02162,0.99517,0.99519,0.50342,0.51027,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Norway,2024-01-02,Adult,Adult,Muscle,Muscular System
29643,SRR27397716,SRX23073963,SRS20033315,SRP480899,PRJNA1060279,EPIFISH,PRJNA1060279,Other,Epigenetic changes in fish during domestication,,,,RRBS library8,LG4,,strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 8|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of danio rerio,RRBS8,RRBS8,Library preparation kit used  Zymo Seq RRBS Library Kit,,,Bisulfite-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP480899,,,LG4_L7_1.fq.gz LG4_L7_2.fq.gz,fastq fastq,1080684300.0,3602281.0,LG4 L7 1.fq.gz,0:150 1:150,A:270759422;C:159278390;G:387693215;T:262907381;N:45892,150,150,,,270759422,159278390,387693215,262907381,45892,SRX23073963,SRS20033315,SRA1777947,Nord University|Bioscience and Aquaculture,Nord University,2,0.01698,0.00033,0.01593,0.00026,0.99675,0.99979,0.4974,0.2,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Norway,2024-01-02,Adult,Adult,Muscle,Muscular System
29644,SRR27397717,SRX23073962,SRS20033314,SRP480899,PRJNA1060279,EPIFISH,PRJNA1060279,Other,Epigenetic changes in fish during domestication,,,,RRBS library7,LG3,,strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 7|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of danio rerio,RRBS7,RRBS7,Library preparation kit used  Zymo Seq RRBS Library Kit,,,Bisulfite-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP480899,,,LG3_L7_1.fq.gz LG3_L7_2.fq.gz,fastq fastq,1223063700.0,4076879.0,LG3 L7 1.fq.gz,0:150 1:150,A:301167012;C:182106743;G:443329321;T:296409064;N:51560,150,150,,,301167012,182106743,443329321,296409064,51560,SRX23073962,SRS20033314,SRA1777947,Nord University|Bioscience and Aquaculture,Nord University,2,0.01787,0.01759,0.01644,0.01622,0.99545,0.99582,0.56826,0.56126,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Norway,2024-01-02,Adult,Adult,Muscle,Muscular System
29645,SRR27397718,SRX23073961,SRS20033313,SRP480899,PRJNA1060279,EPIFISH,PRJNA1060279,Other,Epigenetic changes in fish during domestication,,,,RRBS library6,LG2,,strain:ab|age:adult|collection date:2023 02 07|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 6|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of danio rerio,RRBS6,RRBS6,Library preparation kit used  Zymo Seq RRBS Library Kit,,,Bisulfite-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP480899,,,LG2_L7_1.fq.gz LG2_L7_2.fq.gz,fastq fastq,1188600300.0,3962001.0,LG2 L7 1.fq.gz,0:150 1:150,A:294477343;C:172669379;G:418732939;T:302669966;N:50673,150,150,,,294477343,172669379,418732939,302669966,50673,SRX23073961,SRS20033313,SRA1777947,Nord University|Bioscience and Aquaculture,Nord University,2,0.0205,0.02042,0.01903,0.01894,0.99584,0.99577,0.51685,0.51824,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Norway,2024-01-02,Adult,Adult,Muscle,Muscular System
29646,SRR27397719,SRX23073960,SRS20033312,SRP480899,PRJNA1060279,EPIFISH,PRJNA1060279,Other,Epigenetic changes in fish during domestication,,,,RRBS library5,LG1,,strain:ab|age:adult|collection date:2023 02 06|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 5|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of danio rerio,RRBS5,RRBS5,Library preparation kit used  Zymo Seq RRBS Library Kit,,,Bisulfite-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP480899,,,LG1_L7_1.fq.gz LG1_L7_2.fq.gz,fastq fastq,1048183200.0,3493944.0,LG1 L7 1.fq.gz,0:150 1:150,A:260330612;C:163890192;G:372783427;T:251133569;N:45400,150,150,,,260330612,163890192,372783427,251133569,45400,SRX23073960,SRS20033312,SRA1777947,Nord University|Bioscience and Aquaculture,Nord University,2,0.01999,0.00059,0.01851,0.00045,0.99563,0.99961,0.49816,0.36842,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Norway,2024-01-02,Adult,Adult,Muscle,Muscular System
29647,SRR27397720,SRX23073959,SRS20033311,SRP480899,PRJNA1060279,EPIFISH,PRJNA1060279,Other,Epigenetic changes in fish during domestication,,,,RRBS library4,CG4,,strain:ab|age:adult|collection date:2023 02 05|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 4|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of danio rerio,RRBS4,RRBS4,Library preparation kit used  Zymo Seq RRBS Library Kit,,,Bisulfite-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP480899,,,CG4_L7_1.fq.gz CG4_L7_2.fq.gz,fastq fastq,1547200200.0,5157334.0,CG4 L7 1.fq.gz,0:150 1:150,A:389261224;C:230650937;G:559928386;T:367293552;N:66101,150,150,,,389261224,230650937,559928386,367293552,66101,SRX23073959,SRS20033311,SRA1777947,Nord University|Bioscience and Aquaculture,Nord University,2,0.01121,0.00022,0.01024,0.00018,0.99713,0.99991,0.56111,1.0,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Norway,2024-01-02,Adult,Adult,Muscle,Muscular System
29648,SRR27397721,SRX23073958,SRS20033310,SRP480899,PRJNA1060279,EPIFISH,PRJNA1060279,Other,Epigenetic changes in fish during domestication,,,,RRBS library3,CG3,,strain:ab|age:adult|collection date:2023 02 04|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of danio rerio,RRBS3,RRBS3,Library preparation kit used  Zymo Seq RRBS Library Kit,,,Bisulfite-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP480899,,,CG3_L7_1.fq.gz CG3_L7_2.fq.gz,fastq fastq,1164022500.0,3880075.0,CG3 L7 1.fq.gz,0:150 1:150,A:281490630;C:172929357;G:423757698;T:285795200;N:49615,150,150,,,281490630,172929357,423757698,285795200,49615,SRX23073958,SRS20033310,SRA1777947,Nord University|Bioscience and Aquaculture,Nord University,2,0.0188,0.00046,0.01744,0.00039,0.99626,0.99981,0.55421,0.6,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Norway,2024-01-02,Adult,Adult,Muscle,Muscular System
29649,SRR27397722,SRX23073957,SRS20033309,SRP480899,PRJNA1060279,EPIFISH,PRJNA1060279,Other,Epigenetic changes in fish during domestication,,,,RRBS library12,PG4,,strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 12|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of danio rerio,RRBS12,RRBS12,Library preparation kit used  Zymo Seq RRBS Library Kit,,,Bisulfite-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP480899,,,PG4_L7_1.fq.gz PG4_L7_2.fq.gz,fastq fastq,937521000.0,3125070.0,PG4 L7 1.fq.gz,0:150 1:150,A:230277419;C:145742183;G:328432893;T:233027715;N:40790,150,150,,,230277419,145742183,328432893,233027715,40790,SRX23073957,SRS20033309,SRA1777947,Nord University|Bioscience and Aquaculture,Nord University,2,0.01943,0.01926,0.01799,0.01786,0.99575,0.99588,0.51136,0.48062,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Norway,2024-01-02,Adult,Adult,Muscle,Muscular System
29650,SRR27397723,SRX23073956,SRS20033308,SRP480899,PRJNA1060279,EPIFISH,PRJNA1060279,Other,Epigenetic changes in fish during domestication,,,,RRBS library11,PG3,,strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 11|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of danio rerio,RRBS11,RRBS11,Library preparation kit used  Zymo Seq RRBS Library Kit,,,Bisulfite-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP480899,,,PG3_L7_1.fq.gz PG3_L7_2.fq.gz,fastq fastq,1256812500.0,4189375.0,PG3 L7 1.fq.gz,0:150 1:150,A:318736087;C:194540494;G:434374337;T:309107761;N:53821,150,150,,,318736087,194540494,434374337,309107761,53821,SRX23073956,SRS20033308,SRA1777947,Nord University|Bioscience and Aquaculture,Nord University,2,0.01424,0.00046,0.01316,0.00036,0.99683,0.99975,0.49746,0.5,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Norway,2024-01-02,Adult,Adult,Muscle,Muscular System
29651,SRR27397724,SRX23073955,SRS20033307,SRP480899,PRJNA1060279,EPIFISH,PRJNA1060279,Other,Epigenetic changes in fish during domestication,,,,RRBS library2,CG2,,strain:ab|age:adult|collection date:2023 02 03|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of danio rerio,RRBS2,RRBS2,Library preparation kit used  Zymo Seq RRBS Library Kit,,,Bisulfite-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP480899,,,CG2_L7_1.fq.gz CG2_L7_2.fq.gz,fastq fastq,1157888400.0,3859628.0,CG2 L7 1.fq.gz,0:150 1:150,A:292628434;C:171796176;G:406707172;T:286706357;N:50261,150,150,,,292628434,171796176,406707172,286706357,50261,SRX23073955,SRS20033307,SRA1777947,Nord University|Bioscience and Aquaculture,Nord University,2,0.02036,0.02023,0.01903,0.01889,0.99616,0.99614,0.55102,0.57894,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Norway,2024-01-02,Adult,Adult,Muscle,Muscular System
29652,SRR27397725,SRX23073954,SRS20033306,SRP480899,PRJNA1060279,EPIFISH,PRJNA1060279,Other,Epigenetic changes in fish during domestication,,,,RRBS library1,CG1,,strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of danio rerio,RRBS1,RRBS1,Library preparation kit used  Zymo Seq RRBS Library Kit,,,Bisulfite-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP480899,,,CG1_L7_1.fq.gz CG1_L7_2.fq.gz,fastq fastq,1004867700.0,3349559.0,CG1 L7 1.fq.gz,0:150 1:150,A:247727849;C:158203386;G:350367173;T:248526527;N:42765,150,150,,,247727849,158203386,350367173,248526527,42765,SRX23073954,SRS20033306,SRA1777947,Nord University|Bioscience and Aquaculture,Nord University,2,0.02764,0.00147,0.0252,0.00121,0.99233,0.99926,0.51541,0.5,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Norway,2024-01-02,Adult,Adult,Muscle,Muscular System
33817,SRR30712573,SRX26116362,SRS22679901,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,mut I 4,GSM8523061,,source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured|geo loc name:missing|collection date:missing,mut I 4,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured,GSM8523061,GSM8523061: mut I 4; Danio rerio; RNA Seq,GSM8523061 r1,GSM8523061,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525069_S34_R1_001.fastq.gz 1525069_S34_R2_001.fastq.gz,fastq fastq,6968777444.0,23075422.0,GSM8523061 r1,0:151 1:151,A:1784361774;C:1727895848;G:1635536759;T:1820585862;N:397201,151,151,,,1784361774,1727895848,1635536759,1820585862,397201,SRX26116362,SRS22679901,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33818,SRR30712574,SRX26116361,SRS22679900,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,mut I 3,GSM8523060,,source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured|geo loc name:missing|collection date:missing,mut I 3,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured,GSM8523060,GSM8523060: mut I 3; Danio rerio; RNA Seq,GSM8523060 r1,GSM8523060,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525068_S33_R1_001.fastq.gz 1525068_S33_R2_001.fastq.gz,fastq fastq,6689942656.0,22152128.0,GSM8523060 r1,0:151 1:151,A:1712641463;C:1649736138;G:1564669718;T:1762517154;N:378183,151,151,,,1712641463,1649736138,1564669718,1762517154,378183,SRX26116361,SRS22679900,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33819,SRR30712575,SRX26116360,SRS22679899,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,mut I 2,GSM8523059,,source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured|geo loc name:missing|collection date:missing,mut I 2,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured,GSM8523059,GSM8523059: mut I 2; Danio rerio; RNA Seq,GSM8523059 r1,GSM8523059,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525067_S32_R1_001.fastq.gz 1525067_S32_R2_001.fastq.gz,fastq fastq,6838079394.0,22642647.0,GSM8523059 r1,0:151 1:151,A:1753283488;C:1683533113;G:1593714937;T:1807162545;N:385311,151,151,,,1753283488,1683533113,1593714937,1807162545,385311,SRX26116360,SRS22679899,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33820,SRR30712576,SRX26116359,SRS22679898,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,mut I 1,GSM8523058,,source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured|geo loc name:missing|collection date:missing,mut I 1,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured,GSM8523058,GSM8523058: mut I 1; Danio rerio; RNA Seq,GSM8523058 r1,GSM8523058,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525066_S31_R1_001.fastq.gz 1525066_S31_R2_001.fastq.gz,fastq fastq,6913447118.0,22892209.0,GSM8523058 r1,0:151 1:151,A:1777855775;C:1703268831;G:1606126723;T:1825808576;N:387213,151,151,,,1777855775,1703268831,1606126723,1825808576,387213,SRX26116359,SRS22679898,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33821,SRR30712577,SRX26116358,SRS22679897,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,mut NI 4,GSM8523057,,source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured|geo loc name:missing|collection date:missing,mut NI 4,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured,GSM8523057,GSM8523057: mut NI 4; Danio rerio; RNA Seq,GSM8523057 r1,GSM8523057,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525065_S30_R1_001.fastq.gz 1525065_S30_R2_001.fastq.gz,fastq fastq,7146614372.0,23664286.0,GSM8523057 r1,0:151 1:151,A:1820135371;C:1776367719;G:1681029667;T:1868675511;N:406104,151,151,,,1820135371,1776367719,1681029667,1868675511,406104,SRX26116358,SRS22679897,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33822,SRR30712578,SRX26116357,SRS22679896,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,mut NI 3,GSM8523056,,source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured|geo loc name:missing|collection date:missing,mut NI 3,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured,GSM8523056,GSM8523056: mut NI 3; Danio rerio; RNA Seq,GSM8523056 r1,GSM8523056,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525064_S29_R1_001.fastq.gz 1525064_S29_R2_001.fastq.gz,fastq fastq,7041561558.0,23316429.0,GSM8523056 r1,0:151 1:151,A:1817821542;C:1726630082;G:1641523411;T:1855187749;N:398774,151,151,,,1817821542,1726630082,1641523411,1855187749,398774,SRX26116357,SRS22679896,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33823,SRR30712579,SRX26116356,SRS22679895,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,mut NI 2,GSM8523055,,source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured|geo loc name:missing|collection date:missing,mut NI 2,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured,GSM8523055,GSM8523055: mut NI 2; Danio rerio; RNA Seq,GSM8523055 r1,GSM8523055,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525063_S28_R1_001.fastq.gz 1525063_S28_R2_001.fastq.gz,fastq fastq,6855229974.0,22699437.0,GSM8523055 r1,0:151 1:151,A:1773305175;C:1678771882;G:1578466224;T:1824300431;N:386262,151,151,,,1773305175,1678771882,1578466224,1824300431,386262,SRX26116356,SRS22679895,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33824,SRR30712580,SRX26116355,SRS22679894,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,mut NI 1,GSM8523054,,source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured|geo loc name:missing|collection date:missing,mut NI 1,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured,GSM8523054,GSM8523054: mut NI 1; Danio rerio; RNA Seq,GSM8523054 r1,GSM8523054,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525062_S27_R1_001.fastq.gz 1525062_S27_R2_001.fastq.gz,fastq fastq,7650351278.0,25332289.0,GSM8523054 r1,0:151 1:151,A:1981492979;C:1869766013;G:1772110806;T:2026550473;N:431007,151,151,,,1981492979,1869766013,1772110806,2026550473,431007,SRX26116355,SRS22679894,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33825,SRR30712581,SRX26116354,SRS22679893,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,wt I 4,GSM8523053,,source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:injured|geo loc name:missing|collection date:missing,wt I 4,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:wt|treatment:injured,GSM8523053,GSM8523053: wt I 4; Danio rerio; RNA Seq,GSM8523053 r1,GSM8523053,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525061_S26_R1_001.fastq.gz 1525061_S26_R2_001.fastq.gz,fastq fastq,9052754718.0,29976009.0,GSM8523053 r1,0:151 1:151,A:2314195920;C:2237646210;G:2107364469;T:2393040833;N:507286,151,151,,,2314195920,2237646210,2107364469,2393040833,507286,SRX26116354,SRS22679893,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33826,SRR30712582,SRX26116353,SRS22679892,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,wt I 3,GSM8523052,,source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:injured|geo loc name:missing|collection date:missing,wt I 3,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:wt|treatment:injured,GSM8523052,GSM8523052: wt I 3; Danio rerio; RNA Seq,GSM8523052 r1,GSM8523052,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525060_S25_R1_001.fastq.gz 1525060_S25_R2_001.fastq.gz,fastq fastq,9028185508.0,29894654.0,GSM8523052 r1,0:151 1:151,A:2276450364;C:2258194222;G:2134851710;T:2358181229;N:507983,151,151,,,2276450364,2258194222,2134851710,2358181229,507983,SRX26116353,SRS22679892,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33827,SRR30712583,SRX26116352,SRS22679891,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,wt I 2,GSM8523051,,source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:injured|geo loc name:missing|collection date:missing,wt I 2,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:wt|treatment:injured,GSM8523051,GSM8523051: wt I 2; Danio rerio; RNA Seq,GSM8523051 r1,GSM8523051,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525059_S24_R1_001.fastq.gz 1525059_S24_R2_001.fastq.gz,fastq fastq,8553382920.0,28322460.0,GSM8523051 r1,0:151 1:151,A:2189680208;C:2131369869;G:1994221174;T:2237623798;N:487871,151,151,,,2189680208,2131369869,1994221174,2237623798,487871,SRX26116352,SRS22679891,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33828,SRR30712584,SRX26116351,SRS22679890,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,wt I 1,GSM8523050,,source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:injured|geo loc name:missing|collection date:missing,wt I 1,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:wt|treatment:injured,GSM8523050,GSM8523050: wt I 1; Danio rerio; RNA Seq,GSM8523050 r1,GSM8523050,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525058_S23_R1_001.fastq.gz 1525058_S23_R2_001.fastq.gz,fastq fastq,9259618074.0,30660987.0,GSM8523050 r1,0:151 1:151,A:2353088871;C:2323613307;G:2175738215;T:2406648342;N:529339,151,151,,,2353088871,2323613307,2175738215,2406648342,529339,SRX26116351,SRS22679890,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33829,SRR30712585,SRX26116350,SRS22679889,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,wt NI 4,GSM8523049,,source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:non injured|geo loc name:missing|collection date:missing,wt NI 4,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:wt|treatment:non injured,GSM8523049,GSM8523049: wt NI 4; Danio rerio; RNA Seq,GSM8523049 r1,GSM8523049,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525057_S22_R1_001.fastq.gz 1525057_S22_R2_001.fastq.gz,fastq fastq,8893456966.0,29448533.0,GSM8523049 r1,0:151 1:151,A:2300319776;C:2180302865;G:2044621569;T:2367713263;N:499493,151,151,,,2300319776,2180302865,2044621569,2367713263,499493,SRX26116350,SRS22679889,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33830,SRR30712586,SRX26116349,SRS22679888,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,wt NI 3,GSM8523048,,source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:non injured|geo loc name:missing|collection date:missing,wt NI 3,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:wt|treatment:non injured,GSM8523048,GSM8523048: wt NI 3; Danio rerio; RNA Seq,GSM8523048 r1,GSM8523048,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525056_S21_R1_001.fastq.gz 1525056_S21_R2_001.fastq.gz,fastq fastq,9463183590.0,31335045.0,GSM8523048 r1,0:151 1:151,A:2390372740;C:2375512221;G:2247572478;T:2449199968;N:526183,151,151,,,2390372740,2375512221,2247572478,2449199968,526183,SRX26116349,SRS22679888,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33831,SRR30712587,SRX26116348,SRS22679887,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,wt NI 2,GSM8523047,,source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:non injured|geo loc name:missing|collection date:missing,wt NI 2,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:wt|treatment:non injured,GSM8523047,GSM8523047: wt NI 2; Danio rerio; RNA Seq,GSM8523047 r1,GSM8523047,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525055_S20_R1_001.fastq.gz 1525055_S20_R2_001.fastq.gz,fastq fastq,9106987274.0,30155587.0,GSM8523047 r1,0:151 1:151,A:2302703752;C:2289138612;G:2158041789;T:2356585481;N:517640,151,151,,,2302703752,2289138612,2158041789,2356585481,517640,SRX26116348,SRS22679887,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
33832,SRR30712588,SRX26116347,SRS22679886,SRP533374,PRJNA1162497,Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish,GSE277480,Transcriptome Analysis,The ANKRD1 gene is responsive to different forms of mechanical stress  including injury  stretching  resistance exercise  and eccentric contractions. We showed that ankrd1a  zebrafish homologue of mammalian ANKRD1  gets activated in the heart  post cryoinjury of the ventricle and in skeletal muscle post stab wound  suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction  muscle cell differentiation  MAPK and integrin mediated signaling pathways  and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery  RNA was isolated from the muscle tissue around the injury  anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt  non injured wt  injured mutant  and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.,,,,wt NI 1,GSM8523046,,source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:non injured|geo loc name:missing|collection date:missing,wt NI 1,fastp v0.23.4  STAR v2.7.0  RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20  nqualified percent limit=30  average qual=25  low complexity filter=True  complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110  Ensembl v110  using STAR v2.7.10 with standard parameters  except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3  to estimate transcript and gene abundances. Subsequently  the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110  Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample,skeletal muscle,Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail  in line with the anal opening. Immediately  post the injury  fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle  just behind the anal opening and containing the injury area anterior and posterior to the needle lesion  was dissected by a razor blade and used for RNA isolation.,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions  in circulating water system  under 14 h light/10 h dark cycle and at 28.5 ◦C.,tissue:skeletal muscle|genotype:wt|treatment:non injured,GSM8523046,GSM8523046: wt NI 1; Danio rerio; RNA Seq,GSM8523046 r1,GSM8523046,1,Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a /  fish was homogenized in TRIzol Reagen Invitorgen  Thermo Fisher Scientific  USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research  USA  according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase free water and its quantity and purity were measured promptly post isolation  using BioSpec nano Shimadzu  Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher  USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina  California  USA,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP533374,,,1525054_S19_R1_001.fastq.gz 1525054_S19_R2_001.fastq.gz,fastq fastq,6862974160.0,22725080.0,GSM8523046 r1,0:151 1:151,A:1767442745;C:1673075382;G:1598164146;T:1823910942;N:380945,151,151,,,1767442745,1673075382,1598164146,1823910942,380945,SRX26116347,SRS22679886,SRA2089519,Institute of Molecular Genetic and Genetic Engineering,Institute of Molecular Genetic and Genetic Engineering,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Serbia,2024-09-18,Adult,Adult,Muscle,Muscular System
36665,SRR800045,SRX257154,SRS405708,SRP020008,PRJNA193544,Danio rerio strain:Tubingen Epigenomics,PRJNA193544,Other,Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.,,pubmed:23663776,Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,Generic sample from Danio rerio,muscle RNAseq totalRNARibominus,,strain:Tubingen|label:PE: paired end  SE: single end|development stage:muscle,,,,,,,,,muscle RNAseq totalRNARibominus,muscle RNAseq totalRNARibominus,9084X1,Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 1000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP020008,,,muscle_RNAseq_totalRNARibominus_SE_9084X1_120420_SN141_0500_AD0TG5ACXX_5.txt.gz,Illumina native,3506573750.0,70131475.0,9084X1 120420 SN141 0500 AD0TG5ACXX 5,0:50,A:872717534;C:808774955;G:1036781008;T:777391447;N:10908806,50,,,,872717534,808774955,1036781008,777391447,10908806,SRX257154,SRS405708,SRA072148,University of Utah|Brad Cairns Lab,University of Utah,1,0.61428,,0.09813,,0.89305,,0.6908,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,unknown,bulk,unknown,unknown,,United States,2013-05-07,Undetermined,Embryo,Muscle,Muscular System
37105,SRR891510,SRX298190,SRS673880,SRP024369,PRJNA207719,Tissue specific transcriptome profiling of zebrafish,PRJNA207719,Other,Tissue specific transcriptome profiling of zebrafish.,,,,,Danio rerio muscle,,sex:missing|strain:wild type|tissue:muscle|health state:normal|collection date:2013|geo loc name:India|biomaterial provider:CSIR Institute of Genomics and Integrative Biology|age:adult|BioSampleModel:Model organism or animal,,,,,,,,,Tissue specific transcriptome of zebrafish,Transcriptome of zebrafish Danio rerio muscle,zebrafish muscle,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP024369,,,lane4_NoIndex_L004_R1_cat.fastq lane4_NoIndex_L004_R2_cat.fastq,fastq fastq,1895673468.0,18585034.0,Transcriptome of zebrafish Danio rerio muscle,0:51 1:51,A:461627994;C:495899684;G:489490468;T:448396921;N:258401,51,51,,,461627994,495899684,489490468,448396921,258401,SRX298190,SRS673880,SRA089174,CSIR-IGIB,CSIR-Institute of Genomics and Integrative Biology CSIR-Institute of Genomics and Integrative Biology,2,0.90619,0.93507,0.0338,0.03473,0.79267,0.78683,0.45256,0.45438,51,51,B,B,biological fallback assumption,illumina,early_illumina,unknown,random_priming,unknown,bulk,unknown,unknown,,India,2013-10-10,Adult,Adult,Muscle,Muscular System
38063,SRR1524241,SRX661006,SRS665981,SRP044781,PRJNA255848,Danio rerio Transcriptome,PRJNA255848,Transcriptome Analysis,Transcriptome analysis of 12 zebrafish tissues,parent bioproject:PRJNA255979,pubmed:27189481,Zebrafish Muscle,Zebrafish Muscle,F Dr 5,,strain:AB|age:5 month|biomaterial provider:INRA|sex:female|tissue:Muscle|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Muscle,F Dr 5,F Dr 5,Total RNA was qualified using an Agilent BioAnalyzer and 1 µg was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP044781,,,F_Dr_5_CGATGT_L002_R1.fastq.gz F_Dr_5_CGATGT_L002_R2.fastq.gz,fastq fastq,6806595200.0,34032976.0,F Dr 5 files,0:100 1:100,A:1732271631;C:1678982446;G:1678662020;T:1710896201;N:5782902,100,100,,,1732271631,1678982446,1678662020,1710896201,5782902,SRX661006,SRS665981,SRA176464,INRA|Fish Physiology and Genomics,INRA PhyloFish,2,0.9665,0.96619,0.03055,0.03064,0.78336,0.78366,0.51756,0.51698,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,France,2015-07-24,Adult,Adult,Muscle,Muscular System
38260,SRR1609755,SRX730408,SRS719629,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28°C to mild 18°C and severe 10°C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,muscle10,GSM1523050,,source name:muscle|tissue:muscle|temperature:10°C|strain:Tubingen|age:6 mpf,muscle10,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,muscle,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:muscle|temperature:10°C|strain:Tubingen|age:6 mpf,GSM1523050,GSM1523050: muscle10; Danio rerio; RNA Seq,GSM1523050,,1,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523050,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,muscle10_1.fq.gz muscle10_2.fq.gz,fastq fastq,3526303600.0,17631518.0,GSM1523050 r1,0:100 1:100,A:907821899;C:862068806;G:861677127;T:894668376;N:67392,100,100,,,907821899,862068806,861677127,894668376,67392,SRX730408,SRS719629,SRA189240,GEO,Shanghai Ocean University,2,0.97117,0.96598,0.02645,0.02677,0.78376,0.78819,0.49847,0.49607,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Muscle,Muscular System
38261,SRR1609754,SRX730407,SRS719627,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28°C to mild 18°C and severe 10°C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,muscle18,GSM1523049,,source name:muscle|tissue:muscle|temperature:18°C|strain:Tubingen|age:6 mpf,muscle18,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,muscle,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:muscle|temperature:18°C|strain:Tubingen|age:6 mpf,GSM1523049,GSM1523049: muscle18; Danio rerio; RNA Seq,GSM1523049,,1,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523049,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,muscle18_2.fq.gz muscle18_1.fq.gz,fastq fastq,3052105000.0,15260525.0,GSM1523049 r1,0:100 1:100,A:792718670;C:735445281;G:733127780;T:781512064;N:9301205,100,100,,,792718670,735445281,733127780,781512064,9301205,SRX730407,SRS719627,SRA189240,GEO,Shanghai Ocean University,2,0.95747,0.94738,0.02778,0.0283,0.83313,0.84064,0.50113,0.48506,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Muscle,Muscular System
38262,SRR1609753,SRX730406,SRS719626,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28°C to mild 18°C and severe 10°C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,muscle28,GSM1523048,,source name:muscle|tissue:muscle|temperature:28°C|strain:Tubingen|age:6 mpf,muscle28,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,muscle,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:muscle|temperature:28°C|strain:Tubingen|age:6 mpf,GSM1523048,GSM1523048: muscle28; Danio rerio; RNA Seq,GSM1523048,,1,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523048,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,muscle28_2.fq.gz muscle28_1.fq.gz,fastq fastq,3631962400.0,18159812.0,GSM1523048 r1,0:100 1:100,A:939417649;C:881759212;G:878258318;T:932460271;N:66950,100,100,,,939417649,881759212,878258318,932460271,66950,SRX730406,SRS719626,SRA189240,GEO,Shanghai Ocean University,2,0.96957,0.96709,0.02715,0.02728,0.80748,0.80947,0.52321,0.52681,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Muscle,Muscular System
40779,SRR3381875,SRX1704286,SRS1396337,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 3 muscle,GSM2122877,,source name:muscle  cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,Treated 3 muscle,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,muscle  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,GSM2122877,GSM2122877: Treated 3 muscle; Danio rerio; RNA Seq,GSM2122877,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122877,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_2_GSLv3-7_44_SL139801.fastq.gz C8DY1ANXX_s6_1_GSLv3-7_44_SL139801.fastq.gz,fastq fastq,1424344100.0,14243441.0,GSM2122877 r1,0:50 1:50,A:373105926;C:339772973;G:338044082;T:373286793;N:134326,50,50,,,373105926,339772973,338044082,373286793,134326,SRX1704286,SRS1396337,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.95482,0.95657,0.03881,0.03832,0.73038,0.73046,0.518,0.51502,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Muscle,Muscular System
40780,SRR3381876,SRX1704286,SRS1396337,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 3 muscle,GSM2122877,,source name:muscle  cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,Treated 3 muscle,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,muscle  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,GSM2122877,GSM2122877: Treated 3 muscle; Danio rerio; RNA Seq,GSM2122877,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122877,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_1_GSLv3-7_44_SL139801.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_44_SL139801.fastq.gz,fastq fastq,1067179600.0,10671796.0,GSM2122877 r2,0:50 1:50,A:277281148;C:254793697;G:251033742;T:284052011;N:19002,50,50,,,277281148,254793697,251033742,284052011,19002,SRX1704286,SRS1396337,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.95567,0.95769,0.03847,0.03979,0.74862,0.73651,0.52799,0.52237,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Muscle,Muscular System
40781,SRR3381877,SRX1704286,SRS1396337,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 3 muscle,GSM2122877,,source name:muscle  cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,Treated 3 muscle,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,muscle  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,GSM2122877,GSM2122877: Treated 3 muscle; Danio rerio; RNA Seq,GSM2122877,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122877,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_44_SL139801.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_44_SL139801.fastq.gz,fastq fastq,1419623200.0,14196232.0,GSM2122877 r3,0:50 1:50,A:371804107;C:338707464;G:337012958;T:371929117;N:169554,50,50,,,371804107,338707464,337012958,371929117,169554,SRX1704286,SRS1396337,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.95359,0.95717,0.0391,0.03926,0.73219,0.73225,0.5178,0.51875,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Muscle,Muscular System
40782,SRR3381878,SRX1704286,SRS1396337,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 3 muscle,GSM2122877,,source name:muscle  cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,Treated 3 muscle,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,muscle  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,GSM2122877,GSM2122877: Treated 3 muscle; Danio rerio; RNA Seq,GSM2122877,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122877,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_44_SL139801.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_44_SL139801.fastq.gz,fastq fastq,1080171600.0,10801716.0,GSM2122877 r4,0:50 1:50,A:280638393;C:258100474;G:254205905;T:287207620;N:19208,50,50,,,280638393,258100474,254205905,287207620,19208,SRX1704286,SRS1396337,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.95677,0.95714,0.03833,0.03933,0.74994,0.73937,0.52539,0.52283,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Muscle,Muscular System
40783,SRR3381871,SRX1704285,SRS1396338,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 2 muscle,GSM2122876,,source name:muscle  cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,Treated 2 muscle,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,muscle  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,GSM2122876,GSM2122876: Treated 2 muscle; Danio rerio; RNA Seq,GSM2122876,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122876,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_43_SL139800.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_43_SL139800.fastq.gz,fastq fastq,1066008900.0,10660089.0,GSM2122876 r1,0:50 1:50,A:275324871;C:257800561;G:252695833;T:280167714;N:19921,50,50,,,275324871,257800561,252695833,280167714,19921,SRX1704285,SRS1396338,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.96433,0.96552,0.05349,0.05444,0.78151,0.77007,0.56137,0.54847,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Muscle,Muscular System
40784,SRR3381872,SRX1704285,SRS1396338,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 2 muscle,GSM2122876,,source name:muscle  cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,Treated 2 muscle,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,muscle  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,GSM2122876,GSM2122876: Treated 2 muscle; Danio rerio; RNA Seq,GSM2122876,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122876,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_1_GSLv3-7_43_SL139800.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_43_SL139800.fastq.gz,fastq fastq,1389737800.0,13897378.0,GSM2122876 r2,0:50 1:50,A:362133250;C:335227403;G:331835484;T:360399948;N:141715,50,50,,,362133250,335227403,331835484,360399948,141715,SRX1704285,SRS1396338,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.96312,0.96504,0.05473,0.05481,0.76096,0.76327,0.54262,0.53783,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Muscle,Muscular System
40785,SRR3381873,SRX1704285,SRS1396338,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 2 muscle,GSM2122876,,source name:muscle  cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,Treated 2 muscle,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,muscle  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,GSM2122876,GSM2122876: Treated 2 muscle; Danio rerio; RNA Seq,GSM2122876,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122876,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_1_GSLv3-7_43_SL139800.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_43_SL139800.fastq.gz,fastq fastq,1049220700.0,10492207.0,GSM2122876 r3,0:50 1:50,A:271022900;C:253544145;G:248558843;T:276075122;N:19690,50,50,,,271022900,253544145,248558843,276075122,19690,SRX1704285,SRS1396338,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.96446,0.96516,0.05382,0.05449,0.78269,0.77072,0.55933,0.54576,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Muscle,Muscular System
40786,SRR3381874,SRX1704285,SRS1396338,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 2 muscle,GSM2122876,,source name:muscle  cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,Treated 2 muscle,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,muscle  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,GSM2122876,GSM2122876: Treated 2 muscle; Danio rerio; RNA Seq,GSM2122876,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122876,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_43_SL139800.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_43_SL139800.fastq.gz,fastq fastq,1394669100.0,13946691.0,GSM2122876 r4,0:50 1:50,A:363332129;C:336439374;G:333102129;T:361606902;N:188566,50,50,,,363332129,336439374,333102129,361606902,188566,SRX1704285,SRS1396338,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.96262,0.96516,0.05541,0.05531,0.76262,0.76516,0.54009,0.54486,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Muscle,Muscular System
40787,SRR3381865,SRX1704284,SRS1396339,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 1 muscle,GSM2122875,,source name:muscle  cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,Treated 1 muscle,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,muscle  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,GSM2122875,GSM2122875: Treated 1 muscle; Danio rerio; RNA Seq,GSM2122875,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122875,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_1_GSLv3-7_42_SL139799.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_42_SL139799.fastq.gz,fastq fastq,848332400.0,8483324.0,GSM2122875 r1,0:50 1:50,A:222562905;C:202678911;G:201260703;T:221751638;N:78243,50,50,,,222562905,202678911,201260703,221751638,78243,SRX1704284,SRS1396339,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.95805,0.961,0.04973,0.0491,0.74509,0.74446,0.53696,0.53656,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Muscle,Muscular System
40788,SRR3381866,SRX1704284,SRS1396339,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 1 muscle,GSM2122875,,source name:muscle  cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,Treated 1 muscle,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,muscle  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,GSM2122875,GSM2122875: Treated 1 muscle; Danio rerio; RNA Seq,GSM2122875,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122875,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_42_SL139799.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_42_SL139799.fastq.gz,fastq fastq,847234900.0,8472349.0,GSM2122875 r2,0:50 1:50,A:222218092;C:202466432;G:201066152;T:221372059;N:112165,50,50,,,222218092,202466432,201066152,221372059,112165,SRX1704284,SRS1396339,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.95894,0.96214,0.04899,0.04888,0.74332,0.74353,0.53693,0.53748,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Muscle,Muscular System
40789,SRR3381867,SRX1704284,SRS1396339,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 1 muscle,GSM2122875,,source name:muscle  cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,Treated 1 muscle,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,muscle  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,GSM2122875,GSM2122875: Treated 1 muscle; Danio rerio; RNA Seq,GSM2122875,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122875,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DKGANXX_s8_2_GSLv3-7_42_SL139799.fastq.gz C8DKGANXX_s8_1_GSLv3-7_42_SL139799.fastq.gz,fastq fastq,1573927200.0,15739272.0,GSM2122875 r3,0:50 1:50,A:413612028;C:375148773;G:371885800;T:412450020;N:830579,50,50,,,413612028,375148773,371885800,412450020,830579,SRX1704284,SRS1396339,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.95668,0.96042,0.05044,0.04996,0.74588,0.74763,0.54005,0.5409,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Muscle,Muscular System
40790,SRR3381868,SRX1704284,SRS1396339,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 1 muscle,GSM2122875,,source name:muscle  cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,Treated 1 muscle,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,muscle  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,GSM2122875,GSM2122875: Treated 1 muscle; Danio rerio; RNA Seq,GSM2122875,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122875,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_42_SL139799.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_42_SL139799.fastq.gz,fastq fastq,646111500.0,6461115.0,GSM2122875 r4,0:50 1:50,A:168189077;C:154670722;G:152078186;T:171161973;N:11542,50,50,,,168189077,154670722,152078186,171161973,11542,SRX1704284,SRS1396339,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.96133,0.96206,0.04804,0.04976,0.76568,0.75126,0.5261,0.54393,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Muscle,Muscular System
40791,SRR3381869,SRX1704284,SRS1396339,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 1 muscle,GSM2122875,,source name:muscle  cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,Treated 1 muscle,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,muscle  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,GSM2122875,GSM2122875: Treated 1 muscle; Danio rerio; RNA Seq,GSM2122875,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122875,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DKGANXX_s7_1_GSLv3-7_42_SL139799.fastq.gz C8DKGANXX_s7_2_GSLv3-7_42_SL139799.fastq.gz,fastq fastq,1577881700.0,15778817.0,GSM2122875 r5,0:50 1:50,A:414672587;C:376155159;G:372910894;T:413443352;N:699708,50,50,,,414672587,376155159,372910894,413443352,699708,SRX1704284,SRS1396339,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.95735,0.96122,0.05005,0.0498,0.74789,0.7486,0.53779,0.52556,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Muscle,Muscular System
40792,SRR3381870,SRX1704284,SRS1396339,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 1 muscle,GSM2122875,,source name:muscle  cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,Treated 1 muscle,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,muscle  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol,GSM2122875,GSM2122875: Treated 1 muscle; Danio rerio; RNA Seq,GSM2122875,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122875,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_2_GSLv3-7_42_SL139799.fastq.gz C8BH2ANXX_s6_1_GSLv3-7_42_SL139799.fastq.gz,fastq fastq,637889100.0,6378891.0,GSM2122875 r6,0:50 1:50,A:166073650;C:152564175;G:150056875;T:169183109;N:11291,50,50,,,166073650,152564175,150056875,169183109,11291,SRX1704284,SRS1396339,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.95944,0.96139,0.04768,0.04952,0.7651,0.75126,0.544,0.52652,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Muscle,Muscular System