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
29165,SRR27180613,SRX22861017,SRS19836056,SRP477408,PRJNA1051145,laser captured chondrocyte transcriptomes from cranial base,GSE249932,Transcriptome Analysis,similar methods as in Gomez Picos et al. 2022 and Nguyen et al. 2023 Overall design: mRNA profiles of wild type Danio rerio chondrocytes,,pubmed:38117077,,Z6 WT,GSM7967333,,source name:laser captured cartilage without xxx from cranial base in occipital region|tissue:cartilage|age:6dpf|genotype:wild type|geo loc name:missing|collection date:missing,Z6 WT,The paired end Illumina reads were trimmed using Trimmomatic v0.36 Bolger et al. 2014. Mapped to the Danio rerio Zv9 fom Ensembl. TMM normalization Robinson and Oshlack 2010 was performed using edgeR. Cutoff of genes considered expressed was determined by calculationg the minimum value of the bimodal distribution of counts. Assembly: Danio rerio Ensembl Zv9 Supplementary files format and content: Comma delimited text file includes counts for wildtype samples,laser captured cartilage without xxx from cranial base in occipital region,N/A,RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit ThermoFisher Scientific; Cat# KIT0204 according to the manufacturer’s instructions and DNase treatment was done using RNase Free DNase Qiagen; Cat#79254. RNA was amplified one round using MessageAmp II aRNA Kit ThermoFisher Scientific; Cat# AM1751. The RNA integrity was evaluated on the observation of a signature electropherogram pattern Bioanalyzer. A minimum of 5 10 ng of amplified RNA was used per sample for the construction of each library. RNA seq libraries were prepared by the National Research Council NRC  Saskatoon using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute  Prime  Fragment step using5 µl amplified mRNA the minimum amount was 5 10 ng mRNA as determined using Quant iT RiboGreen RNA Assay Kit Invitrogen. The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer Agilent Technologies Inc..,standard conditions EM filled dishes at 28.5C,tissue:cartilage|age:6dpf|genotype:wild type,GSM7967333,GSM7967333: Z6 WT; Danio rerio; RNA Seq,GSM7967333 r1,GSM7967333,1,RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit ThermoFisher Scientific; Cat# KIT0204 according to the manufacturer's instructions and DNase treatment was done using RNase Free DNase Qiagen; Cat#79254. RNA was amplified one round using MessageAmp II aRNA Kit ThermoFisher Scientific; Cat# AM1751. The RNA integrity was evaluated on the observation of a signature electropherogram pattern Bioanalyzer. A minimum of 5 10 ng of amplified RNA was used per sample for the construction of each library. RNA seq libraries were prepared by the National Research Council NRC  Saskatoon using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute  Prime  Fragment step using5 µl amplified mRNA the minimum amount was 5 10 ng mRNA as determined using Quant iT RiboGreen RNA Assay Kit Invitrogen. The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer Agilent Technologies Inc..,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP477408,,,Z6_R1.fastq.gz Z6_R2.fastq.gz,fastq fastq,7236720902.0,35825351.0,GSM7967333 r1,0:101 1:101,A:2065141509;C:1515489646;G:1508477450;T:2145425270;N:2187027,101,101,,,2065141509,1515489646,1508477450,2145425270,2187027,SRX22861017,SRS19836056,SRA1767043,"3B14 HSC, Anatomy and Cell Biology, University of Saskatchewan","3B14 HSC, Anatomy and Cell Biology, University of Saskatchewan",2,0.92486,0.92406,0.2589,0.2586,0.81836,0.81937,0.64846,0.64959,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Canada,2023-12-11,Larval,Larval,Bone or Cartilage,Skeletal Element
29166,SRR27180614,SRX22861016,SRS19836057,SRP477408,PRJNA1051145,laser captured chondrocyte transcriptomes from cranial base,GSE249932,Transcriptome Analysis,similar methods as in Gomez Picos et al. 2022 and Nguyen et al. 2023 Overall design: mRNA profiles of wild type Danio rerio chondrocytes,,pubmed:38117077,,Z3 WT,GSM7967332,,source name:laser captured cartilage without xxx from cranial base in occipital region|tissue:cartilage|age:6dpf|genotype:wild type|geo loc name:missing|collection date:missing,Z3 WT,The paired end Illumina reads were trimmed using Trimmomatic v0.36 Bolger et al. 2014. Mapped to the Danio rerio Zv9 fom Ensembl. TMM normalization Robinson and Oshlack 2010 was performed using edgeR. Cutoff of genes considered expressed was determined by calculationg the minimum value of the bimodal distribution of counts. Assembly: Danio rerio Ensembl Zv9 Supplementary files format and content: Comma delimited text file includes counts for wildtype samples,laser captured cartilage without xxx from cranial base in occipital region,N/A,RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit ThermoFisher Scientific; Cat# KIT0204 according to the manufacturer’s instructions and DNase treatment was done using RNase Free DNase Qiagen; Cat#79254. RNA was amplified one round using MessageAmp II aRNA Kit ThermoFisher Scientific; Cat# AM1751. The RNA integrity was evaluated on the observation of a signature electropherogram pattern Bioanalyzer. A minimum of 5 10 ng of amplified RNA was used per sample for the construction of each library. RNA seq libraries were prepared by the National Research Council NRC  Saskatoon using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute  Prime  Fragment step using5 µl amplified mRNA the minimum amount was 5 10 ng mRNA as determined using Quant iT RiboGreen RNA Assay Kit Invitrogen. The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer Agilent Technologies Inc..,standard conditions EM filled dishes at 28.5C,tissue:cartilage|age:6dpf|genotype:wild type,GSM7967332,GSM7967332: Z3 WT; Danio rerio; RNA Seq,GSM7967332 r1,GSM7967332,1,RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit ThermoFisher Scientific; Cat# KIT0204 according to the manufacturer's instructions and DNase treatment was done using RNase Free DNase Qiagen; Cat#79254. RNA was amplified one round using MessageAmp II aRNA Kit ThermoFisher Scientific; Cat# AM1751. The RNA integrity was evaluated on the observation of a signature electropherogram pattern Bioanalyzer. A minimum of 5 10 ng of amplified RNA was used per sample for the construction of each library. RNA seq libraries were prepared by the National Research Council NRC  Saskatoon using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute  Prime  Fragment step using5 µl amplified mRNA the minimum amount was 5 10 ng mRNA as determined using Quant iT RiboGreen RNA Assay Kit Invitrogen. The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer Agilent Technologies Inc..,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP477408,,,Z3_R1.fastq.gz Z3_R2.fastq.gz,fastq fastq,8154876754.0,40370677.0,GSM7967332 r1,0:101 1:101,A:2326535807;C:1739502467;G:1727655779;T:2358724699;N:2458002,101,101,,,2326535807,1739502467,1727655779,2358724699,2458002,SRX22861016,SRS19836057,SRA1767043,"3B14 HSC, Anatomy and Cell Biology, University of Saskatchewan","3B14 HSC, Anatomy and Cell Biology, University of Saskatchewan",2,0.91893,0.92052,0.27086,0.27178,0.83489,0.83615,0.7337,0.73303,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Canada,2023-12-11,Larval,Larval,Bone or Cartilage,Skeletal Element
29167,SRR27180615,SRX22861015,SRS19836055,SRP477408,PRJNA1051145,laser captured chondrocyte transcriptomes from cranial base,GSE249932,Transcriptome Analysis,similar methods as in Gomez Picos et al. 2022 and Nguyen et al. 2023 Overall design: mRNA profiles of wild type Danio rerio chondrocytes,,pubmed:38117077,,Z1 WT,GSM7967331,,source name:laser captured cartilage without xxx from cranial base in occipital region|tissue:cartilage|age:6dpf|genotype:wild type|geo loc name:missing|collection date:missing,Z1 WT,The paired end Illumina reads were trimmed using Trimmomatic v0.36 Bolger et al. 2014. Mapped to the Danio rerio Zv9 fom Ensembl. TMM normalization Robinson and Oshlack 2010 was performed using edgeR. Cutoff of genes considered expressed was determined by calculationg the minimum value of the bimodal distribution of counts. Assembly: Danio rerio Ensembl Zv9 Supplementary files format and content: Comma delimited text file includes counts for wildtype samples,laser captured cartilage without xxx from cranial base in occipital region,N/A,RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit ThermoFisher Scientific; Cat# KIT0204 according to the manufacturer’s instructions and DNase treatment was done using RNase Free DNase Qiagen; Cat#79254. RNA was amplified one round using MessageAmp II aRNA Kit ThermoFisher Scientific; Cat# AM1751. The RNA integrity was evaluated on the observation of a signature electropherogram pattern Bioanalyzer. A minimum of 5 10 ng of amplified RNA was used per sample for the construction of each library. RNA seq libraries were prepared by the National Research Council NRC  Saskatoon using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute  Prime  Fragment step using5 µl amplified mRNA the minimum amount was 5 10 ng mRNA as determined using Quant iT RiboGreen RNA Assay Kit Invitrogen. The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer Agilent Technologies Inc..,standard conditions EM filled dishes at 28.5C,tissue:cartilage|age:6dpf|genotype:wild type,GSM7967331,GSM7967331: Z1 WT; Danio rerio; RNA Seq,GSM7967331 r1,GSM7967331,1,RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit ThermoFisher Scientific; Cat# KIT0204 according to the manufacturer's instructions and DNase treatment was done using RNase Free DNase Qiagen; Cat#79254. RNA was amplified one round using MessageAmp II aRNA Kit ThermoFisher Scientific; Cat# AM1751. The RNA integrity was evaluated on the observation of a signature electropherogram pattern Bioanalyzer. A minimum of 5 10 ng of amplified RNA was used per sample for the construction of each library. RNA seq libraries were prepared by the National Research Council NRC  Saskatoon using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute  Prime  Fragment step using5 µl amplified mRNA the minimum amount was 5 10 ng mRNA as determined using Quant iT RiboGreen RNA Assay Kit Invitrogen. The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer Agilent Technologies Inc..,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP477408,,,Z1_R1.fastq.gz Z1_R2.fastq.gz,fastq fastq,9727948522.0,48158161.0,GSM7967331 r1,0:101 1:101,A:2710612972;C:2124743635;G:2101950141;T:2787702029;N:2939745,101,101,,,2710612972,2124743635,2101950141,2787702029,2939745,SRX22861015,SRS19836055,SRA1767043,"3B14 HSC, Anatomy and Cell Biology, University of Saskatchewan","3B14 HSC, Anatomy and Cell Biology, University of Saskatchewan",2,0.92553,0.92633,0.25474,0.25434,0.83362,0.83615,0.76464,0.75351,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Canada,2023-12-11,Larval,Larval,Bone or Cartilage,Skeletal Element
30210,SRR27722348,SRX23388314,SRS20249507,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,2 F5 NPs,,isolate:b1 F5|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,2 F5 NPs,2 F5 NPs,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701134_L1EGI0701134--WT_M5.R1.raw.fastq.gz L1EGI0701134_L1EGI0701134--WT_M5.R2.raw.fastq.gz,fastq fastq,6858985646.0,22711873.0,L1EGI0701134 L1EGI0701134  WT M5.R1.raw.fastq.gz,0:151 1:151,A:1775374486;C:1607590004;G:1736749854;T:1739241353;N:29949,151,151,,,1775374486,1607590004,1736749854,1739241353,29949,SRX23388314,SRS20249507,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30211,SRR27722349,SRX23388313,SRS20249506,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,2 F4 NPs,,isolate:b1 F4|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,2 F4 NPs,2 F4 NPs,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701133--WT_M4.R1.raw.fastq.gz L1EGI0701133--WT_M4.R2.raw.fastq.gz,fastq fastq,8367706978.0,27707639.0,L1EGI0701133  WT M4.R1.raw.fastq.gz,0:151 1:151,A:2190978299;C:1972956945;G:2068607164;T:2135130434;N:34136,151,151,,,2190978299,1972956945,2068607164,2135130434,34136,SRX23388313,SRS20249506,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30212,SRR27722350,SRX23388312,SRS20249505,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,2 F3 NPs,,isolate:b1 F3|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,2 F3 NPs,2 F3 NPs,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701132--WT_M3.R1.raw.fastq.gz L1EGI0701132--WT_M3.R2.raw.fastq.gz,fastq fastq,8356526334.0,27670617.0,L1EGI0701132  WT M3.R1.raw.fastq.gz,0:151 1:151,A:2162579680;C:1984443655;G:2083109306;T:2126359754;N:33939,151,151,,,2162579680,1984443655,2083109306,2126359754,33939,SRX23388312,SRS20249505,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30213,SRR27722351,SRX23388311,SRS20249504,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,2 F2 NPs,,isolate:b1 F2|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,2 F2 NPs,2 F2 NPs,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701131--WT_M2.R1.raw.fastq.gz L1EGI0701131--WT_M2.R2.raw.fastq.gz,fastq fastq,8143546874.0,26965387.0,L1EGI0701131  WT M2.R1.raw.fastq.gz,0:151 1:151,A:2114633540;C:1938964033;G:2015877300;T:2074038855;N:33146,151,151,,,2114633540,1938964033,2015877300,2074038855,33146,SRX23388311,SRS20249504,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30214,SRR27722352,SRX23388310,SRS20249503,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,2 F1 NPs,,isolate:b1 F1|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,2 F1 NPs,2 F1 NPs,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701130--WT_M1.R1.raw.fastq.gz L1EGI0701130--WT_M1.R2.raw.fastq.gz,fastq fastq,9004594174.0,29816537.0,L1EGI0701130  WT M1.R1.raw.fastq.gz,0:151 1:151,A:2356139884;C:2114457727;G:2228436842;T:2305522562;N:37159,151,151,,,2356139884,2114457727,2228436842,2305522562,37159,SRX23388310,SRS20249503,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30215,SRR27722353,SRX23388309,SRS20249502,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,1 F5 WT,,isolate:b1 F5|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,1 F5 WT,1 F5 WT,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701128--WT_F5.R1.raw.fastq.gz L1EGI0701128--WT_F5.R2.raw.fastq.gz,fastq fastq,9595399794.0,31772847.0,L1EGI0701128  WT F5.R1.raw.fastq.gz,0:151 1:151,A:2471647902;C:2293433569;G:2400056012;T:2430223486;N:38825,151,151,,,2471647902,2293433569,2400056012,2430223486,38825,SRX23388309,SRS20249502,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30216,SRR27722354,SRX23388308,SRS20249501,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,1 F4 WT,,isolate:b1 F4|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,1 F4 WT,1 F4 WT,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701127--WT_F4.R1.raw.fastq.gz L1EGI0701127--WT_F4.R2.raw.fastq.gz,fastq fastq,7628679456.0,25260528.0,L1EGI0701127  WT F4.R1.raw.fastq.gz,0:151 1:151,A:2006324404;C:1789150133;G:1873940582;T:1959232617;N:31720,151,151,,,2006324404,1789150133,1873940582,1959232617,31720,SRX23388308,SRS20249501,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30217,SRR27722355,SRX23388307,SRS20249500,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,1 F3 WT,,isolate:b1 F3|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,1 F3 WT,1 F3 WT,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701126--WT_F3.R1.raw.fastq.gz L1EGI0701126--WT_F3.R2.raw.fastq.gz,fastq fastq,8853107954.0,29314927.0,L1EGI0701126  WT F3.R1.raw.fastq.gz,0:151 1:151,A:2281668777;C:2122390553;G:2205818678;T:2243193679;N:36267,151,151,,,2281668777,2122390553,2205818678,2243193679,36267,SRX23388307,SRS20249500,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30218,SRR27722356,SRX23388306,SRS20249499,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,4 M5 NPs,,isolate:b1 M5|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,4 M5 NPs,4 M5 NPs,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701146--NPs_M5.R1.raw.fastq.gz L1EGI0701146--NPs_M5.R2.raw.fastq.gz,fastq fastq,7440341686.0,24636893.0,L1EGI0701146  NPs M5.R1.raw.fastq.gz,0:151 1:151,A:1926837197;C:1774447312;G:1865805171;T:1873221668;N:30338,151,151,,,1926837197,1774447312,1865805171,1873221668,30338,SRX23388306,SRS20249499,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30219,SRR27722357,SRX23388305,SRS20249498,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,4 M4 NPs,,isolate:b1 M4|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,4 M4 NPs,4 M4 NPs,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701145_L1EGI0701145--NPs_M4.R1.raw.fastq.gz L1EGI0701145_L1EGI0701145--NPs_M4.R2.raw.fastq.gz,fastq fastq,7482324518.0,24775909.0,L1EGI0701145 L1EGI0701145  NPs M4.R1.raw.fastq.gz,0:151 1:151,A:2074937139;C:1646093888;G:1749156387;T:2012102736;N:34368,151,151,,,2074937139,1646093888,1749156387,2012102736,34368,SRX23388305,SRS20249498,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30220,SRR27722358,SRX23388304,SRS20249497,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,4 M3 NPs,,isolate:b1 M3|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,4 M3 NPs,4 M3 NPs,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701144--NPs_M3.R1.raw.fastq.gz L1EGI0701144--NPs_M3.R2.raw.fastq.gz,fastq fastq,8439432280.0,27945140.0,L1EGI0701144  NPs M3.R1.raw.fastq.gz,0:151 1:151,A:2168219326;C:2022693060;G:2132822366;T:2115662612;N:34916,151,151,,,2168219326,2022693060,2132822366,2115662612,34916,SRX23388304,SRS20249497,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30221,SRR27722359,SRX23388303,SRS20249496,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,4 M2 NPs,,isolate:b1 M2|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,4 M2 NPs,4 M2 NPs,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701143--NPs_M2.R1.raw.fastq.gz L1EGI0701143--NPs_M2.R2.raw.fastq.gz,fastq fastq,7033808614.0,23290757.0,L1EGI0701143  NPs M2.R1.raw.fastq.gz,0:151 1:151,A:1828789906;C:1675914023;G:1760006026;T:1769068832;N:29827,151,151,,,1828789906,1675914023,1760006026,1769068832,29827,SRX23388303,SRS20249496,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30222,SRR27722360,SRX23388302,SRS20249495,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,4 M1 NPs,,isolate:b1 M1|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,4 M1 NPs,4 M1 NPs,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701142--NPs_M1.R1.raw.fastq.gz L1EGI0701142--NPs_M1.R2.raw.fastq.gz,fastq fastq,8087463964.0,26779682.0,L1EGI0701142  NPs M1.R1.raw.fastq.gz,0:151 1:151,A:2097695704;C:1931279917;G:2029894750;T:2028560473;N:33120,151,151,,,2097695704,1931279917,2029894750,2028560473,33120,SRX23388302,SRS20249495,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30223,SRR27722361,SRX23388301,SRS20249494,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,3 M5 WT,,isolate:b1 M5|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,3 M5 WT,3 M5 WT,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701140--NPs_F5.R1.raw.fastq.gz L1EGI0701140--NPs_F5.R2.raw.fastq.gz,fastq fastq,8478344376.0,28073988.0,L1EGI0701140  NPs F5.R1.raw.fastq.gz,0:151 1:151,A:2202734913;C:2015133130;G:2106431143;T:2154009977;N:35213,151,151,,,2202734913,2015133130,2106431143,2154009977,35213,SRX23388301,SRS20249494,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30224,SRR27722362,SRX23388300,SRS20249493,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,3 M4 WT,,isolate:b1 M4|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,3 M4 WT,3 M4 WT,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701139--NPs_F4.R1.raw.fastq.gz L1EGI0701139--NPs_F4.R2.raw.fastq.gz,fastq fastq,8569883596.0,28377098.0,L1EGI0701139  NPs F4.R1.raw.fastq.gz,0:151 1:151,A:2215047248;C:2038336388;G:2145335785;T:2171128844;N:35331,151,151,,,2215047248,2038336388,2145335785,2171128844,35331,SRX23388300,SRS20249493,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30225,SRR27722363,SRX23388299,SRS20249492,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,3 M3 WT,,isolate:b1 M3|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,3 M3 WT,3 M3 WT,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701138--NPs_F3.R1.raw.fastq.gz L1EGI0701138--NPs_F3.R2.raw.fastq.gz,fastq fastq,7930364168.0,26259484.0,L1EGI0701138  NPs F3.R1.raw.fastq.gz,0:151 1:151,A:2046759305;C:1898600276;G:1959125241;T:2025847086;N:32260,151,151,,,2046759305,1898600276,1959125241,2025847086,32260,SRX23388299,SRS20249492,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30226,SRR27722364,SRX23388298,SRS20249491,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,3 M2 WT,,isolate:b1 M2|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,3 M2 WT,3 M2 WT,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701137--NPs_F2.R1.raw.fastq.gz L1EGI0701137--NPs_F2.R2.raw.fastq.gz,fastq fastq,6914965272.0,22897236.0,L1EGI0701137  NPs F2.R1.raw.fastq.gz,0:151 1:151,A:1789644342;C:1644676301;G:1738643678;T:1741972870;N:28081,151,151,,,1789644342,1644676301,1738643678,1741972870,28081,SRX23388298,SRS20249491,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30227,SRR27722365,SRX23388297,SRS20249490,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,3 M1 WT,,isolate:b1 M1|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,3 M1 WT,3 M1 WT,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701136--NPs_F1.R1.raw.fastq.gz L1EGI0701136--NPs_F1.R2.raw.fastq.gz,fastq fastq,7957071840.0,26347920.0,L1EGI0701136  NPs F1.R1.raw.fastq.gz,0:151 1:151,A:2056500264;C:1899503313;G:1979706436;T:2021329536;N:32291,151,151,,,2056500264,1899503313,1979706436,2021329536,32291,SRX23388297,SRS20249490,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30228,SRR27722366,SRX23388296,SRS20249489,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,1 F2 WT,,isolate:b1 F2|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,1 F2 WT,1 F2 WT,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701125--WT_F2.R1.raw.fastq.gz L1EGI0701125--WT_F2.R2.raw.fastq.gz,fastq fastq,7960683760.0,26359880.0,L1EGI0701125  WT F2.R1.raw.fastq.gz,0:151 1:151,A:2087534093;C:1862286963;G:1962292721;T:2048536454;N:33529,151,151,,,2087534093,1862286963,1962292721,2048536454,33529,SRX23388296,SRS20249489,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
30229,SRR27722367,SRX23388295,SRS20249488,SRP485828,PRJNA1068830,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,PRJNA1068830,Other,Employing standard polystyrene NPs as the representative  the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.,,,,,1 F1 WT,,isolate:b1 F1|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate,,,,,,,,,skeletal toxicity studies of polystyrene nanoplastic in zebrafish,1 F1 WT,1 F1 WT,bone,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP485828,,,L1EGI0701124--WT_F1.R1.raw.fastq.gz L1EGI0701124--WT_F1.R2.raw.fastq.gz,fastq fastq,8373285522.0,27726111.0,L1EGI0701124  WT F1.R1.raw.fastq.gz,0:151 1:151,A:2148645285;C:1996284185;G:2121066399;T:2107255525;N:34128,151,151,,,2148645285,1996284185,2121066399,2107255525,34128,SRX23388295,SRS20249488,SRA1791477,zhejiang university|the college of animal science,zhejiang university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-01-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
34618,SRR32145149,SRX27491071,SRS23912869,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 4,GSM8760186,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760186,GSM8760186: kat6a Replicate 4; Danio rerio; RNA Seq,GSM8760186 r1,GSM8760186,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a4_S4_L001_R1_001.fastq.gz,fastq,1185101288.0,15593438.0,GSM8760186 r1,0:76,A:300559300;C:260467735;G:266433586;T:357432372;N:208295,76,,,,300559300,260467735,266433586,357432372,208295,SRX27491071,SRS23912869,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34619,SRR32145150,SRX27491071,SRS23912869,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 4,GSM8760186,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760186,GSM8760186: kat6a Replicate 4; Danio rerio; RNA Seq,GSM8760186 r1,GSM8760186,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a4_S4_L002_R1_001.fastq.gz,fastq,1131352948.0,14886223.0,GSM8760186 r2,0:76,A:286383575;C:248947288;G:254084926;T:341733278;N:203881,76,,,,286383575,248947288,254084926,341733278,203881,SRX27491071,SRS23912869,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34620,SRR32145151,SRX27491071,SRS23912869,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 4,GSM8760186,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760186,GSM8760186: kat6a Replicate 4; Danio rerio; RNA Seq,GSM8760186 r1,GSM8760186,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a4_S4_L003_R1_001.fastq.gz,fastq,1166160188.0,15344213.0,GSM8760186 r3,0:76,A:296592701;C:256034122;G:261605331;T:351825369;N:102665,76,,,,296592701,256034122,261605331,351825369,102665,SRX27491071,SRS23912869,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34621,SRR32145152,SRX27491071,SRS23912869,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 4,GSM8760186,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760186,GSM8760186: kat6a Replicate 4; Danio rerio; RNA Seq,GSM8760186 r1,GSM8760186,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a4_S4_L004_R1_001.fastq.gz,fastq,1123430480.0,14781980.0,GSM8760186 r4,0:76,A:285427665;C:246734929;G:251428534;T:339753027;N:86325,76,,,,285427665,246734929,251428534,339753027,86325,SRX27491071,SRS23912869,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34622,SRR32145153,SRX27491070,SRS23912868,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 3,GSM8760185,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760185,GSM8760185: kat6a Replicate 3; Danio rerio; RNA Seq,GSM8760185 r1,GSM8760185,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a3_S3_L001_R1_001.fastq.gz,fastq,1130086940.0,14869565.0,GSM8760185 r1,0:76,A:271600754;C:270119369;G:267701531;T:320468732;N:196554,76,,,,271600754,270119369,267701531,320468732,196554,SRX27491070,SRS23912868,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34623,SRR32145154,SRX27491070,SRS23912868,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 3,GSM8760185,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760185,GSM8760185: kat6a Replicate 3; Danio rerio; RNA Seq,GSM8760185 r1,GSM8760185,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a3_S3_L002_R1_001.fastq.gz,fastq,1084172604.0,14265429.0,GSM8760185 r2,0:76,A:260060383;C:259442661;G:256603224;T:307867713;N:198623,76,,,,260060383,259442661,256603224,307867713,198623,SRX27491070,SRS23912868,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34624,SRR32145155,SRX27491070,SRS23912868,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 3,GSM8760185,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760185,GSM8760185: kat6a Replicate 3; Danio rerio; RNA Seq,GSM8760185 r1,GSM8760185,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a3_S3_L003_R1_001.fastq.gz,fastq,1110196904.0,14607854.0,GSM8760185 r3,0:76,A:267507867;C:265237928;G:262455688;T:314899764;N:95657,76,,,,267507867,265237928,262455688,314899764,95657,SRX27491070,SRS23912868,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34625,SRR32145156,SRX27491070,SRS23912868,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 3,GSM8760185,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760185,GSM8760185: kat6a Replicate 3; Danio rerio; RNA Seq,GSM8760185 r1,GSM8760185,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a3_S3_L004_R1_001.fastq.gz,fastq,1075741468.0,14154493.0,GSM8760185 r4,0:76,A:259028301;C:257097498;G:253796080;T:305738292;N:81297,76,,,,259028301,257097498,253796080,305738292,81297,SRX27491070,SRS23912868,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34626,SRR32145157,SRX27491069,SRS23912867,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 2,GSM8760184,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760184,GSM8760184: kat6a Replicate 2; Danio rerio; RNA Seq,GSM8760184 r1,GSM8760184,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a2_S2_L001_R1_001.fastq.gz,fastq,1020140400.0,13422900.0,GSM8760184 r1,0:76,A:246705959;C:238000533;G:239066122;T:296188699;N:179087,76,,,,246705959,238000533,239066122,296188699,179087,SRX27491069,SRS23912867,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34627,SRR32145158,SRX27491069,SRS23912867,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 2,GSM8760184,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760184,GSM8760184: kat6a Replicate 2; Danio rerio; RNA Seq,GSM8760184 r1,GSM8760184,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a2_S2_L002_R1_001.fastq.gz,fastq,977643632.0,12863732.0,GSM8760184 r2,0:76,A:235933957;C:228339408;G:228898216;T:284296721;N:175330,76,,,,235933957,228339408,228898216,284296721,175330,SRX27491069,SRS23912867,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34628,SRR32145159,SRX27491069,SRS23912867,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 2,GSM8760184,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760184,GSM8760184: kat6a Replicate 2; Danio rerio; RNA Seq,GSM8760184 r1,GSM8760184,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a2_S2_L003_R1_001.fastq.gz,fastq,1003014712.0,13197562.0,GSM8760184 r3,0:76,A:243233308;C:233802542;G:234581740;T:291313383;N:83739,76,,,,243233308,233802542,234581740,291313383,83739,SRX27491069,SRS23912867,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34629,SRR32145160,SRX27491069,SRS23912867,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 2,GSM8760184,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760184,GSM8760184: kat6a Replicate 2; Danio rerio; RNA Seq,GSM8760184 r1,GSM8760184,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a2_S2_L004_R1_001.fastq.gz,fastq,971822564.0,12787139.0,GSM8760184 r4,0:76,A:235490570;C:226606386;G:226825751;T:282823868;N:75989,76,,,,235490570,226606386,226825751,282823868,75989,SRX27491069,SRS23912867,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34630,SRR32145161,SRX27491068,SRS23912866,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 1,GSM8760183,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760183,GSM8760183: kat6a Replicate 1; Danio rerio; RNA Seq,GSM8760183 r1,GSM8760183,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a1_S1_L001_R1_001.fastq.gz,fastq,1199414140.0,15781765.0,GSM8760183 r1,0:76,A:302128648;C:264050936;G:275501956;T:357525321;N:207279,76,,,,302128648,264050936,275501956,357525321,207279,SRX27491068,SRS23912866,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34631,SRR32145162,SRX27491068,SRS23912866,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 1,GSM8760183,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760183,GSM8760183: kat6a Replicate 1; Danio rerio; RNA Seq,GSM8760183 r1,GSM8760183,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a1_S1_L002_R1_001.fastq.gz,fastq,1146031360.0,15079360.0,GSM8760183 r2,0:76,A:288111631;C:252600982;G:262972849;T:342138841;N:207057,76,,,,288111631,252600982,262972849,342138841,207057,SRX27491068,SRS23912866,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34632,SRR32145163,SRX27491068,SRS23912866,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 1,GSM8760183,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760183,GSM8760183: kat6a Replicate 1; Danio rerio; RNA Seq,GSM8760183 r1,GSM8760183,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a1_S1_L003_R1_001.fastq.gz,fastq,1179501760.0,15519760.0,GSM8760183 r3,0:76,A:297785533;C:259437124;G:270403974;T:351772505;N:102624,76,,,,297785533,259437124,270403974,351772505,102624,SRX27491068,SRS23912866,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34633,SRR32145164,SRX27491068,SRS23912866,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,kat6a Replicate 1,GSM8760183,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,kat6a Replicate 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760183,GSM8760183: kat6a Replicate 1; Danio rerio; RNA Seq,GSM8760183 r1,GSM8760183,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,kat6a1_S1_L004_R1_001.fastq.gz,fastq,1138207844.0,14976419.0,GSM8760183 r4,0:76,A:287208643;C:250440049;G:260378372;T:340095505;N:85275,76,,,,287208643,250440049,260378372,340095505,85275,SRX27491068,SRS23912866,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34634,SRR32145165,SRX27491067,SRS23912865,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 4,GSM8760182,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760182,GSM8760182: WT Replicate 4; Danio rerio; RNA Seq,GSM8760182 r1,GSM8760182,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT3_S8_L001_R1_001.fastq.gz,fastq,1105608708.0,14547483.0,GSM8760182 r1,0:76,A:275003530;C:255171379;G:257731739;T:317503855;N:198205,76,,,,275003530,255171379,257731739,317503855,198205,SRX27491067,SRS23912865,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34635,SRR32145166,SRX27491067,SRS23912865,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 4,GSM8760182,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760182,GSM8760182: WT Replicate 4; Danio rerio; RNA Seq,GSM8760182 r1,GSM8760182,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT3_S8_L002_R1_001.fastq.gz,fastq,1057949108.0,13920383.0,GSM8760182 r2,0:76,A:262643868;C:244445110;G:246372974;T:304292800;N:194356,76,,,,262643868,244445110,246372974,304292800,194356,SRX27491067,SRS23912865,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34636,SRR32145167,SRX27491067,SRS23912865,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 4,GSM8760182,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760182,GSM8760182: WT Replicate 4; Danio rerio; RNA Seq,GSM8760182 r1,GSM8760182,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT3_S8_L003_R1_001.fastq.gz,fastq,1087749848.0,14312498.0,GSM8760182 r3,0:76,A:271320835;C:250818322;G:253044246;T:312473326;N:93119,76,,,,271320835,250818322,253044246,312473326,93119,SRX27491067,SRS23912865,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34637,SRR32145168,SRX27491067,SRS23912865,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 4,GSM8760182,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760182,GSM8760182: WT Replicate 4; Danio rerio; RNA Seq,GSM8760182 r1,GSM8760182,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT3_S8_L004_R1_001.fastq.gz,fastq,1051964032.0,13841632.0,GSM8760182 r4,0:76,A:262165724;C:242738788;G:244236708;T:302743784;N:79028,76,,,,262165724,242738788,244236708,302743784,79028,SRX27491067,SRS23912865,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34638,SRR32145169,SRX27491066,SRS23912864,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 3,GSM8760181,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760181,GSM8760181: WT Replicate 3; Danio rerio; RNA Seq,GSM8760181 r1,GSM8760181,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT3_S7_L001_R1_001.fastq.gz,fastq,1039833292.0,13682017.0,GSM8760181 r1,0:76,A:250507910;C:247806634;G:245922610;T:295415371;N:180767,76,,,,250507910,247806634,245922610,295415371,180767,SRX27491066,SRS23912864,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34639,SRR32145170,SRX27491066,SRS23912864,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 3,GSM8760181,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760181,GSM8760181: WT Replicate 3; Danio rerio; RNA Seq,GSM8760181 r1,GSM8760181,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT3_S7_L002_R1_001.fastq.gz,fastq,997262196.0,13121871.0,GSM8760181 r2,0:76,A:239743869;C:237950132;G:235660496;T:283726570;N:181129,76,,,,239743869,237950132,235660496,283726570,181129,SRX27491066,SRS23912864,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34640,SRR32145171,SRX27491066,SRS23912864,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 3,GSM8760181,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760181,GSM8760181: WT Replicate 3; Danio rerio; RNA Seq,GSM8760181 r1,GSM8760181,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT3_S7_L003_R1_001.fastq.gz,fastq,1021625592.0,13442442.0,GSM8760181 r3,0:76,A:246769441;C:243242872;G:241137871;T:290388153;N:87255,76,,,,246769441,243242872,241137871,290388153,87255,SRX27491066,SRS23912864,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34641,SRR32145172,SRX27491066,SRS23912864,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 3,GSM8760181,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760181,GSM8760181: WT Replicate 3; Danio rerio; RNA Seq,GSM8760181 r1,GSM8760181,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT3_S7_L004_R1_001.fastq.gz,fastq,988410400.0,13005400.0,GSM8760181 r4,0:76,A:238549859;C:235494730;G:232864346;T:281426699;N:74766,76,,,,238549859,235494730,232864346,281426699,74766,SRX27491066,SRS23912864,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34642,SRR32145173,SRX27491065,SRS23912863,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 2,GSM8760180,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760180,GSM8760180: WT Replicate 2; Danio rerio; RNA Seq,GSM8760180 r1,GSM8760180,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT2_S6_L001_R1_001.fastq.gz,fastq,1197864500.0,15761375.0,GSM8760180 r1,0:76,A:284440503;C:291285146;G:286388620;T:335544162;N:206069,76,,,,284440503,291285146,286388620,335544162,206069,SRX27491065,SRS23912863,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34643,SRR32145174,SRX27491065,SRS23912863,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 2,GSM8760180,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760180,GSM8760180: WT Replicate 2; Danio rerio; RNA Seq,GSM8760180 r1,GSM8760180,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT2_S6_L002_R1_001.fastq.gz,fastq,1150109368.0,15133018.0,GSM8760180 r2,0:76,A:272466884;C:280134047;G:274738822;T:322560009;N:209606,76,,,,272466884,280134047,274738822,322560009,209606,SRX27491065,SRS23912863,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34644,SRR32145175,SRX27491065,SRS23912863,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 2,GSM8760180,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760180,GSM8760180: WT Replicate 2; Danio rerio; RNA Seq,GSM8760180 r1,GSM8760180,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT2_S6_L003_R1_001.fastq.gz,fastq,1181538408.0,15546558.0,GSM8760180 r3,0:76,A:281618798;C:286909225;G:281700417;T:331210989;N:98979,76,,,,281618798,286909225,281700417,331210989,98979,SRX27491065,SRS23912863,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34645,SRR32145176,SRX27491065,SRS23912863,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 2,GSM8760180,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760180,GSM8760180: WT Replicate 2; Danio rerio; RNA Seq,GSM8760180 r1,GSM8760180,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT2_S6_L004_R1_001.fastq.gz,fastq,1144519796.0,15059471.0,GSM8760180 r4,0:76,A:272627373;C:278113659;G:272292478;T:321399688;N:86598,76,,,,272627373,278113659,272292478,321399688,86598,SRX27491065,SRS23912863,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34646,SRR32145177,SRX27491064,SRS23912862,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 1,GSM8760179,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760179,GSM8760179: WT Replicate 1; Danio rerio; RNA Seq,GSM8760179 r1,GSM8760179,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT1_S5_L001_R1_001.fastq.gz,fastq,1231111156.0,16198831.0,GSM8760179 r1,0:76,A:302054822;C:285868196;G:294755776;T:348218223;N:214139,76,,,,302054822,285868196,294755776,348218223,214139,SRX27491064,SRS23912862,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34647,SRR32145178,SRX27491064,SRS23912862,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 1,GSM8760179,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760179,GSM8760179: WT Replicate 1; Danio rerio; RNA Seq,GSM8760179 r1,GSM8760179,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT1_S5_L002_R1_001.fastq.gz,fastq,1182939392.0,15564992.0,GSM8760179 r2,0:76,A:289611553;C:275053581;G:283000505;T:335062758;N:210995,76,,,,289611553,275053581,283000505,335062758,210995,SRX27491064,SRS23912862,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34648,SRR32145179,SRX27491064,SRS23912862,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 1,GSM8760179,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760179,GSM8760179: WT Replicate 1; Danio rerio; RNA Seq,GSM8760179 r1,GSM8760179,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT1_S5_L003_R1_001.fastq.gz,fastq,1211221728.0,15937128.0,GSM8760179 r3,0:76,A:297941702;C:281047445;G:289384552;T:342744260;N:103769,76,,,,297941702,281047445,289384552,342744260,103769,SRX27491064,SRS23912862,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
34649,SRR32145180,SRX27491064,SRS23912862,SRP560249,PRJNA1216300,Insulin like growth factor signalling regulates zebrafish lymphatic vessel development,GSE288160,Transcriptome Analysis,RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene   pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.,,,,WT Replicate 1,GSM8760179,,tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing,WT Replicate 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column,Chondrocyte,,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.,cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry,GSM8760179,GSM8760179: WT Replicate 1; Danio rerio; RNA Seq,GSM8760179 r1,GSM8760179,1,At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP560249,,,WT1_S5_L004_R1_001.fastq.gz,fastq,1173801836.0,15444761.0,GSM8760179 r4,0:76,A:288534595;C:272469282;G:279986497;T:332720262;N:91200,76,,,,288534595,272469282,279986497,332720262,91200,SRX27491064,SRS23912862,SRA2062832,"Molecular Medicine and Pathology, University of Auckland","Molecular Medicine and Pathology, University of Auckland",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,New Zealand,2025-01-27,Larval,Larval,Bone or Cartilage,Skeletal Element
38060,SRR1524244,SRX661009,SRS665984,SRP044781,PRJNA255848,Danio rerio Transcriptome,PRJNA255848,Transcriptome Analysis,Transcriptome analysis of 12 zebrafish tissues,parent bioproject:PRJNA255979,pubmed:27189481,Zebrafish Bones,Zebrafish B1s,F Dr 8,,strain:AB|age:5 month|biomaterial provider:INRA|sex:female|tissue:B1s|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish B1s,F Dr 8,F Dr 8,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_8_ACAGTG_L003_R2.fastq.gz F_Dr_8_ACAGTG_L003_R1.fastq.gz,fastq fastq,19343193000.0,96715965.0,F Dr 8 files,0:100 1:100,A:5011655819;C:4570121318;G:4634671917;T:4933523152;N:193220794,100,100,,,5011655819,4570121318,4634671917,4933523152,193220794,SRX661009,SRS665984,SRA176464,INRA|Fish Physiology and Genomics,INRA PhyloFish,2,0.88337,0.91338,0.05259,0.05508,0.75103,0.75317,0.51459,0.51744,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,France,2014-07-26,Adult,Adult,Bone or Cartilage,Skeletal Element
53148,SRR9692022,SRX6451056,SRS5104327,SRP214773,PRJNA554788,Gene expression analysis in the zebrafish fractured scale,GSE134330,Transcriptome Analysis,Bone is a connective tissue which undergoes continuous remodeling  including bone resorption and formation by osteoclasts OCs and osteoblasts OBs  respectively. Recently  extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs  OCs  and bone matrix  providing an elegant model to visualize OC OB communication. Here  we developed a double transgenic zebrafish line  trap:GFP; osterix:mCherry  which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer  respectively. Utilizing this double transgenic line  in combination with Hoechst 33342 Hoe staining  we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry  GFP– mCh+ Hoehigh OB fraction  GFPlow mCh+ Hoehigh OC precursor pOC fraction  GFPhigh Hoehigh mature OC mOC fraction  and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study  we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each  fraction. Overall design: mRNA profiles of isolated OBs  pOCs   mOCs  and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.,,pubmed:32327701,,EV 2,GSM3942348,,source name:osteoblast derived extracellular vesicles|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblast derived extracellular vesicles|molecule type:Amplified RNA,EV 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,osteoblast derived extracellular vesicles,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblast derived extracellular vesicles|molecule type:Amplified RNA,GSM3942348,GSM3942348: EV 2; Danio rerio; RNA Seq,GSM3942348,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP214773,,,EV_2_R1.fastq.gz EV_2_R2.fastq.gz,fastq fastq,6759957000.0,22533190.0,GSM3942348 r1,0:150 1:150,A:1706593126;C:1699056754;G:1646763192;T:1707067337;N:476591,150,150,,,1706593126,1699056754,1646763192,1707067337,476591,SRX6451056,SRS5104327,SRA921382,GEO,Kanazawa University,2,0.94501,0.94549,0.02885,0.03033,0.80458,0.80957,0.48799,0.50474,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-07-16,Adult,Adult,Bone or Cartilage,Skeletal Element
53149,SRR9692021,SRX6451055,SRS5104326,SRP214773,PRJNA554788,Gene expression analysis in the zebrafish fractured scale,GSE134330,Transcriptome Analysis,Bone is a connective tissue which undergoes continuous remodeling  including bone resorption and formation by osteoclasts OCs and osteoblasts OBs  respectively. Recently  extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs  OCs  and bone matrix  providing an elegant model to visualize OC OB communication. Here  we developed a double transgenic zebrafish line  trap:GFP; osterix:mCherry  which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer  respectively. Utilizing this double transgenic line  in combination with Hoechst 33342 Hoe staining  we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry  GFP– mCh+ Hoehigh OB fraction  GFPlow mCh+ Hoehigh OC precursor pOC fraction  GFPhigh Hoehigh mature OC mOC fraction  and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study  we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each  fraction. Overall design: mRNA profiles of isolated OBs  pOCs   mOCs  and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.,,pubmed:32327701,,EV 1,GSM3942347,,source name:osteoblast derived extracellular vesicles|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblast derived extracellular vesicles|molecule type:Amplified RNA,EV 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,osteoblast derived extracellular vesicles,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblast derived extracellular vesicles|molecule type:Amplified RNA,GSM3942347,GSM3942347: EV 1; Danio rerio; RNA Seq,GSM3942347,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP214773,,,EV_1_R1.fastq.gz EV_1_R2.fastq.gz,fastq fastq,6368980200.0,21229934.0,GSM3942347 r1,0:150 1:150,A:1609224577;C:1593521490;G:1569729629;T:1596056057;N:448447,150,150,,,1609224577,1593521490,1569729629,1596056057,448447,SRX6451055,SRS5104326,SRA921382,GEO,Kanazawa University,2,0.93738,0.93601,0.02919,0.03087,0.79669,0.80312,0.50627,0.50567,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-07-16,Adult,Adult,Bone or Cartilage,Skeletal Element
53154,SRR9692016,SRX6451050,SRS5104321,SRP214773,PRJNA554788,Gene expression analysis in the zebrafish fractured scale,GSE134330,Transcriptome Analysis,Bone is a connective tissue which undergoes continuous remodeling  including bone resorption and formation by osteoclasts OCs and osteoblasts OBs  respectively. Recently  extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs  OCs  and bone matrix  providing an elegant model to visualize OC OB communication. Here  we developed a double transgenic zebrafish line  trap:GFP; osterix:mCherry  which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer  respectively. Utilizing this double transgenic line  in combination with Hoechst 33342 Hoe staining  we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry  GFP– mCh+ Hoehigh OB fraction  GFPlow mCh+ Hoehigh OC precursor pOC fraction  GFPhigh Hoehigh mature OC mOC fraction  and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study  we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each  fraction. Overall design: mRNA profiles of isolated OBs  pOCs   mOCs  and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.,,pubmed:32327701,,OB 2,GSM3942342,,source name:osteoblasts|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblasts|molecule type:Amplified RNA,OB 2,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,osteoblasts,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblasts|molecule type:Amplified RNA,GSM3942342,GSM3942342: OB 2; Danio rerio; RNA Seq,GSM3942342,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP214773,,,OB_2_R1.fastq.gz OB_2_R2.fastq.gz,fastq fastq,4566907200.0,15223024.0,GSM3942342 r1,0:150 1:150,A:1133280984;C:1162119484;G:1119861724;T:1151514772;N:130236,150,150,,,1133280984,1162119484,1119861724,1151514772,130236,SRX6451050,SRS5104321,SRA921382,GEO,Kanazawa University,2,0.9502,0.9473,0.0382,0.04036,0.77853,0.78719,0.47336,0.4862,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-07-16,Adult,Adult,Bone or Cartilage,Skeletal Element
53155,SRR9692015,SRX6451049,SRS5104320,SRP214773,PRJNA554788,Gene expression analysis in the zebrafish fractured scale,GSE134330,Transcriptome Analysis,Bone is a connective tissue which undergoes continuous remodeling  including bone resorption and formation by osteoclasts OCs and osteoblasts OBs  respectively. Recently  extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs  OCs  and bone matrix  providing an elegant model to visualize OC OB communication. Here  we developed a double transgenic zebrafish line  trap:GFP; osterix:mCherry  which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer  respectively. Utilizing this double transgenic line  in combination with Hoechst 33342 Hoe staining  we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry  GFP– mCh+ Hoehigh OB fraction  GFPlow mCh+ Hoehigh OC precursor pOC fraction  GFPhigh Hoehigh mature OC mOC fraction  and mCh+ Hoe– OB derived extracellular vesicle EV fraction. In this study  we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each  fraction. Overall design: mRNA profiles of isolated OBs  pOCs   mOCs  and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.,,pubmed:32327701,,OB 1,GSM3942341,,source name:osteoblasts|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblasts|molecule type:Amplified RNA,OB 1,Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.,osteoblasts,,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the 3’ ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblasts|molecule type:Amplified RNA,GSM3942341,GSM3942341: OB 1; Danio rerio; RNA Seq,GSM3942341,,1,Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic polycytidylic acid  and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer  which contains oligo dT  T7 promoter  and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara  a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer  which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer  which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP214773,,,OB_1_R1.fastq.gz OB_1_R2.fastq.gz,fastq fastq,3924215700.0,13080719.0,GSM3942341 r1,0:150 1:150,A:983923789;C:989882668;G:965519773;T:984780602;N:108868,150,150,,,983923789,989882668,965519773,984780602,108868,SRX6451049,SRS5104320,SRA921382,GEO,Kanazawa University,2,0.95148,0.94857,0.03822,0.04077,0.77705,0.78729,0.48248,0.49117,150,150,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,nextera,sc,single_cell_plate,quartzseq,,Japan,2019-07-16,Adult,Adult,Bone or Cartilage,Skeletal Element
58579,SRR11425295,SRX8003661,SRS6377641,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus  by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin  we could sort osteoblasts into separate Erk+ and Erk  populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically  dusp2  dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal  which anti correlates with Erk activity.,,pubmed:33408418,,high Erk activity; rep1,GSM4433141,,tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,high Erk activity; rep1,Reads were trimmed by Trim Galore 0.4.1  with  q 15   paired and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,high Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially  events were gated using Forward versus Side Scatter Areas 488 nm laser. Then  single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally  H2A mCherry+ Venus hGeminin  and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales  in three rows  from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp  all regenerating scales were plucked  and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade   Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min  500 µl of supernatant was removed  quenched with 65µl sheep serum Sigma S2263 on ice  and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,GSM4433141,GSM4433141: high Erk activity; rep1; Danio rerio; RNA Seq,GSM4433141,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433141,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,3G_plus_1.fq.gz 3G_plus_2.fq.gz,fastq fastq,4698595200.0,46985952.0,GSM4433141 r1,0:100 1:100,A:1261622105;C:1085007643;G:1066886112;T:1285079340;N:0,100,100,,,1261622105,1085007643,1066886112,1285079340,0,SRX8003661,SRS6377641,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.86576,,0.11767,,0.81262,,0.52377,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
58580,SRR11425294,SRX8003660,SRS6377640,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus  by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin  we could sort osteoblasts into separate Erk+ and Erk  populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically  dusp2  dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal  which anti correlates with Erk activity.,,pubmed:33408418,,low Erk activity; rep3,GSM4433140,,tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,low Erk activity; rep3,Reads were trimmed by Trim Galore 0.4.1  with  q 15   paired and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,low Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially  events were gated using Forward versus Side Scatter Areas 488 nm laser. Then  single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally  H2A mCherry+ Venus hGeminin  and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales  in three rows  from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp  all regenerating scales were plucked  and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade   Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min  500 µl of supernatant was removed  quenched with 65µl sheep serum Sigma S2263 on ice  and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,GSM4433140,GSM4433140: low Erk activity; rep3; Danio rerio; RNA Seq,GSM4433140,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433140,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,6B_minus_1.fq.gz 6B_minus_2.fq.gz,fastq fastq,4707217000.0,47072170.0,GSM4433140 r1,0:100 1:100,A:1268188059;C:1086056259;G:1067448053;T:1285524629;N:0,100,100,,,1268188059,1086056259,1067448053,1285524629,0,SRX8003660,SRS6377640,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.88883,,0.05585,,0.82071,,0.47905,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
58581,SRR11425293,SRX8003659,SRS6377639,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus  by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin  we could sort osteoblasts into separate Erk+ and Erk  populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically  dusp2  dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal  which anti correlates with Erk activity.,,pubmed:33408418,,low Erk activity; rep2,GSM4433139,,tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,low Erk activity; rep2,Reads were trimmed by Trim Galore 0.4.1  with  q 15   paired and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,low Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially  events were gated using Forward versus Side Scatter Areas 488 nm laser. Then  single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally  H2A mCherry+ Venus hGeminin  and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales  in three rows  from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp  all regenerating scales were plucked  and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade   Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min  500 µl of supernatant was removed  quenched with 65µl sheep serum Sigma S2263 on ice  and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,GSM4433139,GSM4433139: low Erk activity; rep2; Danio rerio; RNA Seq,GSM4433139,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,5G_minus_1.fq.gz 5G_minus_2.fq.gz,fastq fastq,4705295600.0,47052956.0,GSM4433139 r1,0:100 1:100,A:1240779500;C:1112511484;G:1096653049;T:1255351567;N:0,100,100,,,1240779500,1112511484,1096653049,1255351567,0,SRX8003659,SRS6377639,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.89254,,0.04065,,0.81197,,0.46307,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
58582,SRR11425292,SRX8003658,SRS6377638,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus  by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin  we could sort osteoblasts into separate Erk+ and Erk  populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically  dusp2  dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal  which anti correlates with Erk activity.,,pubmed:33408418,,low Erk activity; rep1,GSM4433138,,tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,low Erk activity; rep1,Reads were trimmed by Trim Galore 0.4.1  with  q 15   paired and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,low Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially  events were gated using Forward versus Side Scatter Areas 488 nm laser. Then  single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally  H2A mCherry+ Venus hGeminin  and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales  in three rows  from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp  all regenerating scales were plucked  and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade   Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min  500 µl of supernatant was removed  quenched with 65µl sheep serum Sigma S2263 on ice  and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,GSM4433138,GSM4433138: low Erk activity; rep1; Danio rerio; RNA Seq,GSM4433138,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433138,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,3G_minus_1.fq.gz 3G_minus_2.fq.gz,fastq fastq,4707783400.0,47077834.0,GSM4433138 r1,0:100 1:100,A:1275040914;C:1077730597;G:1059242617;T:1295769272;N:0,100,100,,,1275040914,1077730597,1059242617,1295769272,0,SRX8003658,SRS6377638,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.8629,,0.13994,,0.7838,,0.50568,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
58583,SRR11425297,SRX8003657,SRS6377637,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus  by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin  we could sort osteoblasts into separate Erk+ and Erk  populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically  dusp2  dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal  which anti correlates with Erk activity.,,pubmed:33408418,,high Erk activity; rep3,GSM4433143,,tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,high Erk activity; rep3,Reads were trimmed by Trim Galore 0.4.1  with  q 15   paired and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,high Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially  events were gated using Forward versus Side Scatter Areas 488 nm laser. Then  single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally  H2A mCherry+ Venus hGeminin  and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales  in three rows  from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp  all regenerating scales were plucked  and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade   Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min  500 µl of supernatant was removed  quenched with 65µl sheep serum Sigma S2263 on ice  and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,GSM4433143,GSM4433143: high Erk activity; rep3; Danio rerio; RNA Seq,GSM4433143,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433143,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,6B_plus_1.fq.gz 6B_plus_2.fq.gz,fastq fastq,4703728000.0,47037280.0,GSM4433143 r1,0:100 1:100,A:1231849303;C:1116643672;G:1102072724;T:1253162301;N:0,100,100,,,1231849303,1116643672,1102072724,1253162301,0,SRX8003657,SRS6377637,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.89702,,0.07131,,0.82978,,0.49499,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
58584,SRR11425296,SRX8003656,SRS6377636,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus  by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin  we could sort osteoblasts into separate Erk+ and Erk  populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically  dusp2  dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal  which anti correlates with Erk activity.,,pubmed:33408418,,high Erk activity; rep2,GSM4433142,,tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,high Erk activity; rep2,Reads were trimmed by Trim Galore 0.4.1  with  q 15   paired and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,high Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially  events were gated using Forward versus Side Scatter Areas 488 nm laser. Then  single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally  H2A mCherry+ Venus hGeminin  and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales  in three rows  from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp  all regenerating scales were plucked  and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade   Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min  500 µl of supernatant was removed  quenched with 65µl sheep serum Sigma S2263 on ice  and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,GSM4433142,GSM4433142: high Erk activity; rep2; Danio rerio; RNA Seq,GSM4433142,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433142,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,5G_plus_1.fq.gz 5G_plus_2.fq.gz,fastq fastq,4708623600.0,47086236.0,GSM4433142 r1,0:100 1:100,A:1200601624;C:1150903127;G:1136628277;T:1220490572;N:0,100,100,,,1200601624,1150903127,1136628277,1220490572,0,SRX8003656,SRS6377636,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.90729,,0.03751,,0.84433,,0.50342,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element
59343,SRR11862830,SRX8413198,SRS6725509,SRP265073,PRJNA635584,Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton,GSE151354,Transcriptome Analysis,The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD  which is characterized by skeletal defects including scoliosis  large epiphyses  wide growth plates  and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification  yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint  as well as severe dysmorphologies of the facial skeleton  skullcap  and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis  indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently  we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants  including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1  which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants,,pubmed:33462117,,nkx3.2 mutant cartilage,GSM4575943,,tissue:cartilage|strain:Tgfli1a:EGFPy1; Tgsox10:DsRedel10|genotype:nkx3.2 el802/el802|age:22 dpf,nkx3.2 mutant cartilage,Reads were aligned to z11 genome using Cell Ranger 3. Genome build: z11 Supplementary files format and content: barcode  gene and matrix files from Cell Ranger alignment and trimming,cartilage,,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,,strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:nkx3.2 el802/el802|age:22 dpf,GSM4575943,GSM4575943: nkx3.2 mutant cartilage; Danio rerio; RNA Seq,GSM4575943,,1,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,GEO Accession:GSM4575943,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP265073,,,Nkx3-2-MUT-1_S5_R1_001.fastq.gz Nkx3-2-MUT-1_S5_R2_001.fastq.gz,fastq fastq,9697124900.0,65763725.0,GSM4575943 r1,0:27 1:120.45,A:2738148127;C:2079798183;G:2363549380;T:2485374716;N:30254494,27,120,,,2738148127,2079798183,2363549380,2485374716,30254494,SRX8413198,SRS6725509,SRA1080696,GEO,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",2,0.00401,0.94743,0.00111,0.12105,0.99271,0.87099,0.53745,0.48087,27,121,T,B,sc-like readlen,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-28,Larval,Larval,Bone or Cartilage,Skeletal Element
59344,SRR11862831,SRX8413198,SRS6725509,SRP265073,PRJNA635584,Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton,GSE151354,Transcriptome Analysis,The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD  which is characterized by skeletal defects including scoliosis  large epiphyses  wide growth plates  and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification  yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint  as well as severe dysmorphologies of the facial skeleton  skullcap  and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis  indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently  we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants  including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1  which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants,,pubmed:33462117,,nkx3.2 mutant cartilage,GSM4575943,,tissue:cartilage|strain:Tgfli1a:EGFPy1; Tgsox10:DsRedel10|genotype:nkx3.2 el802/el802|age:22 dpf,nkx3.2 mutant cartilage,Reads were aligned to z11 genome using Cell Ranger 3. Genome build: z11 Supplementary files format and content: barcode  gene and matrix files from Cell Ranger alignment and trimming,cartilage,,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,,strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:nkx3.2 el802/el802|age:22 dpf,GSM4575943,GSM4575943: nkx3.2 mutant cartilage; Danio rerio; RNA Seq,GSM4575943,,1,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,GEO Accession:GSM4575943,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP265073,,,Nkx3-2-MUT-2_S6_R1_001.fastq.gz Nkx3-2-MUT-2_S6_R2_001.fastq.gz,fastq fastq,8288960388.0,56212365.0,GSM4575943 r2,0:27 1:120.46,A:2329428215;C:1772611501;G:2036479311;T:2124708625;N:25732736,27,120,,,2329428215,1772611501,2036479311,2124708625,25732736,SRX8413198,SRS6725509,SRA1080696,GEO,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",2,0.00387,0.94449,0.00091,0.12074,0.99287,0.87207,0.52767,0.48355,27,121,T,B,sc-like readlen,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-28,Larval,Larval,Bone or Cartilage,Skeletal Element
59345,SRR11862832,SRX8413198,SRS6725509,SRP265073,PRJNA635584,Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton,GSE151354,Transcriptome Analysis,The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD  which is characterized by skeletal defects including scoliosis  large epiphyses  wide growth plates  and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification  yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint  as well as severe dysmorphologies of the facial skeleton  skullcap  and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis  indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently  we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants  including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1  which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants,,pubmed:33462117,,nkx3.2 mutant cartilage,GSM4575943,,tissue:cartilage|strain:Tgfli1a:EGFPy1; Tgsox10:DsRedel10|genotype:nkx3.2 el802/el802|age:22 dpf,nkx3.2 mutant cartilage,Reads were aligned to z11 genome using Cell Ranger 3. Genome build: z11 Supplementary files format and content: barcode  gene and matrix files from Cell Ranger alignment and trimming,cartilage,,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,,strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:nkx3.2 el802/el802|age:22 dpf,GSM4575943,GSM4575943: nkx3.2 mutant cartilage; Danio rerio; RNA Seq,GSM4575943,,1,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,GEO Accession:GSM4575943,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP265073,,,Nkx3-2-MUT-3_S7_R1_001.fastq.gz Nkx3-2-MUT-3_S7_R2_001.fastq.gz,fastq fastq,10287717159.0,69768062.0,GSM4575943 r3,0:27 1:120.46,A:2893541462;C:2211093397;G:2523388252;T:2627515640;N:32178408,27,120,,,2893541462,2211093397,2523388252,2627515640,32178408,SRX8413198,SRS6725509,SRA1080696,GEO,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",2,0.00413,0.94417,0.00109,0.11868,0.99338,0.87274,0.57301,0.47692,27,121,T,B,sc-like readlen,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-28,Larval,Larval,Bone or Cartilage,Skeletal Element
59346,SRR11862833,SRX8413198,SRS6725509,SRP265073,PRJNA635584,Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton,GSE151354,Transcriptome Analysis,The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD  which is characterized by skeletal defects including scoliosis  large epiphyses  wide growth plates  and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification  yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint  as well as severe dysmorphologies of the facial skeleton  skullcap  and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis  indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently  we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants  including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1  which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants,,pubmed:33462117,,nkx3.2 mutant cartilage,GSM4575943,,tissue:cartilage|strain:Tgfli1a:EGFPy1; Tgsox10:DsRedel10|genotype:nkx3.2 el802/el802|age:22 dpf,nkx3.2 mutant cartilage,Reads were aligned to z11 genome using Cell Ranger 3. Genome build: z11 Supplementary files format and content: barcode  gene and matrix files from Cell Ranger alignment and trimming,cartilage,,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,,strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:nkx3.2 el802/el802|age:22 dpf,GSM4575943,GSM4575943: nkx3.2 mutant cartilage; Danio rerio; RNA Seq,GSM4575943,,1,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,GEO Accession:GSM4575943,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP265073,,,Nkx3-2-MUT-4_S8_R1_001.fastq.gz Nkx3-2-MUT-4_S8_R2_001.fastq.gz,fastq fastq,11403239527.0,77332826.0,GSM4575943 r4,0:27 1:120.46,A:3213260011;C:2448235155;G:2783221057;T:2922954756;N:35568548,27,120,,,3213260011,2448235155,2783221057,2922954756,35568548,SRX8413198,SRS6725509,SRA1080696,GEO,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",2,0.00403,0.9454,0.00096,0.11889,0.99277,0.87249,0.52252,0.48389,27,121,T,B,sc-like readlen,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-28,Larval,Larval,Bone or Cartilage,Skeletal Element
59347,SRR11862826,SRX8413197,SRS6725508,SRP265073,PRJNA635584,Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton,GSE151354,Transcriptome Analysis,The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD  which is characterized by skeletal defects including scoliosis  large epiphyses  wide growth plates  and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification  yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint  as well as severe dysmorphologies of the facial skeleton  skullcap  and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis  indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently  we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants  including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1  which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants,,pubmed:33462117,,WT cartilage,GSM4575942,,tissue:cartilage|strain:Tgfli1a:EGFPy1; Tgsox10:DsRedel10|genotype:WT|age:21 dpf,WT cartilage,Reads were aligned to z11 genome using Cell Ranger 3. Genome build: z11 Supplementary files format and content: barcode  gene and matrix files from Cell Ranger alignment and trimming,cartilage,,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,,strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:WT|age:21 dpf,GSM4575942,GSM4575942: WT cartilage; Danio rerio; RNA Seq,GSM4575942,,1,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,GEO Accession:GSM4575942,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP265073,,,Nkx3-2-WT-1_S1_R1_001.fastq.gz Nkx3-2-WT-1_S1_R2_001.fastq.gz,fastq fastq,5536576254.0,37550556.0,GSM4575942 r1,0:27 1:120.44,A:1572836902;C:1170801448;G:1342556738;T:1433261598;N:17119568,27,120,,,1572836902,1170801448,1342556738,1433261598,17119568,SRX8413197,SRS6725508,SRA1080696,GEO,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",2,0.00474,0.94009,0.00117,0.13657,0.99214,0.87099,0.55795,0.47023,27,120,T,B,sc-like readlen,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-28,Larval,Larval,Bone or Cartilage,Skeletal Element
59348,SRR11862827,SRX8413197,SRS6725508,SRP265073,PRJNA635584,Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton,GSE151354,Transcriptome Analysis,The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD  which is characterized by skeletal defects including scoliosis  large epiphyses  wide growth plates  and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification  yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint  as well as severe dysmorphologies of the facial skeleton  skullcap  and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis  indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently  we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants  including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1  which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants,,pubmed:33462117,,WT cartilage,GSM4575942,,tissue:cartilage|strain:Tgfli1a:EGFPy1; Tgsox10:DsRedel10|genotype:WT|age:21 dpf,WT cartilage,Reads were aligned to z11 genome using Cell Ranger 3. Genome build: z11 Supplementary files format and content: barcode  gene and matrix files from Cell Ranger alignment and trimming,cartilage,,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,,strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:WT|age:21 dpf,GSM4575942,GSM4575942: WT cartilage; Danio rerio; RNA Seq,GSM4575942,,1,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,GEO Accession:GSM4575942,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP265073,,,Nkx3-2-WT-2_S2_R1_001.fastq.gz Nkx3-2-WT-2_S2_R2_001.fastq.gz,fastq fastq,11876388158.0,80550349.0,GSM4575942 r2,0:27 1:120.44,A:3364971535;C:2517119793;G:2894599801;T:3062999066;N:36697963,27,120,,,3364971535,2517119793,2894599801,3062999066,36697963,SRX8413197,SRS6725508,SRA1080696,GEO,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",2,0.00483,0.94036,0.00117,0.13342,0.99159,0.86908,0.55589,0.46271,27,121,T,B,sc-like readlen,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-28,Larval,Larval,Bone or Cartilage,Skeletal Element
59349,SRR11862828,SRX8413197,SRS6725508,SRP265073,PRJNA635584,Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton,GSE151354,Transcriptome Analysis,The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD  which is characterized by skeletal defects including scoliosis  large epiphyses  wide growth plates  and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification  yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint  as well as severe dysmorphologies of the facial skeleton  skullcap  and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis  indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently  we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants  including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1  which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants,,pubmed:33462117,,WT cartilage,GSM4575942,,tissue:cartilage|strain:Tgfli1a:EGFPy1; Tgsox10:DsRedel10|genotype:WT|age:21 dpf,WT cartilage,Reads were aligned to z11 genome using Cell Ranger 3. Genome build: z11 Supplementary files format and content: barcode  gene and matrix files from Cell Ranger alignment and trimming,cartilage,,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,,strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:WT|age:21 dpf,GSM4575942,GSM4575942: WT cartilage; Danio rerio; RNA Seq,GSM4575942,,1,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,GEO Accession:GSM4575942,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP265073,,,Nkx3-2-WT-3_S3_R1_001.fastq.gz Nkx3-2-WT-3_S3_R2_001.fastq.gz,fastq fastq,11069345273.0,75076558.0,GSM4575942 r3,0:27 1:120.44,A:3145549374;C:2343216049;G:2703001091;T:2843206620;N:34372139,27,120,,,3145549374,2343216049,2703001091,2843206620,34372139,SRX8413197,SRS6725508,SRA1080696,GEO,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",2,0.00474,0.94141,0.00114,0.13537,0.99255,0.87428,0.57339,0.47945,27,120,T,B,sc-like readlen,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-28,Larval,Larval,Bone or Cartilage,Skeletal Element
59350,SRR11862829,SRX8413197,SRS6725508,SRP265073,PRJNA635584,Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton,GSE151354,Transcriptome Analysis,The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD  which is characterized by skeletal defects including scoliosis  large epiphyses  wide growth plates  and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification  yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint  as well as severe dysmorphologies of the facial skeleton  skullcap  and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis  indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently  we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants  including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1  which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants,,pubmed:33462117,,WT cartilage,GSM4575942,,tissue:cartilage|strain:Tgfli1a:EGFPy1; Tgsox10:DsRedel10|genotype:WT|age:21 dpf,WT cartilage,Reads were aligned to z11 genome using Cell Ranger 3. Genome build: z11 Supplementary files format and content: barcode  gene and matrix files from Cell Ranger alignment and trimming,cartilage,,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,,strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:WT|age:21 dpf,GSM4575942,GSM4575942: WT cartilage; Danio rerio; RNA Seq,GSM4575942,,1,Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using three prime Gene Expression v2 Library kit.,GEO Accession:GSM4575942,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP265073,,,Nkx3-2-WT-4_S4_R1_001.fastq.gz Nkx3-2-WT-4_S4_R2_001.fastq.gz,fastq fastq,12792371587.0,86758219.0,GSM4575942 r4,0:27 1:120.45,A:3620447166;C:2712466949;G:3120686582;T:3299001093;N:39769797,27,120,,,3620447166,2712466949,3120686582,3299001093,39769797,SRX8413197,SRS6725508,SRA1080696,GEO,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",2,0.00534,0.94032,0.00143,0.13395,0.99159,0.87338,0.53475,0.45536,27,120,T,B,sc-like readlen,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-28,Larval,Larval,Bone or Cartilage,Skeletal Element
74701,SRR24003726,SRX19807142,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,case2 4,case2 4,Qualified total RNA was purified by DNase I  and mRNA was enriched by adding OligodT  attached magnetic beads. Subsequently  fragment buffer was added to cleave the mRNA into small   fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first  cDNA strand  and then the second cDNA strand was generated. End repair and adaptor ligation were  performed by adding A tailing Mix and RNA Index Adapters  and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products.  The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality  of the final library was tested. The qualified library was replicated by rolling circle replication to form  DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently  sequencing was performed on the BGIISEQ500 platform  BGI Shenzhen  Guangdong  China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,case2_4_1.fq.gz case2_4_2.fq.gz,fastq fastq,6631325400.0,22104418.0,case2 4 1.fq.gz,0:150 1:150,A:1790451511;C:1523987494;G:1517049214;T:1799837181;N:0,150,150,,,1790451511,1523987494,1517049214,1799837181,0,SRX19807142,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.94202,0.94054,0.06448,0.06393,0.71415,0.71445,0.52801,0.52947,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element
74702,SRR24003727,SRX19807141,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,case2 3,case2 3,Qualified total RNA was purified by DNase I  and mRNA was enriched by adding OligodT  attached magnetic beads. Subsequently  fragment buffer was added to cleave the mRNA into small   fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first  cDNA strand  and then the second cDNA strand was generated. End repair and adaptor ligation were  performed by adding A tailing Mix and RNA Index Adapters  and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products.  The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality  of the final library was tested. The qualified library was replicated by rolling circle replication to form  DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently  sequencing was performed on the BGIISEQ500 platform  BGI Shenzhen  Guangdong  China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,case2_3_1.fq.gz case2_3_2.fq.gz,fastq fastq,6706743300.0,22355811.0,case2 3 1.fq.gz,0:150 1:150,A:1845685627;C:1507725453;G:1499541624;T:1853790596;N:0,150,150,,,1845685627,1507725453,1499541624,1853790596,0,SRX19807141,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.94268,0.93594,0.08009,0.07937,0.70402,0.70441,0.4556,0.48818,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element
74703,SRR24003728,SRX19807140,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,case2 2,case2 2,Qualified total RNA was purified by DNase I  and mRNA was enriched by adding OligodT  attached magnetic beads. Subsequently  fragment buffer was added to cleave the mRNA into small   fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first  cDNA strand  and then the second cDNA strand was generated. End repair and adaptor ligation were  performed by adding A tailing Mix and RNA Index Adapters  and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products.  The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality  of the final library was tested. The qualified library was replicated by rolling circle replication to form  DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently  sequencing was performed on the BGIISEQ500 platform  BGI Shenzhen  Guangdong  China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,case2_2_1.fq.gz case2_2_2.fq.gz,fastq fastq,6677092200.0,22256974.0,case2 2 1.fq.gz,0:150 1:150,A:1864795230;C:1474224567;G:1465199644;T:1872872759;N:0,150,150,,,1864795230,1474224567,1465199644,1872872759,0,SRX19807140,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.93359,0.92743,0.0959,0.09583,0.69089,0.69234,0.48419,0.48121,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element
74704,SRR24003729,SRX19807139,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,case2 1,case2 1,Qualified total RNA was purified by DNase I  and mRNA was enriched by adding OligodT  attached magnetic beads. Subsequently  fragment buffer was added to cleave the mRNA into small   fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first  cDNA strand  and then the second cDNA strand was generated. End repair and adaptor ligation were  performed by adding A tailing Mix and RNA Index Adapters  and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products.  The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality  of the final library was tested. The qualified library was replicated by rolling circle replication to form  DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently  sequencing was performed on the BGIISEQ500 platform  BGI Shenzhen  Guangdong  China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,case2_1_1.fq.gz case2_1_2.fq.gz,fastq fastq,6644478600.0,22148262.0,case2 1 1.fq.gz,0:150 1:150,A:1863814645;C:1460246773;G:1453279946;T:1867137236;N:0,150,150,,,1863814645,1460246773,1453279946,1867137236,0,SRX19807139,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.93932,0.9379,0.09722,0.09709,0.71985,0.71873,0.49646,0.5522,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element
74705,SRR24003730,SRX19807138,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,control2 6,control2 6,Qualified total RNA was purified by DNase I  and mRNA was enriched by adding OligodT  attached magnetic beads. Subsequently  fragment buffer was added to cleave the mRNA into small   fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first  cDNA strand  and then the second cDNA strand was generated. End repair and adaptor ligation were  performed by adding A tailing Mix and RNA Index Adapters  and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products.  The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality  of the final library was tested. The qualified library was replicated by rolling circle replication to form  DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently  sequencing was performed on the BGIISEQ500 platform  BGI Shenzhen  Guangdong  China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,control2_6_1.fq.gz control2_6_2.fq.gz,fastq fastq,6817849200.0,22726164.0,control2 6 1.fq.gz,0:150 1:150,A:1916198776;C:1480570561;G:1501234091;T:1919845772;N:0,150,150,,,1916198776,1480570561,1501234091,1919845772,0,SRX19807138,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.94697,0.9369,0.06934,0.06812,0.76824,0.77114,0.49005,0.54882,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element
74706,SRR24003731,SRX19807137,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,control2 5,control2 5,Qualified total RNA was purified by DNase I  and mRNA was enriched by adding OligodT  attached magnetic beads. Subsequently  fragment buffer was added to cleave the mRNA into small   fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first  cDNA strand  and then the second cDNA strand was generated. End repair and adaptor ligation were  performed by adding A tailing Mix and RNA Index Adapters  and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products.  The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality  of the final library was tested. The qualified library was replicated by rolling circle replication to form  DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently  sequencing was performed on the BGIISEQ500 platform  BGI Shenzhen  Guangdong  China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,control2_5_1.fq.gz control2_5_2.fq.gz,fastq fastq,6730171500.0,22433905.0,control2 5 1.fq.gz,0:150 1:150,A:1881763818;C:1469481635;G:1493477302;T:1885448745;N:0,150,150,,,1881763818,1469481635,1493477302,1885448745,0,SRX19807137,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.9399,0.92905,0.0832,0.08122,0.70993,0.71228,0.54991,0.58952,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element
74707,SRR24003732,SRX19807136,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,control2 4,control2 4,Qualified total RNA was purified by DNase I  and mRNA was enriched by adding OligodT  attached magnetic beads. Subsequently  fragment buffer was added to cleave the mRNA into small   fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first  cDNA strand  and then the second cDNA strand was generated. End repair and adaptor ligation were  performed by adding A tailing Mix and RNA Index Adapters  and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products.  The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality  of the final library was tested. The qualified library was replicated by rolling circle replication to form  DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently  sequencing was performed on the BGIISEQ500 platform  BGI Shenzhen  Guangdong  China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,control2_4_1.fq.gz control2_4_2.fq.gz,fastq fastq,6660686100.0,22202287.0,control2 4 1.fq.gz,0:150 1:150,A:1846205332;C:1486328129;G:1477889862;T:1850262777;N:0,150,150,,,1846205332,1486328129,1477889862,1850262777,0,SRX19807136,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.94251,0.94001,0.08206,0.082,0.69483,0.69524,0.49193,0.49602,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element
74708,SRR24003733,SRX19807135,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,control2 3,control2 3,Qualified total RNA was purified by DNase I  and mRNA was enriched by adding OligodT  attached magnetic beads. Subsequently  fragment buffer was added to cleave the mRNA into small   fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first  cDNA strand  and then the second cDNA strand was generated. End repair and adaptor ligation were  performed by adding A tailing Mix and RNA Index Adapters  and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products.  The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality  of the final library was tested. The qualified library was replicated by rolling circle replication to form  DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently  sequencing was performed on the BGIISEQ500 platform  BGI Shenzhen  Guangdong  China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,control2_3_1.fq.gz control2_3_2.fq.gz,fastq fastq,6683569500.0,22278565.0,control2 3 1.fq.gz,0:150 1:150,A:1846755716;C:1494194697;G:1482717957;T:1859901130;N:0,150,150,,,1846755716,1494194697,1482717957,1859901130,0,SRX19807135,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.93255,0.93106,0.10717,0.10731,0.67665,0.67791,0.54876,0.52297,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element
74709,SRR24003734,SRX19807134,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,case2 7,case2 7,Qualified total RNA was purified by DNase I  and mRNA was enriched by adding OligodT  attached magnetic beads. Subsequently  fragment buffer was added to cleave the mRNA into small   fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first  cDNA strand  and then the second cDNA strand was generated. End repair and adaptor ligation were  performed by adding A tailing Mix and RNA Index Adapters  and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products.  The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality  of the final library was tested. The qualified library was replicated by rolling circle replication to form  DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently  sequencing was performed on the BGIISEQ500 platform  BGI Shenzhen  Guangdong  China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,case2_7_1.fq.gz case2_7_2.fq.gz,fastq fastq,6770748000.0,22569160.0,case2 7 1.fq.gz,0:150 1:150,A:1918448687;C:1455131518;G:1474277741;T:1922890054;N:0,150,150,,,1918448687,1455131518,1474277741,1922890054,0,SRX19807134,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.94025,0.92953,0.08709,0.0851,0.73864,0.73914,0.5716,0.56037,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element
74710,SRR24003735,SRX19807133,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,case2 6,case2 6,Qualified total RNA was purified by DNase I  and mRNA was enriched by adding OligodT  attached magnetic beads. Subsequently  fragment buffer was added to cleave the mRNA into small   fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first  cDNA strand  and then the second cDNA strand was generated. End repair and adaptor ligation were  performed by adding A tailing Mix and RNA Index Adapters  and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products.  The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality  of the final library was tested. The qualified library was replicated by rolling circle replication to form  DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently  sequencing was performed on the BGIISEQ500 platform  BGI Shenzhen  Guangdong  China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,case2_6_1.fq.gz case2_6_2.fq.gz,fastq fastq,6743372700.0,22477909.0,case2 6 1.fq.gz,0:150 1:150,A:1825699499;C:1533637372;G:1552424547;T:1831611282;N:0,150,150,,,1825699499,1533637372,1552424547,1831611282,0,SRX19807133,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.95425,0.94313,0.05313,0.05246,0.77268,0.77461,0.52616,0.5227,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element
74711,SRR24003736,SRX19807132,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,case2 5,case2 5,Qualified total RNA was purified by DNase I  and mRNA was enriched by adding OligodT  attached magnetic beads. Subsequently  fragment buffer was added to cleave the mRNA into small   fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first  cDNA strand  and then the second cDNA strand was generated. End repair and adaptor ligation were  performed by adding A tailing Mix and RNA Index Adapters  and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products.  The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality  of the final library was tested. The qualified library was replicated by rolling circle replication to form  DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently  sequencing was performed on the BGIISEQ500 platform  BGI Shenzhen  Guangdong  China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,case2_5_1.fq.gz case2_5_2.fq.gz,fastq fastq,6810815400.0,22702718.0,case2 5 1.fq.gz,0:150 1:150,A:1861549181;C:1529649127;G:1553365612;T:1866251480;N:0,150,150,,,1861549181,1529649127,1553365612,1866251480,0,SRX19807132,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.94842,0.93757,0.06448,0.06317,0.74036,0.74097,0.53479,0.52393,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element
74712,SRR24003737,SRX19807131,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,control2 2,control2 2,Qualified total RNA was purified by DNase I  and mRNA was enriched by adding OligodT  attached magnetic beads. Subsequently  fragment buffer was added to cleave the mRNA into small   fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first  cDNA strand  and then the second cDNA strand was generated. End repair and adaptor ligation were  performed by adding A tailing Mix and RNA Index Adapters  and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products.  The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality  of the final library was tested. The qualified library was replicated by rolling circle replication to form  DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently  sequencing was performed on the BGIISEQ500 platform  BGI Shenzhen  Guangdong  China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,control2_2_1.fq.gz control2_2_2.fq.gz,fastq fastq,6693643800.0,22312146.0,control2 2 1.fq.gz,0:150 1:150,A:1846873501;C:1499207913;G:1490122627;T:1857439759;N:0,150,150,,,1846873501,1499207913,1490122627,1857439759,0,SRX19807131,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.93282,0.93092,0.09007,0.0899,0.68672,0.68793,0.55221,0.55318,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element
74713,SRR24003738,SRX19807130,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,control2 1,control2 1,Qualified total RNA was purified by DNase I  and mRNA was enriched by adding OligodT  attached magnetic beads. Subsequently  fragment buffer was added to cleave the mRNA into small   fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first  cDNA strand  and then the second cDNA strand was generated. End repair and adaptor ligation were  performed by adding A tailing Mix and RNA Index Adapters  and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products.  The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality  of the final library was tested. The qualified library was replicated by rolling circle replication to form  DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently  sequencing was performed on the BGIISEQ500 platform  BGI Shenzhen  Guangdong  China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,control2_1_1.fq.gz control2_1_2.fq.gz,fastq fastq,6629354100.0,22097847.0,control2 1 1.fq.gz,0:150 1:150,A:1819412655;C:1492313439;G:1486507818;T:1831120188;N:0,150,150,,,1819412655,1492313439,1486507818,1831120188,0,SRX19807130,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.93273,0.93086,0.08814,0.08711,0.67748,0.67696,0.5355,0.54253,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element
76931,SRR25386906,SRX21125096,SRS18391094,SRP450794,PRJNA997263,Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae,GSE237934,Transcriptome Analysis,The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence  P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated.   The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing  while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv  our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv  the counts table complete with the Sanger data.,,,,RR2a 4dpf osteoblasts P2 rep 1,GSM7656643,,tissue:4dpf osteoblasts|cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS|geo loc name:missing|collection date:missing,RR2a 4dpf osteoblasts P2 rep 1,The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  P. A.  et al.   Nat Biotechnol 2020  38  3  276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID  gene name  baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  P2 baseMean  P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2  RR8b P1  RR3a P2  RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1,4dpf osteoblasts,A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf  the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf  around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec  Leiden  Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C  dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec  Leiden  Netherlands  followed by three runs of m brain 03  2 runs of protocol m brain 02  five runs of m brain 03  each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol  separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS  buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific  Merelbeek  Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf,cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS,GSM7656643,GSM7656643: RR2a 4dpf osteoblasts P2 rep 1; Danio rerio; RNA Seq,GSM7656643 r1,GSM7656643,1,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP450794,,loader:fastq load.py,RR2a-P2_NGS20-O032_HGLCNBGXG_S1_L003_R1_001.fastq.gz,fastq,373177684.0,5548694.0,GSM7656643 r3,0:67.26,A:100760112;C:81480585;G:85122648;T:102415267;N:3399072,67,,,,100760112,81480585,85122648,102415267,3399072,SRX21125096,SRS18391094,SRA1677548,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",1,0.8728,,0.31033,,0.8072,,0.60657,,68,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,Belgium,2023-07-21,Multi-stage,Multi-stage,Bone or Cartilage,Skeletal Element
76932,SRR25386907,SRX21125096,SRS18391094,SRP450794,PRJNA997263,Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae,GSE237934,Transcriptome Analysis,The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence  P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated.   The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing  while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv  our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv  the counts table complete with the Sanger data.,,,,RR2a 4dpf osteoblasts P2 rep 1,GSM7656643,,tissue:4dpf osteoblasts|cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS|geo loc name:missing|collection date:missing,RR2a 4dpf osteoblasts P2 rep 1,The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  P. A.  et al.   Nat Biotechnol 2020  38  3  276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID  gene name  baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  P2 baseMean  P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2  RR8b P1  RR3a P2  RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1,4dpf osteoblasts,A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf  the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf  around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec  Leiden  Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C  dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec  Leiden  Netherlands  followed by three runs of m brain 03  2 runs of protocol m brain 02  five runs of m brain 03  each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol  separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS  buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific  Merelbeek  Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf,cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS,GSM7656643,GSM7656643: RR2a 4dpf osteoblasts P2 rep 1; Danio rerio; RNA Seq,GSM7656643 r1,GSM7656643,1,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP450794,,loader:fastq load.py,RR2a-P2_NGS20-O032_HGLCNBGXG_S1_L004_R1_001.fastq.gz,fastq,373962152.0,5557214.0,GSM7656643 r4,0:67.29,A:100972761;C:81555058;G:85226241;T:102843430;N:3364662,67,,,,100972761,81555058,85226241,102843430,3364662,SRX21125096,SRS18391094,SRA1677548,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",1,0.8736,,0.31177,,0.80667,,0.59856,,70,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,Belgium,2023-07-21,Multi-stage,Multi-stage,Bone or Cartilage,Skeletal Element
76933,SRR25386924,SRX21125096,SRS18391094,SRP450794,PRJNA997263,Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae,GSE237934,Transcriptome Analysis,The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence  P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated.   The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing  while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv  our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv  the counts table complete with the Sanger data.,,,,RR2a 4dpf osteoblasts P2 rep 1,GSM7656643,,tissue:4dpf osteoblasts|cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS|geo loc name:missing|collection date:missing,RR2a 4dpf osteoblasts P2 rep 1,The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  P. A.  et al.   Nat Biotechnol 2020  38  3  276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID  gene name  baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  P2 baseMean  P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2  RR8b P1  RR3a P2  RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1,4dpf osteoblasts,A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf  the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf  around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec  Leiden  Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C  dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec  Leiden  Netherlands  followed by three runs of m brain 03  2 runs of protocol m brain 02  five runs of m brain 03  each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol  separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS  buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific  Merelbeek  Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf,cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS,GSM7656643,GSM7656643: RR2a 4dpf osteoblasts P2 rep 1; Danio rerio; RNA Seq,GSM7656643 r1,GSM7656643,1,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP450794,,loader:fastq load.py,RR2a-P2_NGS20-O032_HGLCNBGXG_S1_L001_R1_001.fastq.gz,fastq,373269811.0,5548624.0,GSM7656643 r1,0:67.27,A:101075219;C:81326431;G:85043234;T:102437099;N:3387828,67,,,,101075219,81326431,85043234,102437099,3387828,SRX21125096,SRS18391094,SRA1677548,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",1,0.87208,,0.30902,,0.80923,,0.62143,,41,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,Belgium,2023-07-21,Multi-stage,Multi-stage,Bone or Cartilage,Skeletal Element
76934,SRR25386925,SRX21125096,SRS18391094,SRP450794,PRJNA997263,Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae,GSE237934,Transcriptome Analysis,The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence  P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated.   The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing  while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv  our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv  the counts table complete with the Sanger data.,,,,RR2a 4dpf osteoblasts P2 rep 1,GSM7656643,,tissue:4dpf osteoblasts|cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS|geo loc name:missing|collection date:missing,RR2a 4dpf osteoblasts P2 rep 1,The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  P. A.  et al.   Nat Biotechnol 2020  38  3  276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID  gene name  baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  P2 baseMean  P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2  RR8b P1  RR3a P2  RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1,4dpf osteoblasts,A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf  the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf  around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec  Leiden  Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C  dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec  Leiden  Netherlands  followed by three runs of m brain 03  2 runs of protocol m brain 02  five runs of m brain 03  each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol  separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS  buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific  Merelbeek  Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf,cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS,GSM7656643,GSM7656643: RR2a 4dpf osteoblasts P2 rep 1; Danio rerio; RNA Seq,GSM7656643 r1,GSM7656643,1,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP450794,,loader:fastq load.py,RR2a-P2_NGS20-O032_HGLCNBGXG_S1_L002_R1_001.fastq.gz,fastq,362918448.0,5391108.0,GSM7656643 r2,0:67.32,A:98186136;C:79161985;G:82672936;T:99657172;N:3240219,67,,,,98186136,79161985,82672936,99657172,3240219,SRX21125096,SRS18391094,SRA1677548,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",1,0.8708,,0.30958,,0.80775,,0.60608,,74,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,Belgium,2023-07-21,Multi-stage,Multi-stage,Bone or Cartilage,Skeletal Element
76935,SRR25386908,SRX21125095,SRS18391093,SRP450794,PRJNA997263,Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae,GSE237934,Transcriptome Analysis,The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence  P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated.   The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing  while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv  our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv  the counts table complete with the Sanger data.,,,,RR6a 4dpf osteoblasts P2 rep 4,GSM7656645,,tissue:4dpf osteoblasts|cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS|geo loc name:missing|collection date:missing,RR6a 4dpf osteoblasts P2 rep 4,The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  P. A.  et al.   Nat Biotechnol 2020  38  3  276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID  gene name  baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  P2 baseMean  P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2  RR8b P1  RR3a P2  RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1,4dpf osteoblasts,A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf  the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf  around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec  Leiden  Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C  dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec  Leiden  Netherlands  followed by three runs of m brain 03  2 runs of protocol m brain 02  five runs of m brain 03  each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol  separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS  buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific  Merelbeek  Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf,cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS,GSM7656645,GSM7656645: RR6a 4dpf osteoblasts P2 rep 4; Danio rerio; RNA Seq,GSM7656645 r1,GSM7656645,1,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP450794,,loader:fastq load.py,RR6a-P2_NGS20-O037_HGLCNBGXG_S6_L001_R1_001.fastq.gz,fastq,354032873.0,4986287.0,GSM7656645 r1,0:71.00,A:94144867;C:80102104;G:82817752;T:95495724;N:1472426,71,,,,94144867,80102104,82817752,95495724,1472426,SRX21125095,SRS18391093,SRA1677548,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",1,0.89937,,0.33561,,0.78624,,0.59931,,75,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,Belgium,2023-07-21,Multi-stage,Multi-stage,Bone or Cartilage,Skeletal Element
76936,SRR25386909,SRX21125095,SRS18391093,SRP450794,PRJNA997263,Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae,GSE237934,Transcriptome Analysis,The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence  P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated.   The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing  while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv  our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv  the counts table complete with the Sanger data.,,,,RR6a 4dpf osteoblasts P2 rep 4,GSM7656645,,tissue:4dpf osteoblasts|cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS|geo loc name:missing|collection date:missing,RR6a 4dpf osteoblasts P2 rep 4,The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  P. A.  et al.   Nat Biotechnol 2020  38  3  276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID  gene name  baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  P2 baseMean  P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2  RR8b P1  RR3a P2  RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1,4dpf osteoblasts,A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf  the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf  around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec  Leiden  Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C  dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec  Leiden  Netherlands  followed by three runs of m brain 03  2 runs of protocol m brain 02  five runs of m brain 03  each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol  separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS  buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific  Merelbeek  Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf,cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS,GSM7656645,GSM7656645: RR6a 4dpf osteoblasts P2 rep 4; Danio rerio; RNA Seq,GSM7656645 r1,GSM7656645,1,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP450794,,loader:fastq load.py,RR6a-P2_NGS20-O037_HGLCNBGXG_S6_L002_R1_001.fastq.gz,fastq,346361358.0,4874773.0,GSM7656645 r2,0:71.05,A:92065302;C:78397028;G:81045788;T:93453382;N:1399858,71,,,,92065302,78397028,81045788,93453382,1399858,SRX21125095,SRS18391093,SRA1677548,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",1,0.90158,,0.33472,,0.78553,,0.5992,,75,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,Belgium,2023-07-21,Multi-stage,Multi-stage,Bone or Cartilage,Skeletal Element
76937,SRR25386910,SRX21125095,SRS18391093,SRP450794,PRJNA997263,Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae,GSE237934,Transcriptome Analysis,The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence  P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated.   The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing  while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv  our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv  the counts table complete with the Sanger data.,,,,RR6a 4dpf osteoblasts P2 rep 4,GSM7656645,,tissue:4dpf osteoblasts|cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS|geo loc name:missing|collection date:missing,RR6a 4dpf osteoblasts P2 rep 4,The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  P. A.  et al.   Nat Biotechnol 2020  38  3  276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID  gene name  baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  P2 baseMean  P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2  RR8b P1  RR3a P2  RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1,4dpf osteoblasts,A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf  the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf  around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec  Leiden  Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C  dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec  Leiden  Netherlands  followed by three runs of m brain 03  2 runs of protocol m brain 02  five runs of m brain 03  each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol  separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS  buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific  Merelbeek  Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf,cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS,GSM7656645,GSM7656645: RR6a 4dpf osteoblasts P2 rep 4; Danio rerio; RNA Seq,GSM7656645 r1,GSM7656645,1,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP450794,,loader:fastq load.py,RR6a-P2_NGS20-O037_HGLCNBGXG_S6_L003_R1_001.fastq.gz,fastq,355035161.0,5000095.0,GSM7656645 r3,0:71.01,A:94319592;C:80407508;G:83110050;T:95730889;N:1467122,71,,,,94319592,80407508,83110050,95730889,1467122,SRX21125095,SRS18391093,SRA1677548,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",1,0.90115,,0.33357,,0.78675,,0.57285,,75,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,Belgium,2023-07-21,Multi-stage,Multi-stage,Bone or Cartilage,Skeletal Element
76938,SRR25386911,SRX21125095,SRS18391093,SRP450794,PRJNA997263,Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae,GSE237934,Transcriptome Analysis,The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence  P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated.   The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing  while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv  our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv  the counts table complete with the Sanger data.,,,,RR6a 4dpf osteoblasts P2 rep 4,GSM7656645,,tissue:4dpf osteoblasts|cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS|geo loc name:missing|collection date:missing,RR6a 4dpf osteoblasts P2 rep 4,The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  P. A.  et al.   Nat Biotechnol 2020  38  3  276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID  gene name  baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  P2 baseMean  P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2  RR8b P1  RR3a P2  RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1,4dpf osteoblasts,A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf  the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf  around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec  Leiden  Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C  dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec  Leiden  Netherlands  followed by three runs of m brain 03  2 runs of protocol m brain 02  five runs of m brain 03  each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol  separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS  buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific  Merelbeek  Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf,cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS,GSM7656645,GSM7656645: RR6a 4dpf osteoblasts P2 rep 4; Danio rerio; RNA Seq,GSM7656645 r1,GSM7656645,1,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP450794,,loader:fastq load.py,RR6a-P2_NGS20-O037_HGLCNBGXG_S6_L004_R1_001.fastq.gz,fastq,356149314.0,5014069.0,GSM7656645 r4,0:71.03,A:94655529;C:80576651;G:83343452;T:96095982;N:1477700,71,,,,94655529,80576651,83343452,96095982,1477700,SRX21125095,SRS18391093,SRA1677548,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",1,0.90138,,0.33348,,0.78455,,0.5911,,75,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,Belgium,2023-07-21,Multi-stage,Multi-stage,Bone or Cartilage,Skeletal Element
76939,SRR25386912,SRX21125094,SRS18391092,SRP450794,PRJNA997263,Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae,GSE237934,Transcriptome Analysis,The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence  P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated.   The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing  while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv  our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv  the counts table complete with the Sanger data.,,,,RR3a 4dpf osteoblasts P2 rep 2,GSM7656644,,tissue:4dpf osteoblasts|cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS|geo loc name:missing|collection date:missing,RR3a 4dpf osteoblasts P2 rep 2,The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  P. A.  et al.   Nat Biotechnol 2020  38  3  276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID  gene name  baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  P2 baseMean  P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2  RR8b P1  RR3a P2  RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1,4dpf osteoblasts,A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf  the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf  around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec  Leiden  Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C  dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec  Leiden  Netherlands  followed by three runs of m brain 03  2 runs of protocol m brain 02  five runs of m brain 03  each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol  separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS  buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific  Merelbeek  Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf,cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS,GSM7656644,GSM7656644: RR3a 4dpf osteoblasts P2 rep 2; Danio rerio; RNA Seq,GSM7656644 r1,GSM7656644,1,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP450794,,loader:fastq load.py,RR3a-P2_NGS20-O034_HGLCNBGXG_S3_L001_R1_001.fastq.gz,fastq,338589143.0,4761586.0,GSM7656644 r1,0:71.11,A:97196593;C:69615487;G:71880789;T:98743111;N:1153163,71,,,,97196593,69615487,71880789,98743111,1153163,SRX21125094,SRS18391092,SRA1677548,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",1,0.8916,,0.25165,,0.77244,,0.58676,,76,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,Belgium,2023-07-21,Multi-stage,Multi-stage,Bone or Cartilage,Skeletal Element
76940,SRR25386913,SRX21125094,SRS18391092,SRP450794,PRJNA997263,Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae,GSE237934,Transcriptome Analysis,The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence  P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated.   The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing  while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv  our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv  the counts table complete with the Sanger data.,,,,RR3a 4dpf osteoblasts P2 rep 2,GSM7656644,,tissue:4dpf osteoblasts|cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS|geo loc name:missing|collection date:missing,RR3a 4dpf osteoblasts P2 rep 2,The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  P. A.  et al.   Nat Biotechnol 2020  38  3  276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID  gene name  baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  P2 baseMean  P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2  RR8b P1  RR3a P2  RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1,4dpf osteoblasts,A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf  the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf  around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec  Leiden  Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C  dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec  Leiden  Netherlands  followed by three runs of m brain 03  2 runs of protocol m brain 02  five runs of m brain 03  each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol  separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS  buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific  Merelbeek  Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf,cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS,GSM7656644,GSM7656644: RR3a 4dpf osteoblasts P2 rep 2; Danio rerio; RNA Seq,GSM7656644 r1,GSM7656644,1,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP450794,,loader:fastq load.py,RR3a-P2_NGS20-O034_HGLCNBGXG_S3_L002_R1_001.fastq.gz,fastq,331811774.0,4663625.0,GSM7656644 r2,0:71.15,A:95222586;C:68212365;G:70454008;T:96805245;N:1117570,71,,,,95222586,68212365,70454008,96805245,1117570,SRX21125094,SRS18391092,SRA1677548,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",1,0.89276,,0.25194,,0.7698,,0.58851,,75,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,Belgium,2023-07-21,Multi-stage,Multi-stage,Bone or Cartilage,Skeletal Element
76941,SRR25386914,SRX21125094,SRS18391092,SRP450794,PRJNA997263,Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae,GSE237934,Transcriptome Analysis,The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence  P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated.   The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing  while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv  our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv  the counts table complete with the Sanger data.,,,,RR3a 4dpf osteoblasts P2 rep 2,GSM7656644,,tissue:4dpf osteoblasts|cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS|geo loc name:missing|collection date:missing,RR3a 4dpf osteoblasts P2 rep 2,The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  P. A.  et al.   Nat Biotechnol 2020  38  3  276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID  gene name  baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  P2 baseMean  P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2  RR8b P1  RR3a P2  RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1,4dpf osteoblasts,A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf  the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf  around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec  Leiden  Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C  dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec  Leiden  Netherlands  followed by three runs of m brain 03  2 runs of protocol m brain 02  five runs of m brain 03  each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol  separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS  buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific  Merelbeek  Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf,cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS,GSM7656644,GSM7656644: RR3a 4dpf osteoblasts P2 rep 2; Danio rerio; RNA Seq,GSM7656644 r1,GSM7656644,1,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP450794,,loader:fastq load.py,RR3a-P2_NGS20-O034_HGLCNBGXG_S3_L003_R1_001.fastq.gz,fastq,339208892.0,4771033.0,GSM7656644 r3,0:71.10,A:97276491;C:69781643;G:72044207;T:98948884;N:1157667,71,,,,97276491,69781643,72044207,98948884,1157667,SRX21125094,SRS18391092,SRA1677548,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",1,0.89219,,0.2516,,0.77102,,0.58563,,75,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,Belgium,2023-07-21,Multi-stage,Multi-stage,Bone or Cartilage,Skeletal Element
76942,SRR25386915,SRX21125094,SRS18391092,SRP450794,PRJNA997263,Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae,GSE237934,Transcriptome Analysis,The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence  P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated.   The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing  while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv  our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv  the counts table complete with the Sanger data.,,,,RR3a 4dpf osteoblasts P2 rep 2,GSM7656644,,tissue:4dpf osteoblasts|cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS|geo loc name:missing|collection date:missing,RR3a 4dpf osteoblasts P2 rep 2,The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  P. A.  et al.   Nat Biotechnol 2020  38  3  276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID  gene name  baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  P2 baseMean  P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2  RR8b P1  RR3a P2  RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1,4dpf osteoblasts,A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf  the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf  around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec  Leiden  Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C  dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec  Leiden  Netherlands  followed by three runs of m brain 03  2 runs of protocol m brain 02  five runs of m brain 03  each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol  separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS  buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific  Merelbeek  Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf,cell type:4dpf osteoblasts|cell population:high P2 fluorescence|genotype:ulg071 Tg|treatment:FACS,GSM7656644,GSM7656644: RR3a 4dpf osteoblasts P2 rep 2; Danio rerio; RNA Seq,GSM7656644 r1,GSM7656644,1,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP450794,,loader:fastq load.py,RR3a-P2_NGS20-O034_HGLCNBGXG_S3_L004_R1_001.fastq.gz,fastq,341114353.0,4796386.0,GSM7656644 r4,0:71.12,A:97859710;C:70136066;G:72385473;T:99567064;N:1166040,71,,,,97859710,70136066,72385473,99567064,1166040,SRX21125094,SRS18391092,SRA1677548,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",1,0.89236,,0.25322,,0.77189,,0.58747,,46,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,Belgium,2023-07-21,Multi-stage,Multi-stage,Bone or Cartilage,Skeletal Element
76943,SRR25386916,SRX21125093,SRS18391091,SRP450794,PRJNA997263,Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae,GSE237934,Transcriptome Analysis,The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence  P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated.   The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing  while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv  our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv  the counts table complete with the Sanger data.,,,,RR8b 4dpf osteoblasts P1 rep 6,GSM7656642,,tissue:4dpf osteoblasts|cell type:4dpf osteoblasts|cell population:low P1 fluorescence|genotype:ulg071 Tg|treatment:FACS|geo loc name:missing|collection date:missing,RR8b 4dpf osteoblasts P1 rep 6,The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  P. A.  et al.   Nat Biotechnol 2020  38  3  276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID  gene name  baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  P2 baseMean  P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2  RR8b P1  RR3a P2  RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1,4dpf osteoblasts,A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf  the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf  around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec  Leiden  Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C  dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec  Leiden  Netherlands  followed by three runs of m brain 03  2 runs of protocol m brain 02  five runs of m brain 03  each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol  separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS  buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific  Merelbeek  Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf,cell type:4dpf osteoblasts|cell population:low P1 fluorescence|genotype:ulg071 Tg|treatment:FACS,GSM7656642,GSM7656642: RR8b 4dpf osteoblasts P1 rep 6; Danio rerio; RNA Seq,GSM7656642 r1,GSM7656642,1,"Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at  80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina  San Diego  CA  USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma  X.  Y. W. Wang  M. Q. Zhang and A. F. Gazdar 2013. ""DNA methylation data analysis and its application to cancer research."" Epigenomics 53: 301 316.",,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP450794,,loader:fastq load.py,RR8b-P1_NGS20-O039_HGLCNBGXG_S8_L001_R1_001.fastq.gz,fastq,330198165.0,4722206.0,GSM7656642 r1,0:69.92,A:93808782;C:67002978;G:70951394;T:96805500;N:1629511,69,,,,93808782,67002978,70951394,96805500,1629511,SRX21125093,SRS18391091,SRA1677548,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",1,0.85804,,0.25861,,0.77918,,0.66339,,76,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,Belgium,2023-07-21,Multi-stage,Multi-stage,Bone or Cartilage,Skeletal Element