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F1 WT", "1 F1 WT", "bone", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP485828", null, null, "L1EGI0701124--WT_F1.R1.raw.fastq.gz L1EGI0701124--WT_F1.R2.raw.fastq.gz", "fastq fastq", 8373285522.0, 27726111.0, "L1EGI0701124 WT F1.R1.raw.fastq.gz", "0:151 1:151", "A:2148645285;C:1996284185;G:2121066399;T:2107255525;N:34128", 151, 151, null, null, 2148645285, 1996284185, 2121066399, 2107255525, 34128, "SRX23388295", "SRS20249488", "SRA1791477", "zhejiang university|the college of animal science", "zhejiang university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-01-25", "Undetermined", "Undetermined", "Bone or Cartilage", "Skeletal Element"], [38060, "SRR1524244", "SRX661009", "SRS665984", "SRP044781", "PRJNA255848", "Danio rerio Transcriptome", "PRJNA255848", "Transcriptome Analysis", "Transcriptome analysis of 12 zebrafish tissues", "parent bioproject:PRJNA255979", "pubmed:27189481", "Zebrafish Bones", "Zebrafish B1s", "F Dr 8", null, "strain:AB|age:5 month|biomaterial provider:INRA|sex:female|tissue:B1s|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish B1s", "F Dr 8", "F Dr 8", "Total RNA was qualified using an Agilent BioAnalyzer and 1 \u00b5g was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "SRP044781", null, null, "F_Dr_8_ACAGTG_L003_R2.fastq.gz F_Dr_8_ACAGTG_L003_R1.fastq.gz", "fastq fastq", 19343193000.0, 96715965.0, "F Dr 8 files", "0:100 1:100", "A:5011655819;C:4570121318;G:4634671917;T:4933523152;N:193220794", 100, 100, null, null, 5011655819, 4570121318, 4634671917, 4933523152, 193220794, "SRX661009", "SRS665984", "SRA176464", "INRA|Fish Physiology and Genomics", "INRA PhyloFish", 2, 0.88337, 0.91338, 0.05259, 0.05508, 0.75103, 0.75317, 0.51459, 0.51744, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "France", "2014-07-26", "Adult", "Adult", "Bone or Cartilage", "Skeletal Element"], [53148, "SRR9692022", "SRX6451056", "SRS5104327", "SRP214773", "PRJNA554788", "Gene expression analysis in the zebrafish fractured scale", "GSE134330", "Transcriptome Analysis", "Bone is a connective tissue which undergoes continuous remodeling including bone resorption and formation by osteoclasts OCs and osteoblasts OBs respectively. Recently extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs OCs and bone matrix providing an elegant model to visualize OC OB communication. Here we developed a double transgenic zebrafish line trap:GFP; osterix:mCherry which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer respectively. Utilizing this double transgenic line in combination with Hoechst 33342 Hoe staining we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry GFP\u2013 mCh+ Hoehigh OB fraction GFPlow mCh+ Hoehigh OC precursor pOC fraction GFPhigh Hoehigh mature OC mOC fraction and mCh+ Hoe\u2013 OB derived extracellular vesicle EV fraction. In this study we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each fraction. Overall design: mRNA profiles of isolated OBs pOCs mOCs and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.", null, "pubmed:32327701", null, "EV 2", "GSM3942348", null, "source name:osteoblast derived extracellular vesicles|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblast derived extracellular vesicles|molecule type:Amplified RNA", "EV 2", "Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.", "osteoblast derived extracellular vesicles", null, "Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 \u03bcg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the 3\u2019 ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.", null, "age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblast derived extracellular vesicles|molecule type:Amplified RNA", "GSM3942348", "GSM3942348: EV 2; Danio rerio; RNA Seq", "GSM3942348", null, "1", "Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 \u03bcg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP214773", null, null, "EV_2_R1.fastq.gz EV_2_R2.fastq.gz", "fastq fastq", 6759957000.0, 22533190.0, "GSM3942348 r1", "0:150 1:150", "A:1706593126;C:1699056754;G:1646763192;T:1707067337;N:476591", 150, 150, null, null, 1706593126, 1699056754, 1646763192, 1707067337, 476591, "SRX6451056", "SRS5104327", "SRA921382", "GEO", "Kanazawa University", 2, 0.94501, 0.94549, 0.02885, 0.03033, 0.80458, 0.80957, 0.48799, 0.50474, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "3prime", "poly_a", "nextera", "sc", "single_cell_plate", "quartzseq", null, "Japan", "2019-07-16", "Adult", "Adult", "Bone or Cartilage", "Skeletal Element"], [53149, "SRR9692021", "SRX6451055", "SRS5104326", "SRP214773", "PRJNA554788", "Gene expression analysis in the zebrafish fractured scale", "GSE134330", "Transcriptome Analysis", "Bone is a connective tissue which undergoes continuous remodeling including bone resorption and formation by osteoclasts OCs and osteoblasts OBs respectively. Recently extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs OCs and bone matrix providing an elegant model to visualize OC OB communication. Here we developed a double transgenic zebrafish line trap:GFP; osterix:mCherry which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer respectively. Utilizing this double transgenic line in combination with Hoechst 33342 Hoe staining we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry GFP\u2013 mCh+ Hoehigh OB fraction GFPlow mCh+ Hoehigh OC precursor pOC fraction GFPhigh Hoehigh mature OC mOC fraction and mCh+ Hoe\u2013 OB derived extracellular vesicle EV fraction. In this study we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each fraction. Overall design: mRNA profiles of isolated OBs pOCs mOCs and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.", null, "pubmed:32327701", null, "EV 1", "GSM3942347", null, "source name:osteoblast derived extracellular vesicles|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblast derived extracellular vesicles|molecule type:Amplified RNA", "EV 1", "Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.", "osteoblast derived extracellular vesicles", null, "Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 \u03bcg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the 3\u2019 ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.", null, "age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblast derived extracellular vesicles|molecule type:Amplified RNA", "GSM3942347", "GSM3942347: EV 1; Danio rerio; RNA Seq", "GSM3942347", null, "1", "Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 \u03bcg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP214773", null, null, "EV_1_R1.fastq.gz EV_1_R2.fastq.gz", "fastq fastq", 6368980200.0, 21229934.0, "GSM3942347 r1", "0:150 1:150", "A:1609224577;C:1593521490;G:1569729629;T:1596056057;N:448447", 150, 150, null, null, 1609224577, 1593521490, 1569729629, 1596056057, 448447, "SRX6451055", "SRS5104326", "SRA921382", "GEO", "Kanazawa University", 2, 0.93738, 0.93601, 0.02919, 0.03087, 0.79669, 0.80312, 0.50627, 0.50567, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "3prime", "poly_a", "nextera", "sc", "single_cell_plate", "quartzseq", null, "Japan", "2019-07-16", "Adult", "Adult", "Bone or Cartilage", "Skeletal Element"], [53154, "SRR9692016", "SRX6451050", "SRS5104321", "SRP214773", "PRJNA554788", "Gene expression analysis in the zebrafish fractured scale", "GSE134330", "Transcriptome Analysis", "Bone is a connective tissue which undergoes continuous remodeling including bone resorption and formation by osteoclasts OCs and osteoblasts OBs respectively. Recently extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs OCs and bone matrix providing an elegant model to visualize OC OB communication. Here we developed a double transgenic zebrafish line trap:GFP; osterix:mCherry which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer respectively. Utilizing this double transgenic line in combination with Hoechst 33342 Hoe staining we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry GFP\u2013 mCh+ Hoehigh OB fraction GFPlow mCh+ Hoehigh OC precursor pOC fraction GFPhigh Hoehigh mature OC mOC fraction and mCh+ Hoe\u2013 OB derived extracellular vesicle EV fraction. In this study we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each fraction. Overall design: mRNA profiles of isolated OBs pOCs mOCs and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.", null, "pubmed:32327701", null, "OB 2", "GSM3942342", null, "source name:osteoblasts|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblasts|molecule type:Amplified RNA", "OB 2", "Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.", "osteoblasts", null, "Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 \u03bcg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the 3\u2019 ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.", null, "age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblasts|molecule type:Amplified RNA", "GSM3942342", "GSM3942342: OB 2; Danio rerio; RNA Seq", "GSM3942342", null, "1", "Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 \u03bcg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP214773", null, null, "OB_2_R1.fastq.gz OB_2_R2.fastq.gz", "fastq fastq", 4566907200.0, 15223024.0, "GSM3942342 r1", "0:150 1:150", "A:1133280984;C:1162119484;G:1119861724;T:1151514772;N:130236", 150, 150, null, null, 1133280984, 1162119484, 1119861724, 1151514772, 130236, "SRX6451050", "SRS5104321", "SRA921382", "GEO", "Kanazawa University", 2, 0.9502, 0.9473, 0.0382, 0.04036, 0.77853, 0.78719, 0.47336, 0.4862, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "3prime", "poly_a", "nextera", "sc", "single_cell_plate", "quartzseq", null, "Japan", "2019-07-16", "Adult", "Adult", "Bone or Cartilage", "Skeletal Element"], [53155, "SRR9692015", "SRX6451049", "SRS5104320", "SRP214773", "PRJNA554788", "Gene expression analysis in the zebrafish fractured scale", "GSE134330", "Transcriptome Analysis", "Bone is a connective tissue which undergoes continuous remodeling including bone resorption and formation by osteoclasts OCs and osteoblasts OBs respectively. Recently extracellular vesicles EVs are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs OCs and bone matrix providing an elegant model to visualize OC OB communication. Here we developed a double transgenic zebrafish line trap:GFP; osterix:mCherry which expresses GFP and mCherry under the control of the OC specific trap tartrate resistant acid phosphatase and OB specific osterix enhancer respectively. Utilizing this double transgenic line in combination with Hoechst 33342 Hoe staining we isolated four distinct fractions from the scale at 1 day post fracture by flow cytometry GFP\u2013 mCh+ Hoehigh OB fraction GFPlow mCh+ Hoehigh OC precursor pOC fraction GFPhigh Hoehigh mature OC mOC fraction and mCh+ Hoe\u2013 OB derived extracellular vesicle EV fraction. In this study we have performed RNA seq analysis using these four fractions to examine the gene expression profile of each fraction. Overall design: mRNA profiles of isolated OBs pOCs mOCs and OB derived EVs in the zebrafish fractured scales were generated by Quartz seq using Illumina NextSeq500.", null, "pubmed:32327701", null, "OB 1", "GSM3942341", null, "source name:osteoblasts|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblasts|molecule type:Amplified RNA", "OB 1", "Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using HiSAT2 version 2.1.0. Reads per million RPM were calculated using the Subread ver. 1.6.4. Genome build: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.", "osteoblasts", null, "Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 \u03bcg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the 3\u2019 ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.", null, "age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoblasts|molecule type:Amplified RNA", "GSM3942341", "GSM3942341: OB 1; Danio rerio; RNA Seq", "GSM3942341", null, "1", "Total RNAs were extracted from sorted cells using RNeasy Mini Kit QIAGEN. Cells were directly sorted in a lysis buffer containing 1 \u03bcg/mL of polyinosinic polycytidylic acid and total RNA was extracted using RNeasy Mini Kit. Reverse transcription RT was performed using Super Script III Thermo Fisher Scientific and an RT primer which contains oligo dT T7 promoter and PCR target region sequences. post digestion of remaining RT primers by exonuclease I Takara a poly A tail was added to the three prime ends of the first strand cDNAs using terminal transferase Sigma. The second strand DNA was then synthesized using MightyAmp DNA polymerase Thermo Fisher Scientific and a tagging primer which contains oligo dT and PCR target region sequences. PCR amplification was performed using a suppression primer which allow to amplify small size DNA that contains complementary sequences at both ends of the template DNA. The amplified double strand cDNA was purified using QIAquick PCR Purification Kit Qiagen. Library preparation was performed using Nextera XT DNA Library Preparation Kit illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP214773", null, null, "OB_1_R1.fastq.gz OB_1_R2.fastq.gz", "fastq fastq", 3924215700.0, 13080719.0, "GSM3942341 r1", "0:150 1:150", "A:983923789;C:989882668;G:965519773;T:984780602;N:108868", 150, 150, null, null, 983923789, 989882668, 965519773, 984780602, 108868, "SRX6451049", "SRS5104320", "SRA921382", "GEO", "Kanazawa University", 2, 0.95148, 0.94857, 0.03822, 0.04077, 0.77705, 0.78729, 0.48248, 0.49117, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "3prime", "poly_a", "nextera", "sc", "single_cell_plate", "quartzseq", null, "Japan", "2019-07-16", "Adult", "Adult", "Bone or Cartilage", "Skeletal Element"], [58579, "SRR11425295", "SRX8003661", "SRS6377641", "SRP254053", "PRJNA615232", "Control of osteoblast regeneration by a train of Erk activity waves", "GSE147551", "Transcriptome Analysis", "We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.", null, "pubmed:33408418", null, "high Erk activity; rep1", "GSM4433141", null, "tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales", "high Erk activity; rep1", "Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq", "high Erk activity", "Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 \u00b5m disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 \u00b5l of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 \u00b5l of supernatant was removed quenched with 65\u00b5l sheep serum Sigma S2263 on ice and 500 \u00b5l of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 \u00b5l filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 \u00b5g/ml DAPI Sigma D9542 was added to the tube.", "fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales", "GSM4433141", "GSM4433141: high Erk activity; rep1; Danio rerio; RNA Seq", "GSM4433141", null, "1", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "GEO Accession:GSM4433141", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP254053", null, null, "3G_plus_1.fq.gz 3G_plus_2.fq.gz", "fastq fastq", 4698595200.0, 46985952.0, "GSM4433141 r1", "0:100 1:100", "A:1261622105;C:1085007643;G:1066886112;T:1285079340;N:0", 100, 100, null, null, 1261622105, 1085007643, 1066886112, 1285079340, 0, "SRX8003661", "SRS6377641", "SRA1059429", "GEO", "Poss, Cell Biology, Duke University", 1, 0.86576, null, 0.11767, null, 0.81262, null, 0.52377, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-25", "Undetermined", "Undetermined", "Bone or Cartilage", "Skeletal Element"], [58580, "SRR11425294", "SRX8003660", "SRS6377640", "SRP254053", "PRJNA615232", "Control of osteoblast regeneration by a train of Erk activity waves", "GSE147551", "Transcriptome Analysis", "We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.", null, "pubmed:33408418", null, "low Erk activity; rep3", "GSM4433140", null, "tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales", "low Erk activity; rep3", "Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq", "low Erk activity", "Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 \u00b5m disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 \u00b5l of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 \u00b5l of supernatant was removed quenched with 65\u00b5l sheep serum Sigma S2263 on ice and 500 \u00b5l of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 \u00b5l filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 \u00b5g/ml DAPI Sigma D9542 was added to the tube.", "fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales", "GSM4433140", "GSM4433140: low Erk activity; rep3; Danio rerio; RNA Seq", "GSM4433140", null, "1", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "GEO Accession:GSM4433140", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP254053", null, null, "6B_minus_1.fq.gz 6B_minus_2.fq.gz", "fastq fastq", 4707217000.0, 47072170.0, "GSM4433140 r1", "0:100 1:100", "A:1268188059;C:1086056259;G:1067448053;T:1285524629;N:0", 100, 100, null, null, 1268188059, 1086056259, 1067448053, 1285524629, 0, "SRX8003660", "SRS6377640", "SRA1059429", "GEO", "Poss, Cell Biology, Duke University", 1, 0.88883, null, 0.05585, null, 0.82071, null, 0.47905, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-25", "Undetermined", "Undetermined", "Bone or Cartilage", "Skeletal Element"], [58581, "SRR11425293", "SRX8003659", "SRS6377639", "SRP254053", "PRJNA615232", "Control of osteoblast regeneration by a train of Erk activity waves", "GSE147551", "Transcriptome Analysis", "We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.", null, "pubmed:33408418", null, "low Erk activity; rep2", "GSM4433139", null, "tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales", "low Erk activity; rep2", "Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq", "low Erk activity", "Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 \u00b5m disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 \u00b5l of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 \u00b5l of supernatant was removed quenched with 65\u00b5l sheep serum Sigma S2263 on ice and 500 \u00b5l of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 \u00b5l filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 \u00b5g/ml DAPI Sigma D9542 was added to the tube.", "fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales", "GSM4433139", "GSM4433139: low Erk activity; rep2; Danio rerio; RNA Seq", "GSM4433139", null, "1", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "GEO Accession:GSM4433139", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP254053", null, null, "5G_minus_1.fq.gz 5G_minus_2.fq.gz", "fastq fastq", 4705295600.0, 47052956.0, "GSM4433139 r1", "0:100 1:100", "A:1240779500;C:1112511484;G:1096653049;T:1255351567;N:0", 100, 100, null, null, 1240779500, 1112511484, 1096653049, 1255351567, 0, "SRX8003659", "SRS6377639", "SRA1059429", "GEO", "Poss, Cell Biology, Duke University", 1, 0.89254, null, 0.04065, null, 0.81197, null, 0.46307, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-25", "Undetermined", "Undetermined", "Bone or Cartilage", "Skeletal Element"], [58582, "SRR11425292", "SRX8003658", "SRS6377638", "SRP254053", "PRJNA615232", "Control of osteoblast regeneration by a train of Erk activity waves", "GSE147551", "Transcriptome Analysis", "We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.", null, "pubmed:33408418", null, "low Erk activity; rep1", "GSM4433138", null, "tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales", "low Erk activity; rep1", "Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq", "low Erk activity", "Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 \u00b5m disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 \u00b5l of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 \u00b5l of supernatant was removed quenched with 65\u00b5l sheep serum Sigma S2263 on ice and 500 \u00b5l of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 \u00b5l filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 \u00b5g/ml DAPI Sigma D9542 was added to the tube.", "fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales", "GSM4433138", "GSM4433138: low Erk activity; rep1; Danio rerio; RNA Seq", "GSM4433138", null, "1", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "GEO Accession:GSM4433138", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP254053", null, null, "3G_minus_1.fq.gz 3G_minus_2.fq.gz", "fastq fastq", 4707783400.0, 47077834.0, "GSM4433138 r1", "0:100 1:100", "A:1275040914;C:1077730597;G:1059242617;T:1295769272;N:0", 100, 100, null, null, 1275040914, 1077730597, 1059242617, 1295769272, 0, "SRX8003658", "SRS6377638", "SRA1059429", "GEO", "Poss, Cell Biology, Duke University", 1, 0.8629, null, 0.13994, null, 0.7838, null, 0.50568, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-25", "Undetermined", "Undetermined", "Bone or Cartilage", "Skeletal Element"], [58583, "SRR11425297", "SRX8003657", "SRS6377637", "SRP254053", "PRJNA615232", "Control of osteoblast regeneration by a train of Erk activity waves", "GSE147551", "Transcriptome Analysis", "We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.", null, "pubmed:33408418", null, "high Erk activity; rep3", "GSM4433143", null, "tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales", "high Erk activity; rep3", "Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq", "high Erk activity", "Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 \u00b5m disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 \u00b5l of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 \u00b5l of supernatant was removed quenched with 65\u00b5l sheep serum Sigma S2263 on ice and 500 \u00b5l of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 \u00b5l filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 \u00b5g/ml DAPI Sigma D9542 was added to the tube.", "fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales", "GSM4433143", "GSM4433143: high Erk activity; rep3; Danio rerio; RNA Seq", "GSM4433143", null, "1", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "GEO Accession:GSM4433143", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP254053", null, null, "6B_plus_1.fq.gz 6B_plus_2.fq.gz", "fastq fastq", 4703728000.0, 47037280.0, "GSM4433143 r1", "0:100 1:100", "A:1231849303;C:1116643672;G:1102072724;T:1253162301;N:0", 100, 100, null, null, 1231849303, 1116643672, 1102072724, 1253162301, 0, "SRX8003657", "SRS6377637", "SRA1059429", "GEO", "Poss, Cell Biology, Duke University", 1, 0.89702, null, 0.07131, null, 0.82978, null, 0.49499, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-25", "Undetermined", "Undetermined", "Bone or Cartilage", "Skeletal Element"], [58584, "SRR11425296", "SRX8003656", "SRS6377636", "SRP254053", "PRJNA615232", "Control of osteoblast regeneration by a train of Erk activity waves", "GSE147551", "Transcriptome Analysis", "We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.", null, "pubmed:33408418", null, "high Erk activity; rep2", "GSM4433142", null, "tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales", "high Erk activity; rep2", "Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq", "high Erk activity", "Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 \u00b5m disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 \u00b5l of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 \u00b5l of supernatant was removed quenched with 65\u00b5l sheep serum Sigma S2263 on ice and 500 \u00b5l of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 \u00b5l filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 \u00b5g/ml DAPI Sigma D9542 was added to the tube.", "fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales", "GSM4433142", "GSM4433142: high Erk activity; rep2; Danio rerio; RNA Seq", "GSM4433142", null, "1", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "GEO Accession:GSM4433142", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP254053", null, null, "5G_plus_1.fq.gz 5G_plus_2.fq.gz", "fastq fastq", 4708623600.0, 47086236.0, "GSM4433142 r1", "0:100 1:100", "A:1200601624;C:1150903127;G:1136628277;T:1220490572;N:0", 100, 100, null, null, 1200601624, 1150903127, 1136628277, 1220490572, 0, "SRX8003656", "SRS6377636", "SRA1059429", "GEO", "Poss, Cell Biology, Duke University", 1, 0.90729, null, 0.03751, null, 0.84433, null, 0.50342, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-25", "Undetermined", "Undetermined", "Bone or Cartilage", "Skeletal Element"], [59343, "SRR11862830", "SRX8413198", "SRS6725509", "SRP265073", "PRJNA635584", "Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton", "GSE151354", "Transcriptome Analysis", "The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD which is characterized by skeletal defects including scoliosis large epiphyses wide growth plates and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint as well as severe dysmorphologies of the facial skeleton skullcap and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1 which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants", null, "pubmed:33462117", null, "nkx3.2 mutant cartilage", "GSM4575943", null, "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", null, "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.", null, "strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:nkx3.2 el802/el802|age:22 dpf", "GSM4575943", "GSM4575943: nkx3.2 mutant cartilage; Danio rerio; RNA Seq", "GSM4575943", null, "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", null, "SRP265073", null, null, "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, null, null, 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", null, "United States", "2020-05-28", "Larval", "Larval", "Bone or Cartilage", "Skeletal Element"], [59344, "SRR11862831", "SRX8413198", "SRS6725509", "SRP265073", "PRJNA635584", "Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton", "GSE151354", "Transcriptome Analysis", "The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD which is characterized by skeletal defects including scoliosis large epiphyses wide growth plates and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint as well as severe dysmorphologies of the facial skeleton skullcap and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1 which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants", null, "pubmed:33462117", null, "nkx3.2 mutant cartilage", "GSM4575943", null, "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", null, "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.", null, "strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:nkx3.2 el802/el802|age:22 dpf", "GSM4575943", "GSM4575943: nkx3.2 mutant cartilage; Danio rerio; RNA Seq", "GSM4575943", null, "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", null, "SRP265073", null, null, "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, null, null, 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", null, "United States", "2020-05-28", "Larval", "Larval", "Bone or Cartilage", "Skeletal Element"], [59345, "SRR11862832", "SRX8413198", "SRS6725509", "SRP265073", "PRJNA635584", "Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton", "GSE151354", "Transcriptome Analysis", "The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD which is characterized by skeletal defects including scoliosis large epiphyses wide growth plates and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint as well as severe dysmorphologies of the facial skeleton skullcap and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1 which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants", null, "pubmed:33462117", null, "nkx3.2 mutant cartilage", "GSM4575943", null, "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", null, "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.", null, "strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:nkx3.2 el802/el802|age:22 dpf", "GSM4575943", "GSM4575943: nkx3.2 mutant cartilage; Danio rerio; RNA Seq", "GSM4575943", null, "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", null, "SRP265073", null, null, "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, null, null, 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", null, "United States", "2020-05-28", "Larval", "Larval", "Bone or Cartilage", "Skeletal Element"], [59346, "SRR11862833", "SRX8413198", "SRS6725509", "SRP265073", "PRJNA635584", "Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton", "GSE151354", "Transcriptome Analysis", "The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD which is characterized by skeletal defects including scoliosis large epiphyses wide growth plates and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint as well as severe dysmorphologies of the facial skeleton skullcap and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1 which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants", null, "pubmed:33462117", null, "nkx3.2 mutant cartilage", "GSM4575943", null, "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", null, "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.", null, "strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:nkx3.2 el802/el802|age:22 dpf", "GSM4575943", "GSM4575943: nkx3.2 mutant cartilage; Danio rerio; RNA Seq", "GSM4575943", null, "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", null, "SRP265073", null, null, "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, null, null, 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", null, "United States", "2020-05-28", "Larval", "Larval", "Bone or Cartilage", "Skeletal Element"], [59347, "SRR11862826", "SRX8413197", "SRS6725508", "SRP265073", "PRJNA635584", "Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton", "GSE151354", "Transcriptome Analysis", "The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD which is characterized by skeletal defects including scoliosis large epiphyses wide growth plates and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint as well as severe dysmorphologies of the facial skeleton skullcap and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1 which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants", null, "pubmed:33462117", null, "WT cartilage", "GSM4575942", null, "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", null, "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.", null, "strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:WT|age:21 dpf", "GSM4575942", "GSM4575942: WT cartilage; Danio rerio; RNA Seq", "GSM4575942", null, "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", null, "SRP265073", null, null, "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, null, null, 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", null, "United States", "2020-05-28", "Larval", "Larval", "Bone or Cartilage", "Skeletal Element"], [59348, "SRR11862827", "SRX8413197", "SRS6725508", "SRP265073", "PRJNA635584", "Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton", "GSE151354", "Transcriptome Analysis", "The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD which is characterized by skeletal defects including scoliosis large epiphyses wide growth plates and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint as well as severe dysmorphologies of the facial skeleton skullcap and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1 which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants", null, "pubmed:33462117", null, "WT cartilage", "GSM4575942", null, "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", null, "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.", null, "strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:WT|age:21 dpf", "GSM4575942", "GSM4575942: WT cartilage; Danio rerio; RNA Seq", "GSM4575942", null, "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", null, "SRP265073", null, null, "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, null, null, 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", null, "United States", "2020-05-28", "Larval", "Larval", "Bone or Cartilage", "Skeletal Element"], [59349, "SRR11862828", "SRX8413197", "SRS6725508", "SRP265073", "PRJNA635584", "Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton", "GSE151354", "Transcriptome Analysis", "The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD which is characterized by skeletal defects including scoliosis large epiphyses wide growth plates and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint as well as severe dysmorphologies of the facial skeleton skullcap and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1 which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants", null, "pubmed:33462117", null, "WT cartilage", "GSM4575942", null, "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", null, "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.", null, "strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:WT|age:21 dpf", "GSM4575942", "GSM4575942: WT cartilage; Danio rerio; RNA Seq", "GSM4575942", null, "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", null, "SRP265073", null, null, "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, null, null, 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", null, "United States", "2020-05-28", "Larval", "Larval", "Bone or Cartilage", "Skeletal Element"], [59350, "SRR11862829", "SRX8413197", "SRS6725508", "SRP265073", "PRJNA635584", "Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton", "GSE151354", "Transcriptome Analysis", "The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through maturity. Rare mutations in the transcription factor NKX3.2 underlie Spondylo megaepiphyseal metaphyseal dysplasia SMMD which is characterized by skeletal defects including scoliosis large epiphyses wide growth plates and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint as well as severe dysmorphologies of the facial skeleton skullcap and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis indicating post embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre hypertrophic growth plate chondrocytes. Single cell RNA sequencing reveals an upregulation of stress induced pathways in mutants including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1 which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint adjacent chondrocytes. Overall design: Single cell RNA sequencing of FACS isolated cartilages fli:GFP/sox10:DsRed+ from wildtype and nkx3.2 mutants", null, "pubmed:33462117", null, "WT cartilage", "GSM4575942", null, "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", null, "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.", null, "strain:Tgfli1a:EGFPy1;Tgsox10:DsRedel10|genotype:WT|age:21 dpf", "GSM4575942", "GSM4575942: WT cartilage; Danio rerio; RNA Seq", "GSM4575942", null, "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", null, "SRP265073", null, null, "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, null, null, 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", null, "United States", "2020-05-28", "Larval", "Larval", "Bone or Cartilage", "Skeletal Element"], [74701, "SRR24003726", "SRX19807142", "SRS17168877", "SRP429947", "PRJNA949785", "Sequencing of zebrafish bone tissues", "PRJNA949785", "Other", "Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass", null, null, null, null, "eight month zebrafish bone tissues", null, "breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of b1 tissue in zebrafish", "case2 4", "case2 4", "Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP429947", null, null, "case2_4_1.fq.gz case2_4_2.fq.gz", "fastq fastq", 6631325400.0, 22104418.0, "case2 4 1.fq.gz", "0:150 1:150", "A:1790451511;C:1523987494;G:1517049214;T:1799837181;N:0", 150, 150, null, null, 1790451511, 1523987494, 1517049214, 1799837181, 0, "SRX19807142", "SRS17168877", "SRA1612461", "Sun Yat-sen University|Department of Epidemiology, School of Public Healt", "Sun Yat-sen University", 2, 0.94202, 0.94054, 0.06448, 0.06393, 0.71415, 0.71445, 0.52801, 0.52947, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-29", "Adult", "Adult", "Bone or Cartilage", "Skeletal Element"], [74702, "SRR24003727", "SRX19807141", "SRS17168877", "SRP429947", "PRJNA949785", "Sequencing of zebrafish bone tissues", "PRJNA949785", "Other", "Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass", null, null, null, null, "eight month zebrafish bone tissues", null, "breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of b1 tissue in zebrafish", "case2 3", "case2 3", "Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP429947", null, null, "case2_3_1.fq.gz case2_3_2.fq.gz", "fastq fastq", 6706743300.0, 22355811.0, "case2 3 1.fq.gz", "0:150 1:150", "A:1845685627;C:1507725453;G:1499541624;T:1853790596;N:0", 150, 150, null, null, 1845685627, 1507725453, 1499541624, 1853790596, 0, "SRX19807141", "SRS17168877", "SRA1612461", "Sun Yat-sen University|Department of Epidemiology, School of Public Healt", "Sun Yat-sen University", 2, 0.94268, 0.93594, 0.08009, 0.07937, 0.70402, 0.70441, 0.4556, 0.48818, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-29", "Adult", "Adult", "Bone or Cartilage", "Skeletal Element"], [74703, "SRR24003728", "SRX19807140", "SRS17168877", "SRP429947", "PRJNA949785", "Sequencing of zebrafish bone tissues", "PRJNA949785", "Other", "Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass", null, null, null, null, "eight month zebrafish bone tissues", null, "breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of b1 tissue in zebrafish", "case2 2", "case2 2", "Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP429947", null, null, "case2_2_1.fq.gz case2_2_2.fq.gz", "fastq fastq", 6677092200.0, 22256974.0, "case2 2 1.fq.gz", "0:150 1:150", "A:1864795230;C:1474224567;G:1465199644;T:1872872759;N:0", 150, 150, null, null, 1864795230, 1474224567, 1465199644, 1872872759, 0, "SRX19807140", "SRS17168877", "SRA1612461", "Sun Yat-sen University|Department of Epidemiology, School of Public Healt", "Sun Yat-sen University", 2, 0.93359, 0.92743, 0.0959, 0.09583, 0.69089, 0.69234, 0.48419, 0.48121, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-29", "Adult", "Adult", "Bone or Cartilage", "Skeletal Element"], [74704, "SRR24003729", "SRX19807139", "SRS17168877", "SRP429947", "PRJNA949785", "Sequencing of zebrafish bone tissues", "PRJNA949785", "Other", "Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass", null, null, null, null, "eight month zebrafish bone tissues", null, "breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of b1 tissue in zebrafish", "case2 1", "case2 1", "Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP429947", null, null, "case2_1_1.fq.gz case2_1_2.fq.gz", "fastq fastq", 6644478600.0, 22148262.0, "case2 1 1.fq.gz", "0:150 1:150", "A:1863814645;C:1460246773;G:1453279946;T:1867137236;N:0", 150, 150, null, null, 1863814645, 1460246773, 1453279946, 1867137236, 0, "SRX19807139", "SRS17168877", "SRA1612461", "Sun Yat-sen University|Department of Epidemiology, School of Public Healt", "Sun Yat-sen University", 2, 0.93932, 0.9379, 0.09722, 0.09709, 0.71985, 0.71873, 0.49646, 0.5522, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-29", "Adult", "Adult", "Bone or Cartilage", "Skeletal Element"], [74705, "SRR24003730", "SRX19807138", "SRS17168877", "SRP429947", "PRJNA949785", "Sequencing of zebrafish bone tissues", "PRJNA949785", "Other", "Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass", null, null, null, null, "eight month zebrafish bone tissues", null, "breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of b1 tissue in zebrafish", "control2 6", "control2 6", "Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP429947", null, null, "control2_6_1.fq.gz control2_6_2.fq.gz", "fastq fastq", 6817849200.0, 22726164.0, "control2 6 1.fq.gz", "0:150 1:150", "A:1916198776;C:1480570561;G:1501234091;T:1919845772;N:0", 150, 150, null, null, 1916198776, 1480570561, 1501234091, 1919845772, 0, "SRX19807138", "SRS17168877", "SRA1612461", "Sun Yat-sen University|Department of Epidemiology, School of Public Healt", "Sun Yat-sen University", 2, 0.94697, 0.9369, 0.06934, 0.06812, 0.76824, 0.77114, 0.49005, 0.54882, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-29", "Adult", "Adult", "Bone or Cartilage", "Skeletal Element"], [74706, "SRR24003731", "SRX19807137", "SRS17168877", "SRP429947", "PRJNA949785", "Sequencing of zebrafish bone tissues", "PRJNA949785", "Other", "Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass", null, null, null, null, "eight month zebrafish bone tissues", null, "breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of b1 tissue in zebrafish", "control2 5", "control2 5", "Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP429947", null, null, "control2_5_1.fq.gz control2_5_2.fq.gz", "fastq fastq", 6730171500.0, 22433905.0, "control2 5 1.fq.gz", "0:150 1:150", "A:1881763818;C:1469481635;G:1493477302;T:1885448745;N:0", 150, 150, null, null, 1881763818, 1469481635, 1493477302, 1885448745, 0, "SRX19807137", "SRS17168877", "SRA1612461", "Sun Yat-sen University|Department of Epidemiology, School of Public Healt", "Sun Yat-sen University", 2, 0.9399, 0.92905, 0.0832, 0.08122, 0.70993, 0.71228, 0.54991, 0.58952, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-29", "Adult", "Adult", "Bone or Cartilage", "Skeletal Element"], [74707, "SRR24003732", "SRX19807136", "SRS17168877", "SRP429947", "PRJNA949785", "Sequencing of zebrafish bone tissues", "PRJNA949785", "Other", "Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass", null, null, null, null, "eight month zebrafish bone tissues", null, "breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of b1 tissue in zebrafish", "control2 4", "control2 4", "Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP429947", null, null, "control2_4_1.fq.gz control2_4_2.fq.gz", "fastq fastq", 6660686100.0, 22202287.0, "control2 4 1.fq.gz", "0:150 1:150", "A:1846205332;C:1486328129;G:1477889862;T:1850262777;N:0", 150, 150, null, null, 1846205332, 1486328129, 1477889862, 1850262777, 0, "SRX19807136", "SRS17168877", "SRA1612461", "Sun Yat-sen University|Department of Epidemiology, School of Public Healt", "Sun Yat-sen University", 2, 0.94251, 0.94001, 0.08206, 0.082, 0.69483, 0.69524, 0.49193, 0.49602, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-29", "Adult", "Adult", "Bone or Cartilage", "Skeletal Element"], [74708, "SRR24003733", "SRX19807135", "SRS17168877", "SRP429947", "PRJNA949785", "Sequencing of zebrafish bone tissues", "PRJNA949785", "Other", "Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass", null, null, null, null, "eight month zebrafish bone tissues", null, "breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of b1 tissue in zebrafish", "control2 3", "control2 3", "Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP429947", null, null, "control2_3_1.fq.gz control2_3_2.fq.gz", "fastq fastq", 6683569500.0, 22278565.0, "control2 3 1.fq.gz", "0:150 1:150", "A:1846755716;C:1494194697;G:1482717957;T:1859901130;N:0", 150, 150, null, null, 1846755716, 1494194697, 1482717957, 1859901130, 0, "SRX19807135", "SRS17168877", "SRA1612461", "Sun Yat-sen University|Department of Epidemiology, School of Public Healt", "Sun Yat-sen University", 2, 0.93255, 0.93106, 0.10717, 0.10731, 0.67665, 0.67791, 0.54876, 0.52297, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-29", "Adult", "Adult", "Bone or Cartilage", "Skeletal Element"], [74709, "SRR24003734", "SRX19807134", "SRS17168877", "SRP429947", "PRJNA949785", "Sequencing of zebrafish bone tissues", "PRJNA949785", "Other", "Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass", null, null, null, null, "eight month zebrafish bone tissues", null, "breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of b1 tissue in zebrafish", "case2 7", "case2 7", "Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. 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