{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"quartzseq\" and tissue_curation = \"Undetermined\"", "rows": [[53150, "SRR9692020", "SRX6451054", "SRS5104325", "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, "mOC 2", "GSM3942346", null, "source name:mature osteoclasts|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:mature osteoclasts|molecule type:Amplified RNA", "mOC 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.", "mature osteoclasts", 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:mature osteoclasts|molecule type:Amplified RNA", "GSM3942346", "GSM3942346: mOC 2; Danio rerio; RNA Seq", "GSM3942346", 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. 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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, "mOC 1", "GSM3942345", null, "source name:mature osteoclasts|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:mature osteoclasts|molecule type:Amplified RNA", "mOC 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.", "mature osteoclasts", 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:mature osteoclasts|molecule type:Amplified RNA", "GSM3942345", "GSM3942345: mOC 1; Danio rerio; RNA Seq", "GSM3942345", 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, "mOC_1_R1.fastq.gz mOC_1_R2.fastq.gz", "fastq fastq", 3725202300.0, 12417341.0, "GSM3942345 r1", "0:150 1:150", "A:939287270;C:932158020;G:913434023;T:940223484;N:99503", 150, 150, null, null, 939287270, 932158020, 913434023, 940223484, 99503, "SRX6451053", "SRS5104324", "SRA921382", "GEO", "Kanazawa University", 2, 0.95139, 0.94882, 0.0326, 0.03471, 0.79393, 0.80507, 0.4667, 0.49924, 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", "Undetermined", "Undetermined"], [53152, "SRR9692018", "SRX6451052", "SRS5104323", "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, "pOC 2", "GSM3942344", null, "source name:osteoclast precursors|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoclast precursors|molecule type:Amplified RNA", "pOC 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.", "osteoclast precursors", 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:osteoclast precursors|molecule type:Amplified RNA", "GSM3942344", "GSM3942344: pOC 2; Danio rerio; RNA Seq", "GSM3942344", 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, "pOC_2_R1.fastq.gz pOC_2_R2.fastq.gz", "fastq fastq", 8180901900.0, 27269673.0, "GSM3942344 r1", "0:150 1:150", "A:2045941714;C:2067950267;G:1981277316;T:2085490817;N:241786", 150, 150, null, null, 2045941714, 2067950267, 1981277316, 2085490817, 241786, "SRX6451052", "SRS5104323", "SRA921382", "GEO", "Kanazawa University", 2, 0.94075, 0.93872, 0.04606, 0.04832, 0.77847, 0.78482, 0.50377, 0.50525, 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", "Undetermined", "Undetermined"], [53153, "SRR9692017", "SRX6451051", "SRS5104322", "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, "pOC 1", "GSM3942343", null, "source name:osteoclast precursors|age:adult|genotype:wild type|tissue:Sorted from the fractured sclae|cell type:osteoclast precursors|molecule type:Amplified RNA", "pOC 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.", "osteoclast precursors", 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:osteoclast precursors|molecule type:Amplified RNA", "GSM3942343", "GSM3942343: pOC 1; Danio rerio; RNA Seq", "GSM3942343", 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, "pOC_1_R1.fastq.gz pOC_1_R2.fastq.gz", "fastq fastq", 8119854000.0, 27066180.0, "GSM3942343 r1", "0:150 1:150", "A:2022941314;C:2067331062;G:1960663076;T:2068678318;N:240230", 150, 150, null, null, 2022941314, 2067331062, 1960663076, 2068678318, 240230, "SRX6451051", "SRS5104322", "SRA921382", "GEO", "Kanazawa University", 2, 0.94544, 0.94406, 0.04202, 0.04348, 0.77979, 0.78624, 0.50479, 0.48269, 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", "Undetermined", "Undetermined"]], "truncated": false, "filtered_table_rows_count": 4, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", 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tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_source\" = :p0 and \"technology\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "TRANSCRIPTOMIC", "p1": "quartzseq", "p2": "Undetermined"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=quartzseq&tissue_curation=Undetermined", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=quartzseq&tissue_curation=Undetermined&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": 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