{"database": "metadata", "table": "run_metadata", "rows": [[29032, "SRR26989304", "SRX22682429", "SRS19676381", "SRP474934", "PRJNA1046494", "Cohesin composition and dosage independently affect early development in zebrafish", "GSE248952", "Transcriptome Analysis", "Cohesin  a chromatin associated protein complex with four core subunits Smc1a  Smc3  Rad21 and either Stag1 or 2  has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed \u201ccohesinopathies\u201d are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However  it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition  we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction  but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2  but not rad21 mutants  implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.", null, "pubmed:38975838", null, "TB  dissected  stag2b NZ207  scRNA seq", "GSM7923481", null, "source name:tailbud|tissue:tailbud|age:16 hpf|genotype:stag2b NZ207|geo loc name:missing|collection date:missing", "TB  dissected  stag2b NZ207  scRNA seq", "FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files", "tailbud", null, "Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.", null, "tissue:tailbud|age:16 hpf|genotype:stag2b NZ207", "GSM7923481", "GSM7923481: TB  dissected  stag2b NZ207  scRNA seq; Danio rerio; RNA Seq", "GSM7923481 r1", "GSM7923481", "1", "Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP474934", null, "loader:fastq load.py", "S2B_bamtofastq_S1_L003_I1_002.fastq.gz S2B_bamtofastq_S1_L003_R1_002.fastq.gz S2B_bamtofastq_S1_L003_R2_002.fastq.gz", "fastq fastq fastq", 31750000000.0, 250000000.0, "GSM7923481 r2", "0:8 1:28 2:91", "A:6518388158;C:4725153194;G:5205254633;T:6300375689;N:828326", 8, 28, 91, null, 6518388158, 4725153194, 5205254633, 6300375689, 828326, "SRX22682429", "SRS19676381", "SRA1760034", "Chromosome structure and development group, Pathology, University of Otago", "Chromosome structure and development group, Pathology, University of Otago", 1, 0.95154, null, 0.12683, null, 0.92429, null, 0.45021, null, 91, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "New Zealand", "2023-11-29", "Segmentation", "Embryo", "Tail", "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": ["29032"], "units": {}, "query_ms": 11.424431999330409}