{"database": "metadata", "table": "run_metadata", "rows": [[25130, "SRR25619750", "SRX21346683", "SRS18591743", "SRP454714", "PRJNA1004663", "Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival", "GSE240721", "Other", "Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq", "GSM7708237", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing", "30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq", "using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", null, "Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer\u2019s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer\u2019s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "GSM7708237", "GSM7708237: 30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq; Danio rerio; RNA Seq", "GSM7708237 r1", "GSM7708237", "1", "Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP454714", null, "loader:fastq load.py", "CEL201106AN_WT-2_S19_L004_I1_001.fastq.gz CEL201106AN_WT-2_S19_L004_R1_001.fastq.gz CEL201106AN_WT-2_S19_L004_R2_001.fastq.gz", "fastq fastq fastq", 15740158766.0, 123938258.0, "GSM7708237 r2", "0:8 1:28 2:91", "A:3499017196;C:2231848518;G:2450171440;T:3096822046;N:522278", 8, 28, 91, null, 3499017196, 2231848518, 2450171440, 3096822046, 522278, "SRX21346683", "SRS18591743", "SRA1691311", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 1, 0.87457, null, 0.27073, null, 0.75278, null, 0.50801, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-11", "Pharyngula", "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": ["25130"], "units": {}, "query_ms": 10.171175999857951}