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43 rows where devstage_curation_coarse = "Larval" and tissue_curation_coarse = "Skeletal Element"

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technology 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Skeletal Element · 43 ✖

tissue_curation 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

devstage_curation_coarse 1

  • Larval · 43 ✖

devstage_curation 1

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
34618 34618 SRR32145149 SRX27491071 SRS23912869 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 4 GSM8760186   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 4 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760186 GSM8760186: kat6a Replicate 4; Danio rerio; RNA Seq GSM8760186 r1 GSM8760186 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a4_S4_L001_R1_001.fastq.gz fastq 1185101288.0 15593438.0 GSM8760186 r1 0:76 A:300559300;C:260467735;G:266433586;T:357432372;N:208295 76       300559300 260467735 266433586 357432372 208295 SRX27491071 SRS23912869 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34619 34619 SRR32145150 SRX27491071 SRS23912869 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 4 GSM8760186   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 4 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760186 GSM8760186: kat6a Replicate 4; Danio rerio; RNA Seq GSM8760186 r1 GSM8760186 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a4_S4_L002_R1_001.fastq.gz fastq 1131352948.0 14886223.0 GSM8760186 r2 0:76 A:286383575;C:248947288;G:254084926;T:341733278;N:203881 76       286383575 248947288 254084926 341733278 203881 SRX27491071 SRS23912869 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34620 34620 SRR32145151 SRX27491071 SRS23912869 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 4 GSM8760186   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 4 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760186 GSM8760186: kat6a Replicate 4; Danio rerio; RNA Seq GSM8760186 r1 GSM8760186 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a4_S4_L003_R1_001.fastq.gz fastq 1166160188.0 15344213.0 GSM8760186 r3 0:76 A:296592701;C:256034122;G:261605331;T:351825369;N:102665 76       296592701 256034122 261605331 351825369 102665 SRX27491071 SRS23912869 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34621 34621 SRR32145152 SRX27491071 SRS23912869 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 4 GSM8760186   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 4 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760186 GSM8760186: kat6a Replicate 4; Danio rerio; RNA Seq GSM8760186 r1 GSM8760186 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a4_S4_L004_R1_001.fastq.gz fastq 1123430480.0 14781980.0 GSM8760186 r4 0:76 A:285427665;C:246734929;G:251428534;T:339753027;N:86325 76       285427665 246734929 251428534 339753027 86325 SRX27491071 SRS23912869 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34622 34622 SRR32145153 SRX27491070 SRS23912868 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 3 GSM8760185   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 3 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760185 GSM8760185: kat6a Replicate 3; Danio rerio; RNA Seq GSM8760185 r1 GSM8760185 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a3_S3_L001_R1_001.fastq.gz fastq 1130086940.0 14869565.0 GSM8760185 r1 0:76 A:271600754;C:270119369;G:267701531;T:320468732;N:196554 76       271600754 270119369 267701531 320468732 196554 SRX27491070 SRS23912868 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34623 34623 SRR32145154 SRX27491070 SRS23912868 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 3 GSM8760185   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 3 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760185 GSM8760185: kat6a Replicate 3; Danio rerio; RNA Seq GSM8760185 r1 GSM8760185 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a3_S3_L002_R1_001.fastq.gz fastq 1084172604.0 14265429.0 GSM8760185 r2 0:76 A:260060383;C:259442661;G:256603224;T:307867713;N:198623 76       260060383 259442661 256603224 307867713 198623 SRX27491070 SRS23912868 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34624 34624 SRR32145155 SRX27491070 SRS23912868 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 3 GSM8760185   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 3 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760185 GSM8760185: kat6a Replicate 3; Danio rerio; RNA Seq GSM8760185 r1 GSM8760185 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a3_S3_L003_R1_001.fastq.gz fastq 1110196904.0 14607854.0 GSM8760185 r3 0:76 A:267507867;C:265237928;G:262455688;T:314899764;N:95657 76       267507867 265237928 262455688 314899764 95657 SRX27491070 SRS23912868 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34625 34625 SRR32145156 SRX27491070 SRS23912868 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 3 GSM8760185   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 3 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760185 GSM8760185: kat6a Replicate 3; Danio rerio; RNA Seq GSM8760185 r1 GSM8760185 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a3_S3_L004_R1_001.fastq.gz fastq 1075741468.0 14154493.0 GSM8760185 r4 0:76 A:259028301;C:257097498;G:253796080;T:305738292;N:81297 76       259028301 257097498 253796080 305738292 81297 SRX27491070 SRS23912868 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34626 34626 SRR32145157 SRX27491069 SRS23912867 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 2 GSM8760184   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 2 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760184 GSM8760184: kat6a Replicate 2; Danio rerio; RNA Seq GSM8760184 r1 GSM8760184 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a2_S2_L001_R1_001.fastq.gz fastq 1020140400.0 13422900.0 GSM8760184 r1 0:76 A:246705959;C:238000533;G:239066122;T:296188699;N:179087 76       246705959 238000533 239066122 296188699 179087 SRX27491069 SRS23912867 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34627 34627 SRR32145158 SRX27491069 SRS23912867 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 2 GSM8760184   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 2 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760184 GSM8760184: kat6a Replicate 2; Danio rerio; RNA Seq GSM8760184 r1 GSM8760184 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a2_S2_L002_R1_001.fastq.gz fastq 977643632.0 12863732.0 GSM8760184 r2 0:76 A:235933957;C:228339408;G:228898216;T:284296721;N:175330 76       235933957 228339408 228898216 284296721 175330 SRX27491069 SRS23912867 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34628 34628 SRR32145159 SRX27491069 SRS23912867 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 2 GSM8760184   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 2 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760184 GSM8760184: kat6a Replicate 2; Danio rerio; RNA Seq GSM8760184 r1 GSM8760184 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a2_S2_L003_R1_001.fastq.gz fastq 1003014712.0 13197562.0 GSM8760184 r3 0:76 A:243233308;C:233802542;G:234581740;T:291313383;N:83739 76       243233308 233802542 234581740 291313383 83739 SRX27491069 SRS23912867 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34629 34629 SRR32145160 SRX27491069 SRS23912867 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 2 GSM8760184   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 2 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760184 GSM8760184: kat6a Replicate 2; Danio rerio; RNA Seq GSM8760184 r1 GSM8760184 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a2_S2_L004_R1_001.fastq.gz fastq 971822564.0 12787139.0 GSM8760184 r4 0:76 A:235490570;C:226606386;G:226825751;T:282823868;N:75989 76       235490570 226606386 226825751 282823868 75989 SRX27491069 SRS23912867 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34630 34630 SRR32145161 SRX27491068 SRS23912866 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 1 GSM8760183   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 1 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760183 GSM8760183: kat6a Replicate 1; Danio rerio; RNA Seq GSM8760183 r1 GSM8760183 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a1_S1_L001_R1_001.fastq.gz fastq 1199414140.0 15781765.0 GSM8760183 r1 0:76 A:302128648;C:264050936;G:275501956;T:357525321;N:207279 76       302128648 264050936 275501956 357525321 207279 SRX27491068 SRS23912866 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34631 34631 SRR32145162 SRX27491068 SRS23912866 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 1 GSM8760183   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 1 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760183 GSM8760183: kat6a Replicate 1; Danio rerio; RNA Seq GSM8760183 r1 GSM8760183 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a1_S1_L002_R1_001.fastq.gz fastq 1146031360.0 15079360.0 GSM8760183 r2 0:76 A:288111631;C:252600982;G:262972849;T:342138841;N:207057 76       288111631 252600982 262972849 342138841 207057 SRX27491068 SRS23912866 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34632 34632 SRR32145163 SRX27491068 SRS23912866 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 1 GSM8760183   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 1 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760183 GSM8760183: kat6a Replicate 1; Danio rerio; RNA Seq GSM8760183 r1 GSM8760183 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a1_S1_L003_R1_001.fastq.gz fastq 1179501760.0 15519760.0 GSM8760183 r3 0:76 A:297785533;C:259437124;G:270403974;T:351772505;N:102624 76       297785533 259437124 270403974 351772505 102624 SRX27491068 SRS23912866 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34633 34633 SRR32145164 SRX27491068 SRS23912866 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       kat6a Replicate 1 GSM8760183   tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing kat6a Replicate 1 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760183 GSM8760183: kat6a Replicate 1; Danio rerio; RNA Seq GSM8760183 r1 GSM8760183 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     kat6a1_S1_L004_R1_001.fastq.gz fastq 1138207844.0 14976419.0 GSM8760183 r4 0:76 A:287208643;C:250440049;G:260378372;T:340095505;N:85275 76       287208643 250440049 260378372 340095505 85275 SRX27491068 SRS23912866 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34634 34634 SRR32145165 SRX27491067 SRS23912865 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 4 GSM8760182   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 4 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760182 GSM8760182: WT Replicate 4; Danio rerio; RNA Seq GSM8760182 r1 GSM8760182 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT3_S8_L001_R1_001.fastq.gz fastq 1105608708.0 14547483.0 GSM8760182 r1 0:76 A:275003530;C:255171379;G:257731739;T:317503855;N:198205 76       275003530 255171379 257731739 317503855 198205 SRX27491067 SRS23912865 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34635 34635 SRR32145166 SRX27491067 SRS23912865 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 4 GSM8760182   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 4 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760182 GSM8760182: WT Replicate 4; Danio rerio; RNA Seq GSM8760182 r1 GSM8760182 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT3_S8_L002_R1_001.fastq.gz fastq 1057949108.0 13920383.0 GSM8760182 r2 0:76 A:262643868;C:244445110;G:246372974;T:304292800;N:194356 76       262643868 244445110 246372974 304292800 194356 SRX27491067 SRS23912865 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34636 34636 SRR32145167 SRX27491067 SRS23912865 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 4 GSM8760182   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 4 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760182 GSM8760182: WT Replicate 4; Danio rerio; RNA Seq GSM8760182 r1 GSM8760182 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT3_S8_L003_R1_001.fastq.gz fastq 1087749848.0 14312498.0 GSM8760182 r3 0:76 A:271320835;C:250818322;G:253044246;T:312473326;N:93119 76       271320835 250818322 253044246 312473326 93119 SRX27491067 SRS23912865 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34637 34637 SRR32145168 SRX27491067 SRS23912865 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 4 GSM8760182   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 4 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760182 GSM8760182: WT Replicate 4; Danio rerio; RNA Seq GSM8760182 r1 GSM8760182 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT3_S8_L004_R1_001.fastq.gz fastq 1051964032.0 13841632.0 GSM8760182 r4 0:76 A:262165724;C:242738788;G:244236708;T:302743784;N:79028 76       262165724 242738788 244236708 302743784 79028 SRX27491067 SRS23912865 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34638 34638 SRR32145169 SRX27491066 SRS23912864 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 3 GSM8760181   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 3 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760181 GSM8760181: WT Replicate 3; Danio rerio; RNA Seq GSM8760181 r1 GSM8760181 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT3_S7_L001_R1_001.fastq.gz fastq 1039833292.0 13682017.0 GSM8760181 r1 0:76 A:250507910;C:247806634;G:245922610;T:295415371;N:180767 76       250507910 247806634 245922610 295415371 180767 SRX27491066 SRS23912864 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34639 34639 SRR32145170 SRX27491066 SRS23912864 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 3 GSM8760181   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 3 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760181 GSM8760181: WT Replicate 3; Danio rerio; RNA Seq GSM8760181 r1 GSM8760181 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT3_S7_L002_R1_001.fastq.gz fastq 997262196.0 13121871.0 GSM8760181 r2 0:76 A:239743869;C:237950132;G:235660496;T:283726570;N:181129 76       239743869 237950132 235660496 283726570 181129 SRX27491066 SRS23912864 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34640 34640 SRR32145171 SRX27491066 SRS23912864 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 3 GSM8760181   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 3 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760181 GSM8760181: WT Replicate 3; Danio rerio; RNA Seq GSM8760181 r1 GSM8760181 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT3_S7_L003_R1_001.fastq.gz fastq 1021625592.0 13442442.0 GSM8760181 r3 0:76 A:246769441;C:243242872;G:241137871;T:290388153;N:87255 76       246769441 243242872 241137871 290388153 87255 SRX27491066 SRS23912864 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34641 34641 SRR32145172 SRX27491066 SRS23912864 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 3 GSM8760181   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 3 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760181 GSM8760181: WT Replicate 3; Danio rerio; RNA Seq GSM8760181 r1 GSM8760181 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT3_S7_L004_R1_001.fastq.gz fastq 988410400.0 13005400.0 GSM8760181 r4 0:76 A:238549859;C:235494730;G:232864346;T:281426699;N:74766 76       238549859 235494730 232864346 281426699 74766 SRX27491066 SRS23912864 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34642 34642 SRR32145173 SRX27491065 SRS23912863 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 2 GSM8760180   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 2 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760180 GSM8760180: WT Replicate 2; Danio rerio; RNA Seq GSM8760180 r1 GSM8760180 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT2_S6_L001_R1_001.fastq.gz fastq 1197864500.0 15761375.0 GSM8760180 r1 0:76 A:284440503;C:291285146;G:286388620;T:335544162;N:206069 76       284440503 291285146 286388620 335544162 206069 SRX27491065 SRS23912863 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34643 34643 SRR32145174 SRX27491065 SRS23912863 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 2 GSM8760180   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 2 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760180 GSM8760180: WT Replicate 2; Danio rerio; RNA Seq GSM8760180 r1 GSM8760180 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT2_S6_L002_R1_001.fastq.gz fastq 1150109368.0 15133018.0 GSM8760180 r2 0:76 A:272466884;C:280134047;G:274738822;T:322560009;N:209606 76       272466884 280134047 274738822 322560009 209606 SRX27491065 SRS23912863 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34644 34644 SRR32145175 SRX27491065 SRS23912863 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 2 GSM8760180   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 2 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760180 GSM8760180: WT Replicate 2; Danio rerio; RNA Seq GSM8760180 r1 GSM8760180 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT2_S6_L003_R1_001.fastq.gz fastq 1181538408.0 15546558.0 GSM8760180 r3 0:76 A:281618798;C:286909225;G:281700417;T:331210989;N:98979 76       281618798 286909225 281700417 331210989 98979 SRX27491065 SRS23912863 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34645 34645 SRR32145176 SRX27491065 SRS23912863 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 2 GSM8760180   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 2 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760180 GSM8760180: WT Replicate 2; Danio rerio; RNA Seq GSM8760180 r1 GSM8760180 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT2_S6_L004_R1_001.fastq.gz fastq 1144519796.0 15059471.0 GSM8760180 r4 0:76 A:272627373;C:278113659;G:272292478;T:321399688;N:86598 76       272627373 278113659 272292478 321399688 86598 SRX27491065 SRS23912863 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34646 34646 SRR32145177 SRX27491064 SRS23912862 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 1 GSM8760179   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 1 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760179 GSM8760179: WT Replicate 1; Danio rerio; RNA Seq GSM8760179 r1 GSM8760179 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT1_S5_L001_R1_001.fastq.gz fastq 1231111156.0 16198831.0 GSM8760179 r1 0:76 A:302054822;C:285868196;G:294755776;T:348218223;N:214139 76       302054822 285868196 294755776 348218223 214139 SRX27491064 SRS23912862 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34647 34647 SRR32145178 SRX27491064 SRS23912862 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 1 GSM8760179   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 1 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760179 GSM8760179: WT Replicate 1; Danio rerio; RNA Seq GSM8760179 r1 GSM8760179 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT1_S5_L002_R1_001.fastq.gz fastq 1182939392.0 15564992.0 GSM8760179 r2 0:76 A:289611553;C:275053581;G:283000505;T:335062758;N:210995 76       289611553 275053581 283000505 335062758 210995 SRX27491064 SRS23912862 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34648 34648 SRR32145179 SRX27491064 SRS23912862 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 1 GSM8760179   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 1 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760179 GSM8760179: WT Replicate 1; Danio rerio; RNA Seq GSM8760179 r1 GSM8760179 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT1_S5_L003_R1_001.fastq.gz fastq 1211221728.0 15937128.0 GSM8760179 r3 0:76 A:297941702;C:281047445;G:289384552;T:342744260;N:103769 76       297941702 281047445 289384552 342744260 103769 SRX27491064 SRS23912862 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
34649 34649 SRR32145180 SRX27491064 SRS23912862 SRP560249 PRJNA1216300 Insulin like growth factor signalling regulates zebrafish lymphatic vessel development GSE288160 Transcriptome Analysis RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.       WT Replicate 1 GSM8760179   tissue:Chondrocyte|cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing WT Replicate 1 The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column Chondrocyte   At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. cell type:Chondrocyte|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry GSM8760179 GSM8760179: WT Replicate 1; Danio rerio; RNA Seq GSM8760179 r1 GSM8760179 1 At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP560249     WT1_S5_L004_R1_001.fastq.gz fastq 1173801836.0 15444761.0 GSM8760179 r4 0:76 A:288534595;C:272469282;G:279986497;T:332720262;N:91200 76       288534595 272469282 279986497 332720262 91200 SRX27491064 SRS23912862 SRA2062832 Molecular Medicine and Pathology, University of Auckland Molecular Medicine and Pathology, University of Auckland                       B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   New Zealand 2025-01-27 Larval Larval Bone or Cartilage Skeletal Element
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

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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");;