run_metadata: 26520

This data as json

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
26520	SRR26050765	SRX21767117	SRS18873422	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 sox10+ cells	GSM7778658		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 1 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		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 sox10+ cells neural crest/chondrocytes\|genotype:psmb1 /	GSM7778658	GSM7778658: psmb1 mutants 72hpf biological replicate 1 cranial sox10+ cells; Danio rerio; RNA Seq	GSM7778658 r1	GSM7778658	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 HiSeq 4000		SRP460207		loader:fastq load.py	sox10_M1_R1_001.fastq.gz sox10_M1_R2_001.fastq.gz	fastq fastq	14363136600.0	47877122.0	GSM7778658 r1	0:150 1:150	A:3843987690;C:3329370255;G:3310959116;T:3878765025;N:54514	150	150			3843987690	3329370255	3310959116	3878765025	54514	SRX21767117	SRS18873422	SRA1711572	BWH	BWH	2	0.92722	0.92625	0.11695	0.11644	0.69611	0.6969	0.52036	0.522	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	nextera	bulk	bulk	bulk		United States	2023-09-13	Larval	Larval	Multi-tissue	Multi-system