{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Larval\" and tissue_curation_coarse = \"Muscular System\"", "rows": [[26511, "SRR26050756", "SRX21767126", "SRS18873431", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 mutants 72hpf biological replicate 4 cranial mylz2+ cells", "GSM7778667", null, "source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1 / |geo loc name:missing|collection date:missing", "psmb1 mutants 72hpf biological replicate 4 cranial mylz2+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial mylz2+ cells muscle", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial mylz2+ cells muscle|genotype:psmb1 / ", "GSM7778667", "GSM7778667: psmb1 mutants 72hpf biological replicate 4 cranial mylz2+ cells; Danio rerio; RNA Seq", "GSM7778667 r1", "GSM7778667", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. 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Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 mutants 72hpf biological replicate 3 cranial mylz2+ cells", "GSM7778666", null, "source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1 / |geo loc name:missing|collection date:missing", "psmb1 mutants 72hpf biological replicate 3 cranial mylz2+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial mylz2+ cells muscle", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial mylz2+ cells muscle|genotype:psmb1 / ", "GSM7778666", "GSM7778666: psmb1 mutants 72hpf biological replicate 3 cranial mylz2+ cells; Danio rerio; RNA Seq", "GSM7778666 r1", "GSM7778666", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. 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Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 mutants 72hpf biological replicate 1 cranial mylz2+ cells", "GSM7778665", null, "source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1 / |geo loc name:missing|collection date:missing", "psmb1 mutants 72hpf biological replicate 1 cranial mylz2+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial mylz2+ cells muscle", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial mylz2+ cells muscle|genotype:psmb1 / ", "GSM7778665", "GSM7778665: psmb1 mutants 72hpf biological replicate 1 cranial mylz2+ cells; Danio rerio; RNA Seq", "GSM7778665 r1", "GSM7778665", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. 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Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 wild type/heterozygous 72hpf biological replicate 4 cranial mylz2+ cells", "GSM7778664", null, "source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing", "psmb1 wild type/heterozygous 72hpf biological replicate 4 cranial mylz2+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial mylz2+ cells muscle", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ ", "GSM7778664", "GSM7778664: psmb1 wild type/heterozygous 72hpf biological replicate 4 cranial mylz2+ cells; Danio rerio; RNA Seq", "GSM7778664 r1", "GSM7778664", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. 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Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 wild type/heterozygous 72hpf biological replicate 3 cranial mylz2+ cells", "GSM7778663", null, "source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing", "psmb1 wild type/heterozygous 72hpf biological replicate 3 cranial mylz2+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial mylz2+ cells muscle", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ ", "GSM7778663", "GSM7778663: psmb1 wild type/heterozygous 72hpf biological replicate 3 cranial mylz2+ cells; Danio rerio; RNA Seq", "GSM7778663 r1", "GSM7778663", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP460207", null, "loader:fastq load.py", "mylz2_WH3_R1_001.fastq.gz mylz2_WH3_R2_001.fastq.gz", "fastq fastq", 14286753900.0, 47622513.0, "GSM7778663 r1", "0:150 1:150", "A:3670719741;C:3471994517;G:3491814119;T:3651899112;N:326411", 150, 150, null, null, 3670719741, 3471994517, 3491814119, 3651899112, 326411, "SRX21767122", "SRS18873427", "SRA1711572", "BWH", "BWH", 2, 0.96159, 0.96038, 0.03967, 0.04054, 0.7749, 0.77644, 0.43006, 0.42107, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Muscle", "Muscular System"], [26516, "SRR26050761", "SRX21767121", "SRS18873426", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 wild type/heterozygous 72hpf biological replicate 2 cranial mylz2+ cells", "GSM7778662", null, "source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing", "psmb1 wild type/heterozygous 72hpf biological replicate 2 cranial mylz2+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial mylz2+ cells muscle", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ ", "GSM7778662", "GSM7778662: psmb1 wild type/heterozygous 72hpf biological replicate 2 cranial mylz2+ cells; Danio rerio; RNA Seq", "GSM7778662 r1", "GSM7778662", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP460207", null, "loader:fastq load.py", "mylz2_WH2_R1_001.fastq.gz mylz2_WH2_R2_001.fastq.gz", "fastq fastq", 13505114700.0, 45017049.0, "GSM7778662 r1", "0:150 1:150", "A:3494078647;C:3258926987;G:3282303631;T:3469494662;N:310773", 150, 150, null, null, 3494078647, 3258926987, 3282303631, 3469494662, 310773, "SRX21767121", "SRS18873426", "SRA1711572", "BWH", "BWH", 2, 0.95944, 0.95769, 0.04602, 0.04619, 0.78557, 0.78748, 0.43504, 0.43352, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Muscle", "Muscular System"], [26517, "SRR26050762", "SRX21767120", "SRS18873425", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall our work demonstrates that psmb1 is required for craniofacial cartilage tendon and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 wild type/heterozygous 72hpf biological replicate 1 cranial mylz2+ cells", "GSM7778661", null, "source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing", "psmb1 wild type/heterozygous 72hpf biological replicate 1 cranial mylz2+ cells", "Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al. 2013 and differential gene expression analysis was performed with DESeq2 Love et al. 2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples", "cranial mylz2+ cells muscle", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ ", "GSM7778661", "GSM7778661: psmb1 wild type/heterozygous 72hpf biological replicate 1 cranial mylz2+ cells; Danio rerio; RNA Seq", "GSM7778661 r1", "GSM7778661", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001 and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells 7000 cells were sorted per sample. For RNA seq on mylz2+ cells 1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara San Jose CA USA and the Illumina Nextera XT kit Illumina San Diego CA USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP460207", null, "loader:fastq load.py", "mylz2_WH1_R1_001.fastq.gz mylz2_WH1_R2_001.fastq.gz", "fastq fastq", 14988184200.0, 49960614.0, "GSM7778661 r1", "0:150 1:150", "A:3819900785;C:3673988527;G:3696333011;T:3797617860;N:344017", 150, 150, null, null, 3819900785, 3673988527, 3696333011, 3797617860, 344017, "SRX21767120", "SRS18873425", "SRA1711572", "BWH", "BWH", 2, 0.96471, 0.96183, 0.03703, 0.03679, 0.77167, 0.7749, 0.43436, 0.43348, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Muscle", "Muscular System"], [49226, "SRR7813757", "SRX4665323", "SRS3760351", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "kdrl positive rep3", "GSM3381540", null, "source name:endothelial cells|tissue:embryonic vascular smooth muscle cells|cell population:endothelial cells|Stage:5 dpf isolated cells", "kdrl positive rep3", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "endothelial cells", "embryos were dissociated and single cell suspensions were fixed acccording to the MARIS protocol; transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed libraries were constructed using the TotalScript kit Epicentre", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:endothelial cells|Stage:5 dpf isolated cells", "GSM3381540", "GSM3381540: kdrl positive rep3; Danio rerio; RNA Seq", "GSM3381540", null, "1", "total RNA was isolated using TRIzol oligo dT primed libraries were constructed using the TotalScript kit Epicentre", "GEO Accession:GSM3381540", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP160900", null, null, "13_WT_kdrl-27678658_R1.fastq.gz 13_WT_kdrl-27678658_R2.fastq.gz", "fastq fastq", 2784479826.0, 19920207.0, "GSM3381540 r1", "0:69.84 1:69.94", "A:804420278;C:586596245;G:593929697;T:791804108;N:7729498", 69, 69, null, null, 804420278, 586596245, 593929697, 791804108, 7729498, "SRX4665323", "SRS3760351", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.89497, 0.89707, 0.24708, 0.24419, 0.72247, 0.73091, 0.55063, 0.55618, 70, 70, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49227, "SRR7813756", "SRX4665322", "SRS3760350", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "kdrl positive rep2", "GSM3381539", null, "source name:endothelial cells|tissue:embryonic vascular smooth muscle cells|cell population:endothelial cells|Stage:5 dpf isolated cells", "kdrl positive rep2", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "endothelial cells", "embryos were dissociated and single cell suspensions were fixed acccording to the MARIS protocol; transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed libraries were constructed using the TotalScript kit Epicentre", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:endothelial cells|Stage:5 dpf isolated cells", "GSM3381539", "GSM3381539: kdrl positive rep2; Danio rerio; RNA Seq", "GSM3381539", null, "1", "total RNA was isolated using TRIzol oligo dT primed libraries were constructed using the TotalScript kit Epicentre", "GEO Accession:GSM3381539", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP160900", null, null, "10_wt_kdrl-27735756_R1.fastq.gz 10_wt_kdrl-27735756_R2.fastq.gz", "fastq fastq", 8458876589.0, 61091982.0, "GSM3381539 r1", "0:69.19 1:69.27", "A:2425193059;C:1768178283;G:1801781331;T:2426019252;N:37704664", 69, 69, null, null, 2425193059, 1768178283, 1801781331, 2426019252, 37704664, "SRX4665322", "SRS3760350", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.90791, 0.90971, 0.26965, 0.26707, 0.71737, 0.7236, 0.52145, 0.51821, 65, 65, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49228, "SRR7813755", "SRX4665321", "SRS3760349", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "kdrl positive rep1", "GSM3381538", null, "source name:endothelial cells|tissue:embryonic vascular smooth muscle cells|cell population:endothelial cells|Stage:5 dpf isolated cells", "kdrl positive rep1", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "endothelial cells", "embryos were dissociated and single cell suspensions were fixed acccording to the MARIS protocol; transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed libraries were constructed using the TotalScript kit Epicentre", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:endothelial cells|Stage:5 dpf isolated cells", "GSM3381538", "GSM3381538: kdrl positive rep1; Danio rerio; RNA Seq", "GSM3381538", null, "1", "total RNA was isolated using TRIzol oligo dT primed libraries were constructed using the TotalScript kit Epicentre", "GEO Accession:GSM3381538", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP160900", null, null, "07_WT_kdrl-27748739_R1.fastq.gz 07_WT_kdrl-27748739_R2.fastq.gz", "fastq fastq", 10869236830.0, 77148249.0, "GSM3381538 r1", "0:70.42 1:70.47", "A:3034144596;C:2341538216;G:2381338157;T:3056353761;N:55862100", 70, 70, null, null, 3034144596, 2341538216, 2381338157, 3056353761, 55862100, "SRX4665321", "SRS3760349", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.90629, 0.90766, 0.31994, 0.31661, 0.70327, 0.70857, 0.50716, 0.50524, 74, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49229, "SRR7813754", "SRX4665320", "SRS3760348", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "kdrl negative rep3", "GSM3381537", null, "source name:non endothelial cells|tissue:embryonic vascular smooth muscle cells|cell population:non endothelial cells|Stage:5 dpf isolated cells", "kdrl negative rep3", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "non endothelial cells", "embryos were dissociated and single cell suspensions were fixed acccording to the MARIS protocol; transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed libraries were constructed using the TotalScript kit Epicentre", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:non endothelial cells|Stage:5 dpf isolated cells", "GSM3381537", "GSM3381537: kdrl negative rep3; Danio rerio; RNA Seq", "GSM3381537", null, "1", "total RNA was isolated using TRIzol oligo dT primed libraries were constructed using the TotalScript kit Epicentre", "GEO Accession:GSM3381537", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP160900", null, null, "14_WT_negative-27667691_R1.fastq.gz 14_WT_negative-27667691_R2.fastq.gz", "fastq fastq", 6455872934.0, 47143102.0, "GSM3381537 r1", "0:68.44 1:68.51", "A:1926477582;C:1293920445;G:1304294531;T:1901480912;N:29699464", 68, 68, null, null, 1926477582, 1293920445, 1304294531, 1901480912, 29699464, "SRX4665320", "SRS3760348", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.88384, 0.88923, 0.37335, 0.37255, 0.69907, 0.71654, 0.55337, 0.55166, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49230, "SRR7813753", "SRX4665319", "SRS3760347", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "kdrl negative rep2", "GSM3381536", null, "source name:non endothelial cells|tissue:embryonic vascular smooth muscle cells|cell population:non endothelial cells|Stage:5 dpf isolated cells", "kdrl negative rep2", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "non endothelial cells", "embryos were dissociated and single cell suspensions were fixed acccording to the MARIS protocol; transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed libraries were constructed using the TotalScript kit Epicentre", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:non endothelial cells|Stage:5 dpf isolated cells", "GSM3381536", "GSM3381536: kdrl negative rep2; Danio rerio; RNA Seq", "GSM3381536", null, "1", "total RNA was isolated using TRIzol oligo dT primed libraries were constructed using the TotalScript kit Epicentre", "GEO Accession:GSM3381536", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP160900", null, null, "11_wt_negative-27727797_R1.fastq.gz 11_wt_negative-27727797_R2.fastq.gz", "fastq fastq", 3126281675.0, 22874205.0, "GSM3381536 r1", "0:68.31 1:68.37", "A:912363111;C:640152236;G:651233552;T:907795346;N:14737430", 68, 68, null, null, 912363111, 640152236, 651233552, 907795346, 14737430, "SRX4665319", "SRS3760347", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.89673, 0.89935, 0.36991, 0.36881, 0.6983, 0.70705, 0.54257, 0.54963, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49231, "SRR7813752", "SRX4665318", "SRS3760346", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "kdrl negative rep1", "GSM3381535", null, "source name:non endothelial cells|tissue:embryonic vascular smooth muscle cells|cell population:non endothelial cells|Stage:5 dpf isolated cells", "kdrl negative rep1", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "non endothelial cells", "embryos were dissociated and single cell suspensions were fixed acccording to the MARIS protocol; transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed libraries were constructed using the TotalScript kit Epicentre", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:non endothelial cells|Stage:5 dpf isolated cells", "GSM3381535", "GSM3381535: kdrl negative rep1; Danio rerio; RNA Seq", "GSM3381535", null, "1", "total RNA was isolated using TRIzol oligo dT primed libraries were constructed using the TotalScript kit Epicentre", "GEO Accession:GSM3381535", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP160900", null, null, "08_WT_negative-27726816_R2.fastq.gz 08_WT_negative-27726816_R1.fastq.gz", "fastq fastq", 6768499011.0, 47415000.0, "GSM3381535 r1", "0:71.36 1:71.39", "A:2052636566;C:1320197120;G:1348340134;T:2032751679;N:14573512", 71, 71, null, null, 2052636566, 1320197120, 1348340134, 2032751679, 14573512, "SRX4665318", "SRS3760346", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.88397, 0.88537, 0.50832, 0.50894, 0.68509, 0.69528, 0.52501, 0.52779, 74, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49232, "SRR7813751", "SRX4665317", "SRS3760345", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "acta2/foxc1b positive rep2", "GSM3381534", null, "source name:mural cells|tissue:embryonic vascular smooth muscle cells|cell population:mural cells|Stage:4 dpf isolated cells", "acta2/foxc1b positive rep2", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "mural cells", "embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:mural cells|Stage:4 dpf isolated cells", "GSM3381534", "GSM3381534: acta2/foxc1b positive rep2; Danio rerio; RNA Seq", "GSM3381534", null, "1", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "GEO Accession:GSM3381534", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP160900", null, null, "pos_pos.Li1845_R1.fastq.gz pos_pos.Li1845_R2.fastq.gz", "fastq fastq", 9492964443.0, 63022242.0, "GSM3381534 r1", "0:75.33 1:75.29", "A:2888704941;C:1868709022;G:1920404824;T:2809205466;N:5940190", 75, 75, null, null, 2888704941, 1868709022, 1920404824, 2809205466, 5940190, "SRX4665317", "SRS3760345", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.80725, 0.80514, 0.29417, 0.29216, 0.79005, 0.79738, 0.54536, 0.5468, 73, 73, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49233, "SRR7813750", "SRX4665316", "SRS3760344", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "acta2/foxc1b positive rep1", "GSM3381533", null, "source name:mural cells|tissue:embryonic vascular smooth muscle cells|cell population:mural cells|Stage:4 dpf isolated cells", "acta2/foxc1b positive rep1", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "mural cells", "embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:mural cells|Stage:4 dpf isolated cells", "GSM3381533", "GSM3381533: acta2/foxc1b positive rep1; Danio rerio; RNA Seq", "GSM3381533", null, "1", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "GEO Accession:GSM3381533", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP160900", null, null, "pos_pos.Li1561_R1.fastq.gz pos_pos.Li1561_R2.fastq.gz", "fastq fastq", 8555412568.0, 56285609.0, "GSM3381533 r1", "0:76 1:76", "A:2553608498;C:1712778302;G:1816917585;T:2465906361;N:6201822", 76, 76, null, null, 2553608498, 1712778302, 1816917585, 2465906361, 6201822, "SRX4665316", "SRS3760344", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.81238, 0.80009, 0.28815, 0.28463, 0.77043, 0.77725, 0.50972, 0.50788, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49234, "SRR7813749", "SRX4665315", "SRS3760343", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "acta2/foxc1b negative rep3", "GSM3381532", null, "source name:non mural cells|tissue:embryonic vascular smooth muscle cells|cell population:non mural cells|Stage:4 dpf isolated cells", "acta2/foxc1b negative rep3", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "non mural cells", "embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:non mural cells|Stage:4 dpf isolated cells", "GSM3381532", "GSM3381532: acta2/foxc1b negative rep3; Danio rerio; RNA Seq", "GSM3381532", null, "1", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "GEO Accession:GSM3381532", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP160900", null, null, "neg_neg.Li1848_R1.fastq.gz neg_neg.Li1848_R2.fastq.gz", "fastq fastq", 9587912836.0, 63628126.0, "GSM3381532 r1", "0:75.36 1:75.32", "A:2946417731;C:1861322053;G:1907371030;T:2867162752;N:5639270", 75, 75, null, null, 2946417731, 1861322053, 1907371030, 2867162752, 5639270, "SRX4665315", "SRS3760343", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.81145, 0.80682, 0.302, 0.30018, 0.73632, 0.74499, 0.57632, 0.57899, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49235, "SRR7813748", "SRX4665314", "SRS3760342", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "acta2/foxc1b negative rep2", "GSM3381531", null, "source name:non mural cells|tissue:embryonic vascular smooth muscle cells|cell population:non mural cells|Stage:4 dpf isolated cells", "acta2/foxc1b negative rep2", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "non mural cells", "embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:non mural cells|Stage:4 dpf isolated cells", "GSM3381531", "GSM3381531: acta2/foxc1b negative rep2; Danio rerio; RNA Seq", "GSM3381531", null, "1", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "GEO Accession:GSM3381531", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP160900", null, null, "neg_neg.Li1687_R1.fastq.gz neg_neg.Li1687_R2.fastq.gz", "fastq fastq", 9992159197.0, 66823964.0, "GSM3381531 r1", "0:74.78 1:74.75", "A:2818032751;C:2193498742;G:2256921183;T:2715973040;N:7733481", 74, 74, null, null, 2818032751, 2193498742, 2256921183, 2715973040, 7733481, "SRX4665314", "SRS3760342", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.77362, 0.7679, 0.09634, 0.09486, 0.8254, 0.83368, 0.56569, 0.57403, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49236, "SRR7813747", "SRX4665313", "SRS3760341", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "acta2/foxc1b negative rep1", "GSM3381530", null, "source name:non mural cells|tissue:embryonic vascular smooth muscle cells|cell population:non mural cells|Stage:4 dpf isolated cells", "acta2/foxc1b negative rep1", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "non mural cells", "embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:non mural cells|Stage:4 dpf isolated cells", "GSM3381530", "GSM3381530: acta2/foxc1b negative rep1; Danio rerio; RNA Seq", "GSM3381530", null, "1", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "GEO Accession:GSM3381530", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP160900", null, null, "neg_neg.Li1558_R2.fastq.gz neg_neg.Li1558_R1.fastq.gz", "fastq fastq", 8236014968.0, 54184309.0, "GSM3381530 r1", "0:76 1:76", "A:2524133327;C:1578601519;G:1685061055;T:2442267908;N:5951159", 76, 76, null, null, 2524133327, 1578601519, 1685061055, 2442267908, 5951159, "SRX4665313", "SRS3760341", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.81074, 0.80182, 0.31766, 0.31586, 0.74397, 0.75136, 0.54376, 0.53855, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49237, "SRR7813746", "SRX4665312", "SRS3760340", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "acta2 positive rep3", "GSM3381529", null, "source name:mural cells|tissue:embryonic vascular smooth muscle cells|cell population:mural cells|Stage:4 dpf isolated cells", "acta2 positive rep3", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "mural cells", "embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:mural cells|Stage:4 dpf isolated cells", "GSM3381529", "GSM3381529: acta2 positive rep3; Danio rerio; RNA Seq", "GSM3381529", null, "1", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "GEO Accession:GSM3381529", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP160900", null, null, "a_pos.Li1678_R2.fastq.gz a_pos.Li1678_R1.fastq.gz", "fastq fastq", 9104744148.0, 60739078.0, "GSM3381529 r1", "0:74.97 1:74.93", "A:2739018981;C:1829269161;G:1872659638;T:2657731297;N:6065071", 74, 74, null, null, 2739018981, 1829269161, 1872659638, 2657731297, 6065071, "SRX4665312", "SRS3760340", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.76629, 0.75883, 0.26875, 0.26569, 0.7931, 0.79967, 0.55379, 0.56015, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49238, "SRR7813745", "SRX4665311", "SRS3760339", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "acta2 positive rep2", "GSM3381528", null, "source name:mural cells|tissue:embryonic vascular smooth muscle cells|cell population:mural cells|Stage:4 dpf isolated cells", "acta2 positive rep2", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "mural cells", "embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:mural cells|Stage:4 dpf isolated cells", "GSM3381528", "GSM3381528: acta2 positive rep2; Danio rerio; RNA Seq", "GSM3381528", null, "1", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "GEO Accession:GSM3381528", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP160900", null, null, "a_pos.Li1556_R1.fastq.gz a_pos.Li1556_R2.fastq.gz", "fastq fastq", 7528037272.0, 49526561.0, "GSM3381528 r1", "0:76 1:76", "A:2305259259;C:1451108207;G:1539596962;T:2226723104;N:5349740", 76, 76, null, null, 2305259259, 1451108207, 1539596962, 2226723104, 5349740, "SRX4665311", "SRS3760339", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.81208, 0.8026, 0.28947, 0.2877, 0.78315, 0.79056, 0.53641, 0.56482, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49239, "SRR7813744", "SRX4665310", "SRS3760338", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "acta2 positive rep1", "GSM3381527", null, "source name:mural cells|tissue:embryonic vascular smooth muscle cells|cell population:mural cells|Stage:4 dpf isolated cells", "acta2 positive rep1", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "mural cells", "embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:mural cells|Stage:4 dpf isolated cells", "GSM3381527", "GSM3381527: acta2 positive rep1; Danio rerio; RNA Seq", "GSM3381527", null, "1", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "GEO Accession:GSM3381527", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP160900", null, null, "a_pos.Li1555_R1.fastq.gz a_pos.Li1555_R2.fastq.gz", "fastq fastq", 8227684760.0, 54129505.0, "GSM3381527 r1", "0:76 1:76", "A:2479170873;C:1617180417;G:1731510884;T:2393879918;N:5942668", 76, 76, null, null, 2479170873, 1617180417, 1731510884, 2393879918, 5942668, "SRX4665310", "SRS3760338", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.80796, 0.79688, 0.19942, 0.19692, 0.8116, 0.81694, 0.64102, 0.6373, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49240, "SRR7813743", "SRX4665309", "SRS3760337", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "acta2 negative rep3", "GSM3381526", null, "source name:non mural cells|tissue:embryonic vascular smooth muscle cells|cell population:non mural cells|Stage:4 dpf isolated cells", "acta2 negative rep3", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "non mural cells", "embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:non mural cells|Stage:4 dpf isolated cells", "GSM3381526", "GSM3381526: acta2 negative rep3; Danio rerio; RNA Seq", "GSM3381526", null, "1", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "GEO Accession:GSM3381526", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP160900", null, null, "a_neg.Li1683_R2.fastq.gz a_neg.Li1683_R1.fastq.gz", "fastq fastq", 9097748237.0, 60650998.0, "GSM3381526 r1", "0:75.02 1:74.98", "A:2772085015;C:1806536310;G:1843884316;T:2669536606;N:5705990", 75, 74, null, null, 2772085015, 1806536310, 1843884316, 2669536606, 5705990, "SRX4665309", "SRS3760337", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.80001, 0.79426, 0.25234, 0.24945, 0.77057, 0.77873, 0.52545, 0.52971, 74, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49241, "SRR7813742", "SRX4665308", "SRS3760336", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "acta2 negative rep2", "GSM3381525", null, "source name:non mural cells|tissue:embryonic vascular smooth muscle cells|cell population:non mural cells|Stage:4 dpf isolated cells", "acta2 negative rep2", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "non mural cells", "embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:non mural cells|Stage:4 dpf isolated cells", "GSM3381525", "GSM3381525: acta2 negative rep2; Danio rerio; RNA Seq", "GSM3381525", null, "1", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "GEO Accession:GSM3381525", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP160900", null, null, "a_neg.Li1679_R2.fastq.gz a_neg.Li1679_R1.fastq.gz", "fastq fastq", 9725777990.0, 64953959.0, "GSM3381525 r1", "0:74.89 1:74.85", "A:2854537926;C:2033544144;G:2091919254;T:2738782399;N:6994267", 74, 74, null, null, 2854537926, 2033544144, 2091919254, 2738782399, 6994267, "SRX4665308", "SRS3760336", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.78479, 0.78087, 0.16516, 0.1643, 0.77277, 0.78021, 0.53113, 0.53398, 75, 74, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [49242, "SRR7813741", "SRX4665307", "SRS3760335", "SRP160900", "PRJNA490132", "Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish", "GSE119718", "Transcriptome Analysis", "Molecular and cellular analysis of mural cell development during zebrafish embryonic development Overall design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos", null, "pubmed:31199900", null, "acta2 negative rep1", "GSM3381524", null, "source name:non mural cells|tissue:embryonic vascular smooth muscle cells|cell population:non mural cells|Stage:4 dpf isolated cells", "acta2 negative rep1", "For mural cellls raw NextSeq500 reads were processed and demultiplexed using bcl2fastq 2.14 Illumina to generate fastq files for each sample. For kdrl cells raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were aligned to 26 chromosomes and 967 primary assembly scaffolds of the zebrafish genome GRCz11 with star 2.5.3a Dobin et al. 2013. Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts 1.5.2 Liao Smyth & Shi 2014. Normalization and differential expression DE analysis was performed with DESeq2 1.20.0 Love Huber & Anders 2014. For DE analysis the original DESeq2 shrinkage estimator was used to estimate log2 fold change LFC for each comparison. Genome build: GRCz11 Refseq GCF 000002035.6 Supplementary files format and content: comma separated text file", "non mural cells", "embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "zebrafish embryos were grown to 4 or 5 dpf", "tissue:embryonic vascular smooth muscle cells|cell population:non mural cells|Stage:4 dpf isolated cells", "GSM3381524", "GSM3381524: acta2 negative rep1; Danio rerio; RNA Seq", "GSM3381524", null, "1", "total RNA was isolated using TRIzol oligo dT primed cDNA was amplified REPLI G followed by library construction using TruSeq adapters", "GEO Accession:GSM3381524", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP160900", null, null, "a_neg.Li1557_R1.fastq.gz a_neg.Li1557_R2.fastq.gz", "fastq fastq", 8677757520.0, 57090510.0, "GSM3381524 r1", "0:76 1:76", "A:2645286253;C:1678145921;G:1806960348;T:2541088187;N:6276811", 76, 76, null, null, 2645286253, 1678145921, 1806960348, 2541088187, 6276811, "SRX4665307", "SRS3760335", "SRA770492", "GEO", "Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School", 2, 0.82318, 0.81353, 0.24196, 0.24064, 0.7668, 0.77435, 0.54087, 0.56155, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2018-09-10", "Larval", "Larval", "Muscle", "Muscular System"], [53507, "SRR9899207", "SRX6651058", "SRS5212730", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish bmpr2b mutant", null, "strain:AB zebrafish|isolate:mutant|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of mutant fish", "mutant1", "mutant1", "Total RNA was isolated from the 15 dpf dpf bmpr2b mutant larval fishes using RNAiso Plus Reagent TaKaRa China according to the manufacturers protocol. post RNA quality and quantity control the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "m1_1.fq.gz m1_2.fq.gz", "fastq fastq", 8332769700.0, 27775899.0, "m1 1.fq.gz", "0:150 1:150", "A:2157086519;C:2009631895;G:2036110721;T:2129846686;N:93879", 150, 150, null, null, 2157086519, 2009631895, 2036110721, 2129846686, 93879, "SRX6651058", "SRS5212730", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.95476, 0.95486, 0.06414, 0.06413, 0.66115, 0.66156, 0.47619, 0.47307, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53508, "SRR9899208", "SRX6651057", "SRS5212731", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish wild", null, "strain:AB zebrafish|isolate:wild fish|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of wild fish", "wild3", "wild3", "Total RNA was isolated from the 15 dpf dpf wild larval fishes using RNAiso Plus Reagent TaKaRa China according to the manufacturers protocol. post RNA quality and quantity control the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "w3_1.fq.gz w3_2.fq.gz", "fastq fastq", 8715170100.0, 29050567.0, "w3 1.fq.gz", "0:150 1:150", "A:2265881414;C:2090871457;G:2123814411;T:2234503490;N:99328", 150, 150, null, null, 2265881414, 2090871457, 2123814411, 2234503490, 99328, "SRX6651057", "SRS5212731", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.95085, 0.95146, 0.06684, 0.0667, 0.65886, 0.6588, 0.47356, 0.48005, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53509, "SRR9899209", "SRX6651056", "SRS5212731", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish wild", null, "strain:AB zebrafish|isolate:wild fish|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of wild fish", "wild2", "wild2", "Total RNA was isolated from the 15 dpf dpf wild larval fishes using RNAiso Plus Reagent TaKaRa China according to the manufacturers protocol. post RNA quality and quantity control the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "w2_1.fq.gz w2_2.fq.gz", "fastq fastq", 9346269600.0, 31154232.0, "w2 1.fq.gz", "0:150 1:150", "A:2421899244;C:2254190061;G:2283375277;T:2386698720;N:106298", 150, 150, null, null, 2421899244, 2254190061, 2283375277, 2386698720, 106298, "SRX6651056", "SRS5212731", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.95445, 0.95603, 0.06361, 0.06276, 0.6616, 0.66121, 0.47635, 0.47716, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53510, "SRR9899210", "SRX6651055", "SRS5212731", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish wild", null, "strain:AB zebrafish|isolate:wild fish|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of wild fish", "wild1", "wild1", "Total RNA was isolated from the 15 dpf dpf wild larval fishes using RNAiso Plus Reagent TaKaRa China according to the manufacturers protocol. post RNA quality and quantity control the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "w1_1.fq.gz w1_2.fq.gz", "fastq fastq", 8756101500.0, 29187005.0, "w1 1.fq.gz", "0:150 1:150", "A:2274557262;C:2102935324;G:2133197715;T:2245310628;N:100571", 150, 150, null, null, 2274557262, 2102935324, 2133197715, 2245310628, 100571, "SRX6651055", "SRS5212731", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.95161, 0.95225, 0.06682, 0.06678, 0.65831, 0.65993, 0.47144, 0.47166, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53511, "SRR9899211", "SRX6651054", "SRS5212730", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish bmpr2b mutant", null, "strain:AB zebrafish|isolate:mutant|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of mutant fish", "mutant3", "mutant3", "Total RNA was isolated from the 15 dpf dpf bmpr2b mutant larval fishes using RNAiso Plus Reagent TaKaRa China according to the manufacturers protocol. post RNA quality and quantity control the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "m3_1.fq.gz m3_2.fq.gz", "fastq fastq", 8385335400.0, 27951118.0, "m3 1.fq.gz", "0:150 1:150", "A:2179183324;C:2013493686;G:2044351918;T:2148211353;N:95119", 150, 150, null, null, 2179183324, 2013493686, 2044351918, 2148211353, 95119, "SRX6651054", "SRS5212730", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.94884, 0.94904, 0.0643, 0.06403, 0.66145, 0.66316, 0.46951, 0.4767, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53512, "SRR9899212", "SRX6651053", "SRS5212730", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish bmpr2b mutant", null, "strain:AB zebrafish|isolate:mutant|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of mutant fish", "mutant2", "mutant2", "Total RNA was isolated from the 15 dpf dpf bmpr2b mutant larval fishes using RNAiso Plus Reagent TaKaRa China according to the manufacturers protocol. post RNA quality and quantity control the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, 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