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 28496,SRR26321412,SRX22029502,SRS19102283,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 1,R27,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R27,R27,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R27.fastq,fastq,23400.0,312.0,R27.fastq,0:75,A:7949;C:4612;G:4730;T:6100;N:9,75,,,,7949,4612,4730,6100,9,SRX22029502,SRS19102283,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89642,,0.06772,,0.99827,,0.75,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28497,SRR26321413,SRX22029501,SRS19102284,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 4,R22,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R22,R22,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R22.fastq,fastq,23400.0,312.0,R22.fastq,0:75,A:7470;C:4460;G:5063;T:6404;N:3,75,,,,7470,4460,5063,6404,3,SRX22029501,SRS19102284,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87073,,0.12167,,0.99801,,0.73157,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28498,SRR26321414,SRX22029500,SRS19102281,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,R21,R21,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R21,R21,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R21.fastq,fastq,23400.0,312.0,R21.fastq,0:75,A:7540;C:4349;G:4857;T:6646;N:8,75,,,,7540,4349,4857,6646,8,SRX22029500,SRS19102281,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.8839,,0.04494,,0.99768,,0.72769,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28499,SRR26321415,SRX22029499,SRS19102282,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 2,R18,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R18,R18,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R18.fastq,fastq,23400.0,312.0,R18.fastq,0:75,A:7380;C:4430;G:5069;T:6518;N:3,75,,,,7380,4430,5069,6518,3,SRX22029499,SRS19102282,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87259,,0.11196,,0.99784,,0.69791,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28500,SRR26321416,SRX22029498,SRS19102280,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 1,R17,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R17,R17,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R17.fastq,fastq,23400.0,312.0,R17.fastq,0:75,A:7322;C:4455;G:5111;T:6507;N:5,75,,,,7322,4455,5111,6507,5,SRX22029498,SRS19102280,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90439,,0.12749,,0.99813,,0.71052,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28501,SRR26321417,SRX22029497,SRS19102279,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 5,R1,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R1,R1,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R1.fastq,fastq,23400.0,312.0,R1.fastq,0:75,A:7934;C:4560;G:4922;T:5980;N:4,75,,,,7934,4560,4922,5980,4,SRX22029497,SRS19102279,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87045,,0.10526,,0.99805,,0.71978,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28502,SRR26321418,SRX22029496,SRS19102277,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 4,R64,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R64,R64,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R64.fastq,fastq,23400.0,312.0,R64.fastq,0:75,A:7844;C:4626;G:4804;T:6126;N:0,75,,,,7844,4626,4804,6126,0,SRX22029496,SRS19102277,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90119,,0.07509,,0.99839,,0.8,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28503,SRR26321419,SRX22029495,SRS19102278,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 3,R61,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R61,R61,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R61.fastq,fastq,23400.0,312.0,R61.fastq,0:75,A:7454;C:4556;G:4960;T:6425;N:5,75,,,,7454,4556,4960,6425,5,SRX22029495,SRS19102278,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89098,,0.06015,,0.99813,,0.77102,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28504,SRR26321420,SRX22029494,SRS19102276,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 4,30,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,30,30,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,30.fastq,fastq,23400.0,312.0,30.fastq,0:75,A:7732;C:4528;G:5150;T:5987;N:3,75,,,,7732,4528,5150,5987,3,SRX22029494,SRS19102276,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.88447,,0.13147,,0.99772,,0.71584,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28505,SRR26321421,SRX22029493,SRS19102275,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,R11,R11,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,R11,R11,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R11.fastq,fastq,23400.0,312.0,R11.fastq,0:75,A:7818;C:4507;G:5107;T:5956;N:12,75,,,,7818,4507,5107,5956,12,SRX22029493,SRS19102275,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89345,,0.11475,,0.99847,,0.82258,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28506,SRR26321422,SRX22029492,SRS19102274,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 2,31,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,31,31,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,31.fastq,fastq,23400.0,312.0,31.fastq,0:75,A:7470;C:4619;G:4802;T:6504;N:5,75,,,,7470,4619,4802,6504,5,SRX22029492,SRS19102274,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87699,,0.11111,,0.99829,,0.78918,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28507,SRR26321423,SRX22029491,SRS19102273,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 1,R9,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,R9,R9,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R9.fastq,fastq,23400.0,312.0,R9.fastq,0:75,A:8130;C:4537;G:4809;T:5917;N:7,75,,,,8130,4537,4809,5917,7,SRX22029491,SRS19102273,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.83588,,0.05725,,0.99801,,0.68586,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28508,SRR26321424,SRX22029490,SRS19102272,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 4,R33,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R33,R33,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R33.fastq,fastq,23400.0,312.0,R33.fastq,0:75,A:7745;C:4421;G:4867;T:6360;N:7,75,,,,7745,4421,4867,6360,7,SRX22029490,SRS19102272,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87259,,0.07335,,0.99805,,0.71428,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28509,SRR26321425,SRX22029489,SRS19102271,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 3,R31,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R31,R31,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R31.fastq,fastq,23400.0,312.0,R31.fastq,0:75,A:7441;C:4483;G:5163;T:6313;N:0,75,,,,7441,4483,5163,6313,0,SRX22029489,SRS19102271,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.9,,0.05925,,0.9977,,0.68325,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28510,SRR26321426,SRX22029488,SRS19102270,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 2,R29,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R29,R29,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R29.fastq,fastq,23400.0,312.0,R29.fastq,0:75,A:7379;C:4698;G:5166;T:6156;N:1,75,,,,7379,4698,5166,6156,1,SRX22029488,SRS19102270,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.91016,,0.05859,,0.99797,,0.74528,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28511,SRR26321427,SRX22029487,SRS19102269,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 2,R62,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R62,R62,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R62.fastq,fastq,23400.0,312.0,R62.fastq,0:75,A:7383;C:4566;G:4713;T:6728;N:10,75,,,,7383,4566,4713,6728,10,SRX22029487,SRS19102269,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.91571,,0.05363,,0.99835,,0.77674,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28512,SRR26321428,SRX22029486,SRS19102268,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,Replicate 1 for SHAM,SHAM 1,R63,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia: Melbourne|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R63,R63,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R63.fastq,fastq,23400.0,312.0,R63.fastq,0:75,A:7516;C:4606;G:4765;T:6508;N:5,75,,,,7516,4606,4765,6508,5,SRX22029486,SRS19102268,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90385,,0.0423,,0.99805,,0.72429,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 32476,SRR29270149,SRX24787634,SRS21505104,SRP511487,PRJNA1119569,RNA seq of zebrafish foxl2l mutant,PRJNA1119569,Other,Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.,,,,,foxl2l Mut 20 1,,strain:AB|age:20|collection date:2023 06 10|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal,,,,,,,,,foxl2l Mut 20 1,E10,E10,50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP511487,,,foxl2l_Mut-20-1_S162_R1.fastq.gz foxl2l_Mut-20-1_S162_R2.fastq.gz,fastq fastq,8940963680.0,29605840.0,foxl2l Mut 20 1 S162 R1.fastq.gz,0:151 1:151,A:2232167098;C:2229744850;G:2271326718;T:2207692629;N:32385,151,151,,,2232167098,2229744850,2271326718,2207692629,32385,SRX24787634,SRS21505104,SRA1887976,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2024-06-03,Undetermined,Undetermined,Gonad,Reproductive System 32477,SRR29270150,SRX24787633,SRS21505103,SRP511487,PRJNA1119569,RNA seq of zebrafish foxl2l mutant,PRJNA1119569,Other,Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.,,,,,foxl2l Het 20 3,,strain:AB|age:20|collection date:2023 06 09|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal,,,,,,,,,foxl2l Het 20 3,E9,E9,50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP511487,,,foxl2l_Het-20-3_S161_R1.fastq.gz foxl2l_Het-20-3_S161_R2.fastq.gz,fastq fastq,7038409282.0,23305991.0,foxl2l Het 20 3 S161 R1.fastq.gz,0:151 1:151,A:1766863186;C:1740008639;G:1787471686;T:1744039429;N:26342,151,151,,,1766863186,1740008639,1787471686,1744039429,26342,SRX24787633,SRS21505103,SRA1887976,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2024-06-03,Undetermined,Undetermined,Gonad,Reproductive System 32478,SRR29270151,SRX24787632,SRS21505102,SRP511487,PRJNA1119569,RNA seq of zebrafish foxl2l mutant,PRJNA1119569,Other,Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.,,,,,foxl2l Het 20 2,,strain:AB|age:20|collection date:2023 06 08|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal,,,,,,,,,foxl2l Het 20 2,E8,E8,50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP511487,,,foxl2l_Het-20-2_S160_R1.fastq.gz foxl2l_Het-20-2_S160_R2.fastq.gz,fastq fastq,6772505832.0,22425516.0,foxl2l Het 20 2 S160 R1.fastq.gz,0:151 1:151,A:1704124986;C:1673138074;G:1713003931;T:1682214009;N:24832,151,151,,,1704124986,1673138074,1713003931,1682214009,24832,SRX24787632,SRS21505102,SRA1887976,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2024-06-03,Undetermined,Undetermined,Gonad,Reproductive System 32479,SRR29270152,SRX24787631,SRS21505101,SRP511487,PRJNA1119569,RNA seq of zebrafish foxl2l mutant,PRJNA1119569,Other,Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.,,,,,foxl2l Het 20 1,,strain:AB|age:20|collection date:2023 06 07|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal,,,,,,,,,foxl2l Het 20 1,E7,E7,50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP511487,,,foxl2l_Het-20-1_S159_R1.fastq.gz foxl2l_Het-20-1_S159_R2.fastq.gz,fastq fastq,11685740812.0,38694506.0,foxl2l Het 20 1 S159 R1.fastq.gz,0:151 1:151,A:2939618668;C:2888861085;G:2958173208;T:2899044704;N:43147,151,151,,,2939618668,2888861085,2958173208,2899044704,43147,SRX24787631,SRS21505101,SRA1887976,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2024-06-03,Undetermined,Undetermined,Gonad,Reproductive System 32480,SRR29270153,SRX24787630,SRS21505100,SRP511487,PRJNA1119569,RNA seq of zebrafish foxl2l mutant,PRJNA1119569,Other,Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.,,,,,foxl2l Mut 15 3,,strain:AB|age:15|collection date:2023 06 06|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal,,,,,,,,,foxl2l Mut 15 3,E6,E6,50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP511487,,,foxl2l_Mut-15-3_S158_R1.fastq.gz foxl2l_Mut-15-3_S158_R2.fastq.gz,fastq fastq,9503789604.0,31469502.0,foxl2l Mut 15 3 S158 R1.fastq.gz,0:151 1:151,A:2393052443;C:2340958111;G:2411502428;T:2358240313;N:36309,151,151,,,2393052443,2340958111,2411502428,2358240313,36309,SRX24787630,SRS21505100,SRA1887976,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2024-06-03,Undetermined,Undetermined,Gonad,Reproductive System 32481,SRR29270154,SRX24787629,SRS21505099,SRP511487,PRJNA1119569,RNA seq of zebrafish foxl2l mutant,PRJNA1119569,Other,Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.,,,,,foxl2l Mut 15 2,,strain:AB|age:15|collection date:2023 06 05|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal,,,,,,,,,foxl2l Mut 15 2,E5,E5,50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP511487,,,foxl2l_Mut-15-2_S157_R1.fastq.gz foxl2l_Mut-15-2_S157_R2.fastq.gz,fastq fastq,7416837026.0,24559063.0,foxl2l Mut 15 2 S157 R1.fastq.gz,0:151 1:151,A:1865711045;C:1830489703;G:1881612508;T:1838995980;N:27790,151,151,,,1865711045,1830489703,1881612508,1838995980,27790,SRX24787629,SRS21505099,SRA1887976,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2024-06-03,Undetermined,Undetermined,Gonad,Reproductive System 32482,SRR29270155,SRX24787628,SRS21505098,SRP511487,PRJNA1119569,RNA seq of zebrafish foxl2l mutant,PRJNA1119569,Other,Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.,,,,,foxl2l Mut 15 1,,strain:AB|age:15|collection date:2023 06 04|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal,,,,,,,,,foxl2l Mut 15 1,E4,E4,50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP511487,,,foxl2l_Mut-15-1_S156_R1.fastq.gz foxl2l_Mut-15-1_S156_R2.fastq.gz,fastq fastq,7092721868.0,23485834.0,foxl2l Mut 15 1 S156 R1.fastq.gz,0:151 1:151,A:1764166761;C:1770534219;G:1820397492;T:1737597123;N:26273,151,151,,,1764166761,1770534219,1820397492,1737597123,26273,SRX24787628,SRS21505098,SRA1887976,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2024-06-03,Undetermined,Undetermined,Gonad,Reproductive System 32483,SRR29270156,SRX24787627,SRS21505097,SRP511487,PRJNA1119569,RNA seq of zebrafish foxl2l mutant,PRJNA1119569,Other,Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.,,,,,foxl2l Het 15 3,,strain:AB|age:15|collection date:2023 06 03|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal,,,,,,,,,foxl2l Het 15 3,E3,E3,50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP511487,,,foxl2l_Het-15-3_S155_R1.fastq.gz foxl2l_Het-15-3_S155_R2.fastq.gz,fastq fastq,8083606820.0,26766910.0,foxl2l Het 15 3 S155 R1.fastq.gz,0:151 1:151,A:2028557443;C:2001113164;G:2050610840;T:2003295953;N:29420,151,151,,,2028557443,2001113164,2050610840,2003295953,29420,SRX24787627,SRS21505097,SRA1887976,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2024-06-03,Undetermined,Undetermined,Gonad,Reproductive System 32484,SRR29270157,SRX24787626,SRS21505096,SRP511487,PRJNA1119569,RNA seq of zebrafish foxl2l mutant,PRJNA1119569,Other,Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.,,,,,foxl2l Mut 20 3,,strain:AB|age:20|collection date:2023 06 12|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal,,,,,,,,,foxl2l Mut 20 3,E12,E12,50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP511487,,,foxl2l_Mut-20-3_S164_R1.fastq.gz foxl2l_Mut-20-3_S164_R2.fastq.gz,fastq fastq,7474861796.0,24751198.0,foxl2l Mut 20 3 S164 R1.fastq.gz,0:151 1:151,A:1878881650;C:1849512621;G:1891142525;T:1855296720;N:28280,151,151,,,1878881650,1849512621,1891142525,1855296720,28280,SRX24787626,SRS21505096,SRA1887976,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2024-06-03,Undetermined,Undetermined,Gonad,Reproductive System 32485,SRR29270158,SRX24787625,SRS21505095,SRP511487,PRJNA1119569,RNA seq of zebrafish foxl2l mutant,PRJNA1119569,Other,Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.,,,,,foxl2l Mut 20 2,,strain:AB|age:20|collection date:2023 06 11|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal,,,,,,,,,foxl2l Mut 20 2,E11,E11,50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP511487,,,foxl2l_Mut-20-2_S163_R1.fastq.gz foxl2l_Mut-20-2_S163_R2.fastq.gz,fastq fastq,8203704066.0,27164583.0,foxl2l Mut 20 2 S163 R1.fastq.gz,0:151 1:151,A:2061693689;C:2030126562;G:2072980952;T:2038873198;N:29665,151,151,,,2061693689,2030126562,2072980952,2038873198,29665,SRX24787625,SRS21505095,SRA1887976,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2024-06-03,Undetermined,Undetermined,Gonad,Reproductive System 32486,SRR29270159,SRX24787624,SRS21505094,SRP511487,PRJNA1119569,RNA seq of zebrafish foxl2l mutant,PRJNA1119569,Other,Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.,,,,,foxl2l Het 15 2,,strain:AB|age:15|collection date:2023 06 02|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal,,,,,,,,,foxl2l Het 15 2,E2,E2,50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP511487,,,foxl2l_Het-15-2_S154_R1.fastq.gz foxl2l_Het-15-2_S154_R2.fastq.gz,fastq fastq,7868286860.0,26053930.0,foxl2l Het 15 2 S154 R1.fastq.gz,0:151 1:151,A:1972210357;C:1946891859;G:2008091153;T:1941064817;N:28674,151,151,,,1972210357,1946891859,2008091153,1941064817,28674,SRX24787624,SRS21505094,SRA1887976,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2024-06-03,Undetermined,Undetermined,Gonad,Reproductive System 32487,SRR29270160,SRX24787623,SRS21505093,SRP511487,PRJNA1119569,RNA seq of zebrafish foxl2l mutant,PRJNA1119569,Other,Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.,,,,,foxl2l Het 15 1,,strain:AB|age:15|collection date:2023 06 01|geo loc name:China|sex:hermaphrodite|tissue:gonad|BioSampleModel:Model organism or animal,,,,,,,,,foxl2l Het 15 1,E1,E1,50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP511487,,,foxl2l_Het-15-1_S153_R1.fastq.gz foxl2l_Het-15-1_S153_R2.fastq.gz,fastq fastq,7117391946.0,23567523.0,foxl2l Het 15 1 S153 R1.fastq.gz,0:151 1:151,A:1795668098;C:1752824783;G:1793720116;T:1775153584;N:25365,151,151,,,1795668098,1752824783,1793720116,1775153584,25365,SRX24787623,SRS21505093,SRA1887976,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2024-06-03,Undetermined,Undetermined,Gonad,Reproductive System 70803,SRR20651070,SRX16674147,SRS14305696,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,klhl40a KO4,klhl40a Mutant 4,,strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal,,,,,,,,,KO4,klhl40a4,klhl40a4,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,KO4_1.fq.gz KO4_2.fq.gz,fastq fastq,6711352800.0,22371176.0,KO4 1.fq.gz,0:150 1:150,A:1777166363;C:1589553466;G:1610514347;T:1734012530;N:106094,150,150,,,1777166363,1589553466,1610514347,1734012530,106094,SRX16674147,SRS14305696,,,Brigham and Women's Hospital,2,0.96541,0.96534,0.04564,0.04561,0.80478,0.80594,0.49645,0.49712,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System 70804,SRR20651071,SRX16674146,SRS14305695,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,klhl40a KO3,klhl40a Mutant 3,,strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal,,,,,,,,,KO3,klhl40a3,klhl40a3,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,KO3_1.fq.gz KO3_2.fq.gz,fastq fastq,6837271200.0,22790904.0,KO3 1.fq.gz,0:150 1:150,A:1889665334;C:1538962427;G:1555674788;T:1852860913;N:107738,150,150,,,1889665334,1538962427,1555674788,1852860913,107738,SRX16674146,SRS14305695,,,Brigham and Women's Hospital,2,0.9394,0.93825,0.07858,0.07822,0.7413,0.74186,0.50534,0.49292,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System 70805,SRR20651072,SRX16674145,SRS14305694,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,klhl40a KO2,klhl40a Mutant 2,,strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal,,,,,,,,,KO2,klhl40a2,klhl40a2,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,KO2_1.fq.gz KO2_2.fq.gz,fastq fastq,6551044800.0,21836816.0,KO2 1.fq.gz,0:150 1:150,A:1793351007;C:1490899611;G:1511714794;T:1754976004;N:103384,150,150,,,1793351007,1490899611,1511714794,1754976004,103384,SRX16674145,SRS14305694,,,Brigham and Women's Hospital,2,0.95416,0.953,0.06534,0.06511,0.76678,0.76668,0.51901,0.49628,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System 70806,SRR20651073,SRX16674144,SRS14305693,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,klh40a KO1,klhl40a Mutant 1,,strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal,,,,,,,,,KO1,klhl40a1,klhl40a1,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,KO1_1.fq.gz KO1_2.fq.gz,fastq fastq,7080009000.0,23600030.0,KO1 1.fq.gz,0:150 1:150,A:1927450674;C:1619718617;G:1639235237;T:1893497462;N:107010,150,150,,,1927450674,1619718617,1639235237,1893497462,107010,SRX16674144,SRS14305693,,,Brigham and Women's Hospital,2,0.94175,0.94193,0.06579,0.06628,0.75045,0.7503,0.49508,0.50075,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System 70807,SRR20651074,SRX16674143,SRS14305692,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,WT4,Wild type Control4,,strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal,,,,,,,,,WT4,WT4,WT4,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,WT4_1.fq.gz WT4_2.fq.gz,fastq fastq,7079022600.0,23596742.0,WT4 1.fq.gz,0:150 1:150,A:1901387601;C:1651068590;G:1657216811;T:1869243020;N:106578,150,150,,,1901387601,1651068590,1657216811,1869243020,106578,SRX16674143,SRS14305692,,,Brigham and Women's Hospital,2,0.95455,0.95486,0.07809,0.07798,0.75491,0.75442,0.49622,0.50833,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System 70808,SRR20651075,SRX16674142,SRS14305691,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,WT3,Wild type Control3,,strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal,,,,,,,,,WT3,WT3,WT3,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,WT3_1.fq.gz WT3_2.fq.gz,fastq fastq,6750141600.0,22500472.0,WT3 1.fq.gz,0:150 1:150,A:1809694888;C:1570721302;G:1597114393;T:1772508410;N:102607,150,150,,,1809694888,1570721302,1597114393,1772508410,102607,SRX16674142,SRS14305691,,,Brigham and Women's Hospital,2,0.95657,0.95647,0.06172,0.06163,0.76252,0.76366,0.49411,0.49204,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System 70809,SRR20651076,SRX16674141,SRS14305690,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,WT2,Wild type Control2,,strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal,,,,,,,,,WT2,WT2,WT2,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,WT2_1.fq.gz WT2_2.fq.gz,fastq fastq,6786893400.0,22622978.0,WT2 1.fq.gz,0:150 1:150,A:1835782156;C:1564402670;G:1586345899;T:1800260025;N:102650,150,150,,,1835782156,1564402670,1586345899,1800260025,102650,SRX16674141,SRS14305690,,,Brigham and Women's Hospital,2,0.95057,0.9495,0.06714,0.06726,0.75266,0.75333,0.50647,0.50457,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System 70810,SRR20651077,SRX16674140,SRS14305689,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,WT1,Wild type Control1,,strain:AB|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:3 Months|dev stage:Adult|sex:male|tissue:Skeletal Muscle|disease:Nemaline Myopathy|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal,,,,,,,,,WT1,WT1,WT1,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,WT1_1.fq.gz WT1_2.fq.gz,fastq fastq,6946359900.0,23154533.0,WT1 1.fq.gz,0:150 1:150,A:1891340276;C:1588097676;G:1606011156;T:1860805584;N:105208,150,150,,,1891340276,1588097676,1606011156,1860805584,105208,SRX16674140,SRS14305689,,,Brigham and Women's Hospital,2,0.94444,0.94509,0.07758,0.07756,0.72943,0.72878,0.50732,0.50723,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System