{"database": "metadata", "table": "run_metadata", "rows": [[26518, "SRR26050763", "SRX21767119", "SRS18873424", "SRP460207", "PRJNA1016321", "The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis", "GSE243072", "Transcriptome Analysis", "Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.", null, "pubmed:39171526", null, "psmb1 mutants  72hpf  biological replicate 4  cranial sox10+ cells", "GSM7778660", null, "source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / |geo loc name:missing|collection date:missing", "psmb1 mutants  72hpf  biological replicate 4  cranial sox10+ 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 sox10+ cells neural crest/chondrocytes", null, "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", "Embryos were raised in E3 at 28.5C until 72hpf.", "tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / ", "GSM7778660", "GSM7778660: psmb1 mutants  72hpf  biological replicate 4  cranial sox10+ cells; Danio rerio; RNA Seq", "GSM7778660 r1", "GSM7778660", "1", "20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 \u03bcm filter. Cells were sorted into Buffer RLT with 1% \u03b2 mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP460207", null, "loader:fastq load.py", "sox10_M4_R1_001.fastq.gz sox10_M4_R2_001.fastq.gz", "fastq fastq", 17203316400.0, 57344388.0, "GSM7778660 r1", "0:150 1:150", "A:4557769784;C:4038080087;G:4028545423;T:4578857383;N:63723", 150, 150, null, null, 4557769784, 4038080087, 4028545423, 4578857383, 63723, "SRX21767119", "SRS18873424", "SRA1711572", "BWH", "BWH", 2, 0.93924, 0.93866, 0.10703, 0.1068, 0.70597, 0.70508, 0.52195, 0.52023, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2023-09-13", "Larval", "Larval", "Multi-tissue", "Multi-system"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["26518"], "units": {}, "query_ms": 9.769060998223722}