{"database": "metadata", "table": "run_metadata", "rows": [[35469, "SRR32818813", "SRX28102231", "SRS24458278", "SRP572436", "PRJNA1240804", "Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset", "GSE292683", "Transcriptome Analysis", "Mechanical forces play a critical role in tendon development and function  influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix ECM remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome wide bulk RNA sequencing of FAC sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Overall design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX alpha bungarotoxin injected paralyzed 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes.", null, "pubmed:40145570", null, "sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 5", "GSM8863189", null, "source name:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos aBTX injected at single cell stage|geo loc name:missing|collection date:missing", "sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 5", "Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1 Assembly: GRCz10 Supplementary files format and content: DESeq2 normalized counts", "FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos", null, "For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O\u2019Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4\u00b0C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit", null, "tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos aBTX injected at single cell stage", "GSM8863189", "GSM8863189: sorted mCherry+ tenocytes from aBTX injected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 5; Danio rerio; RNA Seq", "GSM8863189 r1", "GSM8863189", "1", "For 48 hpf bulk RNA seq alone transgenic Tgscxa:mCherry embryos  BTX injected or un injected siblings  were dissociated using Subtilisin A cold active protease in a stock solution consisting of: 5 ul of 1M CaCl2  100 ul of protease stock solution 100mg of Bacillus licheniformis protease Sigma P5380 solubilized in 1 ml of Ca and Mg free PBS  889ul of PBS  1 ul of 0.5M EDTA Sigma E5134 and 5ul of DNAse I  Roche 10104159001 stock 25U/ul in PBS  stored at  80C adapted from O'Flanagan et al.  2019. Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min  tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took 30 min per samples  and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA 0.01% BSA in PBS  made fresh on the day of dissociation and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4\u00b0C  supernatant is discarded  and cells are resuspended in 1 ml of ice cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio Rad FACS Aria II cell sorter. Clontech SMARTer Stranded Total RNA Seq v3 Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP572436", null, null, "nR284-L2-G5-P48-TACCGAGG-AGTTCAGG-READ1-Sequences.txt nR284-L2-G5-P48-TACCGAGG-AGTTCAGG-READ2-Sequences.txt", "fastq fastq", 9778516798.0, 48408499.0, "GSM8863189 r1", "0:101 1:101", "A:1871707305;C:3053861632;G:3000334130;T:1852564463;N:49268", 101, 101, null, null, 1871707305, 3053861632, 3000334130, 1852564463, 49268, "SRX28102231", "SRS24458278", "SRA2098459", "UC Irvine", "UC Irvine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "United States", "2025-03-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "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": ["35469"], "units": {}, "query_ms": 7.5102319970028475}