{"database": "metadata", "table": "run_metadata", "rows": [[35482, "SRR32818801", "SRX28102218", "SRS24458265", "SRP572438", "PRJNA1240805", "Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force responsive genes. FAC sorted tenocytes from 36 hpf vs. 48 hpf zebrafish embryos bulk RNAseq dataset", "GSE292682", "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 36 hpf and 48 hpf Tgscxa:mCherry zebrafish embryos  labeling tendon fibroblasts tenocytes. 36 hpf embryos have not yet begun active muscle contraction  and 48 hpf embryos are freely swimming  indicating active muscle contraction onset.", null, "pubmed:40145570", null, "sorted mCherry+ tenocytes from 36 hpf Tgscxa:mCherry zebrafish embryos replicate 3", "GSM8863176", 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:36 hpf|geo loc name:missing|collection date:missing", "sorted mCherry+ tenocytes from 36 hpf Tgscxa:mCherry zebrafish embryos replicate 3", "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: csv file includes DESeq2 normalized counts for all samples", "FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos", null, "36 hpf and 48 hpf Tgscxa:mCherry zebrafish embryos labeling tendon fibroblasts/tenocytes were dissociated with Collagenase IV Gibco  17104019 at a concentration of 6.24 mg/ml without xxx addition at a temperature of 28C for roughly 40 min  homogenizing every 5 min with a P1000 pipette. Cells were filtered through a 40um filter Pluriselect usa  43 10040 50. Dissociated cell suspensions were sorted on a Bio Rad FACS Aria II cell sorter. mCherry positive cells were gated and sorted for those expressing at high levels. RNEasy Micro Kit Qiagen  74004 was used for RNA extraction of cell lysates from FAC sorted cells  and the Smart seq2 protocol was utilized for cDNA library construction. Libraries were sequenced using a Hi seq 4000 sequencer Illumina at a read depth of 35M reads per replicate.", null, "tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:36 hpf", "GSM8863176", "GSM8863176: sorted mCherry+ tenocytes from 36 hpf Tgscxa:mCherry zebrafish embryos replicate 3; Danio rerio; RNA Seq", "GSM8863176 r1", "GSM8863176", "1", "36 hpf and 48 hpf Tgscxa:mCherry zebrafish embryos labeling tendon fibroblasts/tenocytes were dissociated with Collagenase IV Gibco  17104019 at a concentration of 6.24 mg/ml without xxx addition at a temperature of 28C for roughly 40 min  homogenizing every 5 min with a P1000 pipette. Cells were filtered through a 40um filter Pluriselect usa  43 10040 50. Dissociated cell suspensions were sorted on a Bio Rad FACS Aria II cell sorter. mCherry positive cells were gated and sorted for those expressing at high levels. RNEasy Micro Kit Qiagen  74004 was used for RNA extraction of cell lysates from FAC sorted cells  and the Smart seq2 protocol was utilized for cDNA library construction. Libraries were sequenced using a Hi seq 4000 sequencer Illumina at a read depth of 35M reads per replicate.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP572438", null, null, "p36-3-READ1-Sequences.txt p36-3-READ2-Sequences.txt", "fastq fastq", 6089823000.0, 30449115.0, "GSM8863176 r1", "0:100 1:100", "A:1565216204;C:1493655703;G:1438012972;T:1592561753;N:376368", 100, 100, null, null, 1565216204, 1493655703, 1438012972, 1592561753, 376368, "SRX28102218", "SRS24458265", "SRA2098458", "UC Irvine", "UC Irvine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2025-03-23", "Multi-stage", "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": ["35482"], "units": {}, "query_ms": 10.8236689993646}