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55 rows where experiment.library_layout = "PAIRED" and tissue_curation_coarse = "Skeletal Element"

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technology 3

experiment.library_selection 3

devstage_curation_coarse 3

devstage_curation 3

experiment.platform 2

tissue_curation_coarse 1

  • Skeletal Element · 55 ✖

tissue_curation 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_layout 1

  • PAIRED · 55 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
29165 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
38060 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;