{"database": "metadata", "table": "run_metadata", "rows": [[28716, "SRR26588128", "SRX22289207", "SRS19340289", "SRP469198", "PRJNA1033661", "scRNAseq of skeletal tissue during zebrafish craniofacial development", "GSE246579", "Transcriptome Analysis", "We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.", null, null, null, "sp7 mutant 5.8 mm", "GSM7871947", null, "source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing", "sp7 mutant 5.8 mm", "Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files", "craniofacial skeletal tissues", null, "Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30\u00b0. Alternating between pipetting and incubation at 30\u00b0  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100\u03bcL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40\u03bcm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.", null, "tissue:craniofacial skeletal tissues|genotype:sp7 / ", "GSM7871947", "GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq", "GSM7871947 r1", "GSM7871947", "1", "Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30\u00b0. Alternating between pipetting and incubation at 30\u00b0  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100\u03bcL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40\u03bcm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP469198", null, "loader:fastq load.py", "FS_Mutant0628_S4_L002_R2_001.fastq.gz FS_Mutant0628_S4_L002_R1_001.fastq.gz FS_Mutant0628_S4_L002_I1_001.fastq.gz", "fastq fastq fastq", 3795705896.0, 29887448.0, "GSM7871947 r2", "0:8 1:28 2:91", "A:769584134;C:598310890;G:715720368;T:635803045;N:339331", 8, 28, 91, null, 769584134, 598310890, 715720368, 635803045, 339331, "SRX22289207", "SRS19340289", "SRA1742079", "Boston University", "Boston University", 1, 0.83992, null, 0.199, null, 0.84094, null, 0.63528, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-10-30", "Undetermined", "Undetermined", "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": ["28716"], "units": {}, "query_ms": 9.881393998512067}