{"database": "metadata", "table": "run_metadata", "rows": [[66010, "SRR15783458", "SRX12076338", "SRS10057004", "SRP336073", "PRJNA761449", "Myostatin is a negative regulator of adult neurogenesis in zebrafish", "GSE183644", "Transcriptome Analysis", "Intrinsic and extrinsic inhibition of axonal and neuronal regeneration obstruct spinal cord SC repair in mammals. In contrast  adult zebrafish achieve functional recovery post SC damage. While studies of innate SC regeneration have focused on axon regrowth as a primary repair mechanism  how local neurogenesis impacts functional recovery is unknown. We uncovered dynamic expression of myostatin b mstnb in a niche of dorsal ependymal progenitors post complete SC transection in zebrafish. Genetic loss of function in mstnb impaired functional recovery  although glial and axonal bridging across the lesion were unaffected. Using a series of transgenic reporter lines  we quantified the numbers of stem  progenitor  and neuronal cells in the absence of mstnb. We found neural stem cell proliferation was reduced  while newborn neurons were increased in mstnb null tissues  suggesting mstnb is a negative regulator of neurogenesis. Molecularly  neuron differentiation genes were upregulated  while the neural stem cell maintenance gene fgf1b was downregulated in mstnb mutants. Finally  we show that human FGF1 treatment rescued neuronal gene expression in mstnb mutants. These studies uncover unanticipated neurogenic functions for mstnb in adult zebrafish  and establish the importance of local neurogenesis for functional SC repair. Overall design: Gene expression profiling of mstn mutants and wildtype at control and one xxx post injury.", null, "pubmed:36417881", null, "SC  mstnb wildtype   Uninjured   replicate 2", "GSM5566277", null, "source name:Spinal cord|tissue:Spinal cord|experiment:Uninjured|time:Control|genotype:wildtype", "SC  mstnb wildtype   Uninjured   replicate 2", "Quality QC and trimming of adapters and short sequences were performed using Fastx. Sequencing reads were mapped to the zebrafish genome Zv11 using Bowtie2  then assembled and quantified using the Cufflinks and Cuffdiff algorithms. Genes with log2fold enrichment between  1 and 1 or adjusted p value \u2265 0.01 were considered insignificant. Genome build: Zv11 Supplementary files format and content: Processed data is store csv format files. All files contain FPKM expression values of all the genes in different replicates and experimental condition. Supplementary files format and content: Additionally  log2 Fold change is calculate between conditions as indicated in the file name.", "Spinal cord", "Zebrafish were anaesthetized using MS 222. Fine scissors were used to make a small incision that transects the SC 4 mm caudal to the brainstem region. Complete transection was visually confirmed at the time of surgery. Injured animals were also assessed at 2 or 3 dpi to confirm loss of swim capacity post surgery. For sham injuries  animals were anaesthetized  and fine scissors were used to transect skin and muscle tissues without xxx SCI.", "Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.", "Adult zebrafish  were maintained at the Washington University Zebrafish Core Facility. All animal experiments were performed in compliance with institutional animal protocols. Male and female animals between 3 month and 9 month of 2 cm in length were used. Experimental fish and control siblings of similar size and equal sex distribution were used for all experiments. SC transection surgeries and regeneration analyses were performed in a blinded manner  and 2 to 4 independent experiments were repeated using different clutches of animals.", "tissue:Spinal cord|experiment:Uninjured|time:Control|genotype:wildtype", "GSM5566277", "GSM5566277: SC  mstnb wildtype   Uninjured   replicate 2; Danio rerio; RNA Seq", "GSM5566277", null, "1", "Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.", "GEO Accession:GSM5566277", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP336073", null, "loader:fastq load.py", "b7-mstnb-wt-uninj-2.AAGCGGATTA-TTCAGATCCA.AAGCGGATTA-TTCAGATCCA_S5_L003_R1_001.fastq.gz b7-mstnb-wt-uninj-2.AAGCGGATTA-TTCAGATCCA.AAGCGGATTA-TTCAGATCCA_S5_L003_R2_001.fastq.gz", "fastq fastq", 16361235956.0, 54176278.0, "GSM5566277 r1", "0:151 1:151", "A:4710356079;C:3362427190;G:3849175583;T:4439093873;N:183231", 151, 151, null, null, 4710356079, 3362427190, 3849175583, 4439093873, 183231, "SRX12076338", "SRS10057004", "SRA1289934", "GEO", "Developmental Biology, Washington University in St. Louis", 2, 0.91784, 0.92473, 0.16572, 0.16836, 0.72255, 0.7349, 0.54847, 0.54107, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2021-09-07", "Adult", "Adult", "Spinal Cord", "Nervous 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": ["66010"], "units": {}, "query_ms": 8.1855429962161}