{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", technology = \"smartseq\" and tissue_curation_coarse = \"Muscular System\"", "rows": [[56291, "SRR10903545", "SRX7571714", "SRS6007290", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle  but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle  we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here  we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse  which enables rapid  direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system  we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids  lysophosphatidic acid LPA and niflumic acid NFA  both linked to activation of intracellular calcium ion flux  which showed conserved  dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells  we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the  with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish DMSO Rep 3", "GSM4274800", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:DMSO", "Zebrafish DMSO Rep 3", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO  20% horse serum Atlanta Biologics  1% penicillin streptomycin Invitrogen  1% GlutaMAX Invitrogen  and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C  respectively.", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells  which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen  35% DMEM Invitrogen  and 15% Ham\u2019s F 12 Invitrogen  with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich  15 mM sodium bicarbonate  15 mM HEPES Invitrogen 1% L glutamine Invitrogen  10 nM sodium selenite Sigma Aldrich  1% N2 Invitrogen  2% B27 Invitrogen  0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:DMSO", "GSM4274800", "GSM4274800: Zebrafish DMSO Rep 3; Danio rerio; RNA Seq", "GSM4274800", null, "1", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274800", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "DMSO-Z3_S3_R2_001.fastq.gz DMSO-Z3_S3_R1_001.fastq.gz", "fastq fastq", 3131766552.0, 41732800.0, "GSM4274800 r1", "0:37.52 1:37.52", "A:885347014;C:656593900;G:658966405;T:930204699;N:654534", 37, 37, null, null, 885347014, 656593900, 658966405, 930204699, 654534, "SRX7571714", "SRS6007290", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.9017, 0.90284, 0.20295, 0.20352, 0.726, 0.72681, 0.4835, 0.48166, 37, 36, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56292, "SRR10903544", "SRX7571713", "SRS6007289", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle  but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle  we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here  we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse  which enables rapid  direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system  we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids  lysophosphatidic acid LPA and niflumic acid NFA  both linked to activation of intracellular calcium ion flux  which showed conserved  dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells  we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the  with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish DMSO Rep 2", "GSM4274799", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:DMSO", "Zebrafish DMSO Rep 2", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO  20% horse serum Atlanta Biologics  1% penicillin streptomycin Invitrogen  1% GlutaMAX Invitrogen  and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C  respectively.", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells  which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen  35% DMEM Invitrogen  and 15% Ham\u2019s F 12 Invitrogen  with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich  15 mM sodium bicarbonate  15 mM HEPES Invitrogen 1% L glutamine Invitrogen  10 nM sodium selenite Sigma Aldrich  1% N2 Invitrogen  2% B27 Invitrogen  0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:DMSO", "GSM4274799", "GSM4274799: Zebrafish DMSO Rep 2; Danio rerio; RNA Seq", "GSM4274799", null, "1", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274799", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "DMSO-Z2_S2_R2_001.fastq.gz DMSO-Z2_S2_R1_001.fastq.gz", "fastq fastq", 3602763184.0, 48016122.0, "GSM4274799 r1", "0:37.52 1:37.52", "A:1036072046;C:737502030;G:741972436;T:1086457828;N:758844", 37, 37, null, null, 1036072046, 737502030, 741972436, 1086457828, 758844, "SRX7571713", "SRS6007289", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.89788, 0.8998, 0.22198, 0.22328, 0.72324, 0.72612, 0.47822, 0.47673, 38, 37, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56293, "SRR10903543", "SRX7571712", "SRS6007288", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle  but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle  we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here  we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse  which enables rapid  direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system  we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids  lysophosphatidic acid LPA and niflumic acid NFA  both linked to activation of intracellular calcium ion flux  which showed conserved  dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells  we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the  with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish DMSO Rep 1", "GSM4274798", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:DMSO", "Zebrafish DMSO Rep 1", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO  20% horse serum Atlanta Biologics  1% penicillin streptomycin Invitrogen  1% GlutaMAX Invitrogen  and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C  respectively.", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells  which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen  35% DMEM Invitrogen  and 15% Ham\u2019s F 12 Invitrogen  with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich  15 mM sodium bicarbonate  15 mM HEPES Invitrogen 1% L glutamine Invitrogen  10 nM sodium selenite Sigma Aldrich  1% N2 Invitrogen  2% B27 Invitrogen  0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:DMSO", "GSM4274798", "GSM4274798: Zebrafish DMSO Rep 1; Danio rerio; RNA Seq", "GSM4274798", null, "1", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274798", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "DMSO-Z1_S1_R2_001.fastq.gz DMSO-Z1_S1_R1_001.fastq.gz", "fastq fastq", 3604342960.0, 48032922.0, "GSM4274798 r1", "0:37.52 1:37.52", "A:1012371470;C:761879249;G:766369377;T:1062980320;N:742544", 37, 37, null, null, 1012371470, 761879249, 766369377, 1062980320, 742544, "SRX7571712", "SRS6007288", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.90147, 0.90411, 0.18135, 0.18178, 0.72756, 0.72989, 0.48286, 0.484, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56294, "SRR10903542", "SRX7571711", "SRS6007287", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle  but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle  we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here  we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse  which enables rapid  direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system  we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids  lysophosphatidic acid LPA and niflumic acid NFA  both linked to activation of intracellular calcium ion flux  which showed conserved  dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells  we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the  with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish NFA Rep 3", "GSM4274797", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:NFA", "Zebrafish NFA Rep 3", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO  20% horse serum Atlanta Biologics  1% penicillin streptomycin Invitrogen  1% GlutaMAX Invitrogen  and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C  respectively.", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells  which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen  35% DMEM Invitrogen  and 15% Ham\u2019s F 12 Invitrogen  with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich  15 mM sodium bicarbonate  15 mM HEPES Invitrogen 1% L glutamine Invitrogen  10 nM sodium selenite Sigma Aldrich  1% N2 Invitrogen  2% B27 Invitrogen  0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:NFA", "GSM4274797", "GSM4274797: Zebrafish NFA Rep 3; Danio rerio; RNA Seq", "GSM4274797", null, "1", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274797", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "NFA-Z3_S9_R2_001.fastq.gz NFA-Z3_S9_R1_001.fastq.gz", "fastq fastq", 2585502086.0, 34448695.0, "GSM4274797 r1", "0:37.53 1:37.53", "A:703025617;C:569504763;G:571097453;T:741333725;N:540528", 37, 37, null, null, 703025617, 569504763, 571097453, 741333725, 540528, "SRX7571711", "SRS6007287", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.90534, 0.90734, 0.17389, 0.17443, 0.72569, 0.72689, 0.47635, 0.47915, 36, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56295, "SRR10903541", "SRX7571710", "SRS6007286", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle  but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle  we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here  we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse  which enables rapid  direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system  we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids  lysophosphatidic acid LPA and niflumic acid NFA  both linked to activation of intracellular calcium ion flux  which showed conserved  dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells  we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the  with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish NFA Rep 2", "GSM4274796", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:NFA", "Zebrafish NFA Rep 2", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO  20% horse serum Atlanta Biologics  1% penicillin streptomycin Invitrogen  1% GlutaMAX Invitrogen  and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C  respectively.", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells  which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen  35% DMEM Invitrogen  and 15% Ham\u2019s F 12 Invitrogen  with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich  15 mM sodium bicarbonate  15 mM HEPES Invitrogen 1% L glutamine Invitrogen  10 nM sodium selenite Sigma Aldrich  1% N2 Invitrogen  2% B27 Invitrogen  0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:NFA", "GSM4274796", "GSM4274796: Zebrafish NFA Rep 2; Danio rerio; RNA Seq", "GSM4274796", null, "1", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274796", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "NFA-Z2_S8_R2_001.fastq.gz NFA-Z2_S8_R1_001.fastq.gz", "fastq fastq", 3166928712.0, 42208361.0, "GSM4274796 r1", "0:37.52 1:37.52", "A:922958966;C:638285887;G:640244924;T:964802852;N:636083", 37, 37, null, null, 922958966, 638285887, 640244924, 964802852, 636083, "SRX7571710", "SRS6007286", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.8974, 0.89826, 0.21803, 0.21778, 0.72679, 0.72825, 0.48119, 0.48197, 37, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56296, "SRR10903540", "SRX7571709", "SRS6007285", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle  but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle  we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here  we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse  which enables rapid  direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system  we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids  lysophosphatidic acid LPA and niflumic acid NFA  both linked to activation of intracellular calcium ion flux  which showed conserved  dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells  we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the  with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish NFA Rep 1", "GSM4274795", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:NFA", "Zebrafish NFA Rep 1", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO  20% horse serum Atlanta Biologics  1% penicillin streptomycin Invitrogen  1% GlutaMAX Invitrogen  and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C  respectively.", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells  which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen  35% DMEM Invitrogen  and 15% Ham\u2019s F 12 Invitrogen  with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich  15 mM sodium bicarbonate  15 mM HEPES Invitrogen 1% L glutamine Invitrogen  10 nM sodium selenite Sigma Aldrich  1% N2 Invitrogen  2% B27 Invitrogen  0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:NFA", "GSM4274795", "GSM4274795: Zebrafish NFA Rep 1; Danio rerio; RNA Seq", "GSM4274795", null, "1", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274795", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "NFA-Z1_S7_R2_001.fastq.gz NFA-Z1_S7_R1_001.fastq.gz", "fastq fastq", 2962555966.0, 39481568.0, "GSM4274795 r1", "0:37.52 1:37.52", "A:850455036;C:607610800;G:611012952;T:892860213;N:616965", 37, 37, null, null, 850455036, 607610800, 611012952, 892860213, 616965, "SRX7571709", "SRS6007285", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.89392, 0.89571, 0.25628, 0.25686, 0.72153, 0.72297, 0.47614, 0.47823, 38, 37, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56297, "SRR10903539", "SRX7571708", "SRS6007284", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle  but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle  we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here  we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse  which enables rapid  direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system  we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids  lysophosphatidic acid LPA and niflumic acid NFA  both linked to activation of intracellular calcium ion flux  which showed conserved  dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells  we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the  with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish LPA Rep 3", "GSM4274794", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:LPA", "Zebrafish LPA Rep 3", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO  20% horse serum Atlanta Biologics  1% penicillin streptomycin Invitrogen  1% GlutaMAX Invitrogen  and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C  respectively.", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells  which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen  35% DMEM Invitrogen  and 15% Ham\u2019s F 12 Invitrogen  with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich  15 mM sodium bicarbonate  15 mM HEPES Invitrogen 1% L glutamine Invitrogen  10 nM sodium selenite Sigma Aldrich  1% N2 Invitrogen  2% B27 Invitrogen  0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:LPA", "GSM4274794", "GSM4274794: Zebrafish LPA Rep 3; Danio rerio; RNA Seq", "GSM4274794", null, "1", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274794", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "LPA-Z3_S6_R2_001.fastq.gz LPA-Z3_S6_R1_001.fastq.gz", "fastq fastq", 3066652967.0, 40865355.0, "GSM4274794 r1", "0:37.52 1:37.52", "A:864150135;C:645040202;G:648074884;T:908748285;N:639461", 37, 37, null, null, 864150135, 645040202, 648074884, 908748285, 639461, "SRX7571708", "SRS6007284", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.89879, 0.89988, 0.21861, 0.21824, 0.72705, 0.72953, 0.47984, 0.48124, 36, 37, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56298, "SRR10903538", "SRX7571707", "SRS6007283", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle  but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle  we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here  we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse  which enables rapid  direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system  we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids  lysophosphatidic acid LPA and niflumic acid NFA  both linked to activation of intracellular calcium ion flux  which showed conserved  dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells  we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the  with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish LPA Rep 2", "GSM4274793", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:LPA", "Zebrafish LPA Rep 2", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO  20% horse serum Atlanta Biologics  1% penicillin streptomycin Invitrogen  1% GlutaMAX Invitrogen  and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C  respectively.", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells  which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen  35% DMEM Invitrogen  and 15% Ham\u2019s F 12 Invitrogen  with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich  15 mM sodium bicarbonate  15 mM HEPES Invitrogen 1% L glutamine Invitrogen  10 nM sodium selenite Sigma Aldrich  1% N2 Invitrogen  2% B27 Invitrogen  0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:LPA", "GSM4274793", "GSM4274793: Zebrafish LPA Rep 2; Danio rerio; RNA Seq", "GSM4274793", null, "1", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274793", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "LPA-Z2_S5_R2_001.fastq.gz LPA-Z2_S5_R1_001.fastq.gz", "fastq fastq", 3259713731.0, 43430992.0, "GSM4274793 r1", "0:37.53 1:37.53", "A:889586274;C:714766857;G:716243885;T:938441843;N:674872", 37, 37, null, null, 889586274, 714766857, 716243885, 938441843, 674872, "SRX7571707", "SRS6007283", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.90057, 0.90315, 0.2034, 0.20364, 0.72583, 0.72819, 0.48128, 0.48201, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56299, "SRR10903537", "SRX7571706", "SRS6007282", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle  but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle  we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here  we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse  which enables rapid  direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system  we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids  lysophosphatidic acid LPA and niflumic acid NFA  both linked to activation of intracellular calcium ion flux  which showed conserved  dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells  we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the  with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish LPA Rep 1", "GSM4274792", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:LPA", "Zebrafish LPA Rep 1", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO  20% horse serum Atlanta Biologics  1% penicillin streptomycin Invitrogen  1% GlutaMAX Invitrogen  and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C  respectively.", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells  which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen  35% DMEM Invitrogen  and 15% Ham\u2019s F 12 Invitrogen  with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich  15 mM sodium bicarbonate  15 mM HEPES Invitrogen 1% L glutamine Invitrogen  10 nM sodium selenite Sigma Aldrich  1% N2 Invitrogen  2% B27 Invitrogen  0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:LPA", "GSM4274792", "GSM4274792: Zebrafish LPA Rep 1; Danio rerio; RNA Seq", "GSM4274792", null, "1", "Treated freshly isolated mice muscle stem cells  and zebrafish myogenic progenitor cells were washed with DPBS  then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit 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