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30 rows where devstage_curation = "Larval" and tissue_curation = "Muscle"

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  • Muscle · 30 ✖

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devstage_curation 1

  • Larval · 30 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
26511 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.   pubmed:39171526   psmb1 mutants 72hpf biological replicate 4 cranial mylz2+ cells GSM7778667   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   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 μm filter. Cells were sorted into Buffer RLT with 1% β 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 μm filter. Cells were sorted into Buffer RLT with 1% β 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP460207   loader:fastq load.py mylz2_M4_R2_001.fastq.gz mylz2_M4_R1_001.fastq.gz fastq fastq 16253832000.0 54179440.0 GSM7778667 r1 0:150 1:150 A:4172321085;C:3956578712;G:3980023180;T:4144541347;N:367676 150 150     4172321085 3956578712 3980023180 4144541347 367676 SRX21767126 SRS18873431 SRA1711572 BWH BWH 2 0.95935 0.95662 0.03769 0.03765 0.76556 0.76741 0.42151 0.41972 150 150 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified nextera bulk bulk bulk   United States 2023-09-13 Larval Larval Muscle Muscular System
26512 26512 SRR26050757 SRX21767125 SRS18873430 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.   pubmed:39171526   psmb1 mutants 72hpf biological replicate 3 cranial mylz2+ cells GSM7778666   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   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 μm filter. Cells were sorted into Buffer RLT with 1% β 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 μm filter. Cells were sorted into Buffer RLT with 1% β 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP460207   loader:fastq load.py mylz2_M2_R1_001.fastq.gz mylz2_M2_R2_001.fastq.gz fastq fastq 20441581200.0 68138604.0 GSM7778666 r1 0:150 1:150 A:5286416350;C:4932599128;G:4952935975;T:5269152687;N:477060 150 150     5286416350 4932599128 4952935975 5269152687 477060 SRX21767125 SRS18873430 SRA1711572 BWH BWH 2 0.95599 0.95338 0.04497 0.04514 0.74811 0.74974 0.43348 0.43839 150 150 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified nextera bulk bulk bulk   United States 2023-09-13 Larval Larval Muscle Muscular System
26513 26513 SRR26050758 SRX21767124 SRS18873429 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.   pubmed:39171526   psmb1 mutants 72hpf biological replicate 1 cranial mylz2+ cells GSM7778665   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   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 μm filter. Cells were sorted into Buffer RLT with 1% β 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 μm filter. Cells were sorted into Buffer RLT with 1% β 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP460207   loader:fastq load.py mylz2_M1_R2_001.fastq.gz mylz2_M1_R1_001.fastq.gz fastq fastq 16429988100.0 54766627.0 GSM7778665 r1 0:150 1:150 A:4233929382;C:3979539796;G:4000710274;T:4215435332;N:373316 150 150     4233929382 3979539796 4000710274 4215435332 373316 SRX21767124 SRS18873429 SRA1711572 BWH BWH 2 0.95781 0.95546 0.04249 0.04266 0.75359 0.7556 0.42698 0.43387 150 150 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified nextera bulk bulk bulk   United States 2023-09-13 Larval Larval Muscle Muscular System
26514 26514 SRR26050759 SRX21767123 SRS18873428 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.   pubmed:39171526   psmb1 wild type/heterozygous 72hpf biological replicate 4 cranial mylz2+ cells GSM7778664   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   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 μm filter. Cells were sorted into Buffer RLT with 1% β 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 μm filter. Cells were sorted into Buffer RLT with 1% β 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP460207   loader:fastq load.py mylz2_WH4_R1_001.fastq.gz mylz2_WH4_R2_001.fastq.gz fastq fastq 14554941600.0 48516472.0 GSM7778664 r1 0:150 1:150 A:3762464429;C:3514503319;G:3535806865;T:3741838861;N:328126 150 150     3762464429 3514503319 3535806865 3741838861 328126 SRX21767123 SRS18873428 SRA1711572 BWH BWH 2 0.96121 0.95881 0.04249 0.04242 0.77745 0.77999 0.43011 0.42743 150 150 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified nextera bulk bulk bulk   United States 2023-09-13 Larval Larval Muscle Muscular System
26515 26515 SRR26050760 SRX21767122 SRS18873427 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.   pubmed:39171526   psmb1 wild type/heterozygous 72hpf biological replicate 3 cranial mylz2+ cells GSM7778663   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   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 μm filter. Cells were sorted into Buffer RLT with 1% β 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 μm filter. Cells were sorted into Buffer RLT with 1% β 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP460207   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     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   United States 2023-09-13 Larval Larval Muscle Muscular System
26516 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.   pubmed:39171526   psmb1 wild type/heterozygous 72hpf biological replicate 2 cranial mylz2+ cells GSM7778662   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   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 μm filter. Cells were sorted into Buffer RLT with 1% β 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 μm filter. Cells were sorted into Buffer RLT with 1% β 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP460207   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     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   United States 2023-09-13 Larval Larval Muscle Muscular System
26517 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.   pubmed:39171526   psmb1 wild type/heterozygous 72hpf biological replicate 1 cranial mylz2+ cells GSM7778661   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   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 μm filter. Cells were sorted into Buffer RLT with 1% β 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 μm filter. Cells were sorted into Buffer RLT with 1% β 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP460207   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     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   United States 2023-09-13 Larval Larval Muscle Muscular System
49226 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   pubmed:31199900   kdrl positive rep3 GSM3381540   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49227 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   pubmed:31199900   kdrl positive rep2 GSM3381539   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49228 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   pubmed:31199900   kdrl positive rep1 GSM3381538   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49229 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   pubmed:31199900   kdrl negative rep3 GSM3381537   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49230 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   pubmed:31199900   kdrl negative rep2 GSM3381536   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49231 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   pubmed:31199900   kdrl negative rep1 GSM3381535   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49232 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   pubmed:31199900   acta2/foxc1b positive rep2 GSM3381534   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49233 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   pubmed:31199900   acta2/foxc1b positive rep1 GSM3381533   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49234 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   pubmed:31199900   acta2/foxc1b negative rep3 GSM3381532   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49235 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   pubmed:31199900   acta2/foxc1b negative rep2 GSM3381531   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49236 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   pubmed:31199900   acta2/foxc1b negative rep1 GSM3381530   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49237 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   pubmed:31199900   acta2 positive rep3 GSM3381529   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49238 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   pubmed:31199900   acta2 positive rep2 GSM3381528   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49239 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   pubmed:31199900   acta2 positive rep1 GSM3381527   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49240 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   pubmed:31199900   acta2 negative rep3 GSM3381526   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49241 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   pubmed:31199900   acta2 negative rep2 GSM3381525   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
49242 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   pubmed:31199900   acta2 negative rep1 GSM3381524   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   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   SRP160900     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     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   United States 2018-09-10 Larval Larval Muscle Muscular System
53507 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.         zebrafish bmpr2b mutant   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                 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.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2000   SRP217299     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     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   China 2019-08-03 Larval Larval Muscle Muscular System
53508 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.         zebrafish wild   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                 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.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2000   SRP217299     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     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   China 2019-08-03 Larval Larval Muscle Muscular System
53509 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.         zebrafish wild   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                 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.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2000   SRP217299     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     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   China 2019-08-03 Larval Larval Muscle Muscular System
53510 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.         zebrafish wild   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                 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.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2000   SRP217299     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     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   China 2019-08-03 Larval Larval Muscle Muscular System
53511 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.         zebrafish bmpr2b mutant   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                 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.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2000   SRP217299     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     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   China 2019-08-03 Larval Larval Muscle Muscular System
53512 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.         zebrafish bmpr2b mutant   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                 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.     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2000   SRP217299     m2_1.fq.gz m2_2.fq.gz fastq fastq 8728240500.0 29094135.0 m2 1.fq.gz 0:150 1:150 A:2262292258;C:2101600854;G:2129980194;T:2234266968;N:100226 150 150     2262292258 2101600854 2129980194 2234266968 100226 SRX6651053 SRS5212730 SRA932406 Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal Huazhong Agricultural University 2 0.95297 0.95358 0.06449 0.06417 0.65965 0.65918 0.47932 0.4645 150 150 B B biological fallback assumption illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   China 2019-08-03 Larval Larval Muscle Muscular System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;