{"database": "metadata", "table": "run_metadata", "rows": [[25238, "SRR25721802", "SRX21445937", "SRS18680715", "SRP456253", "PRJNA1007646", "Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival [larva]", "GSE241296", "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: About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 \u00b0C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 \u00b5m respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 \u00b0C for 25 min. The digestion was terminated by adding 500 \u00b5l stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4\u00b0C  washed once with L15 and resuspended in 200 \u00b5l of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 \u00b5m opening. The solution was filtered through a 35 \u00b5m strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing", null, null, null, "zebrafish larva  neurons and glia  scRNAseq", "GSM7720759", null, "source name:zebrafish larva|cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf loc name:missing|collection date:missing", "zebrafish larva  neurons and glia  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 larva", null, "About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 \u00b0C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 \u03bcm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 \u00b0C for 25 min. The digestion was terminated by adding 500 \u03bcl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4\u00b0C  washed once with L15 and resuspended in 200 \u03bcl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 \u03bcm opening. The solution was filtered through a 35 \u03bcm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf", "GSM7720759", "GSM7720759: zebrafish larva  neurons and glia  scRNAseq; Danio rerio; RNA Seq", "GSM7720759 r1", "GSM7720759", "1", "About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 \u00b0C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 \u03bcm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 \u00b0C for 25 min. The digestion was terminated by adding 500 \u03bcl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4\u00b0C  washed once with L15 and resuspended in 200 \u03bcl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 \u03bcm opening. The solution was filtered through a 35 \u03bcm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing 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, "SRP456253", null, "loader:fastq load.py", "CEL210928PB_HW1008_SAIG_D7_S1_L001_I1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_I2_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_R1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 54474841080.0, 247612914.0, "GSM7720759 r2", "0:10 1:10 2:100 3:100", "A:12887048507;C:10210716068;G:10683375130;T:15740176261;N:1266834", 10, 10, 100, 100, 12887048507, 10210716068, 10683375130, 15740176261, 1266834, "SRX21445937", "SRS18680715", "SRA1696793", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 2, 0.0, 0.82189, 0.0, 0.19349, 1.0, 0.85025, null, 0.6092, 100, 100, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-21", "Larval", "Larval", "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": ["25238"], "units": {}, "query_ms": 9.931792999850586}