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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
35464 SRR32818808 SRX28102236 SRS24458283 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.   pubmed:40145570   sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 4 GSM8863194   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 uninjected control|geo loc name:missing|collection date:missing sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 4 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   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°C 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   tissue:FAC sorted mCherry+ tenocytes from whole Tgscxa:mCherry embryos|cell type:mCherry+ tenocytes|genotype:WT Tgscxa:mCherry background|treatment:48 hpf embryos uninjected control GSM8863194 GSM8863194: sorted mCherry+ tenocytes from uninjected 48 hpf Tgscxa:mCherry zebrafish embryos replicate 4; Danio rerio; RNA Seq GSM8863194 r1 GSM8863194 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°C 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP572436     nR284-L2-G5-P53-AAGATACT-ATGTAAGT-READ1-Sequences.txt nR284-L2-G5-P53-AAGATACT-ATGTAAGT-READ2-Sequences.txt fastq fastq 11273189336.0 55807868.0 GSM8863194 r1 0:101 1:101 A:2204760360;C:3477277778;G:3404605220;T:2186489012;N:56966 101 101     2204760360 3477277778 3404605220 2186489012 56966 SRX28102236 SRS24458283 SRA2098459 UC Irvine UC Irvine                       B B biological fallback assumption illumina nextseq full_length cdna_unspecified smarter bulk bulk bulk   United States 2025-03-23 Hatching Embryo Embryo Imprecise All anatomical structures