{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", technology = \"unknown\" and tissue_curation = \"Spinal Cord\"", "rows": [[44, "DRR668250", "DRX648352", "DRS458865", "DRP012880", "PRJDB18466", "Comparison of spinal cord regeneration capacity in zebrafish and medaka", "PRJDB18466", "Other", "Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. 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Libraries were constructed from the amplified total RNA.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "DRP012880", "DNBSEQ G400 paired end sequencing of SAMD00799622", null, null, null, 13687641800.0, 68438209.0, "DRR668249", "0:100 1:100", "A:3759784620;C:3087398782;G:3083881581;T:3754378915;N:2197902", 100, 100, null, null, 3759784620, 3087398782, 3083881581, 3754378915, 2197902, "DRX648351", "DRS458864", "DRA020617", "Osaka University", "Osaka University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2025-05-12", "Adult", "Adult", "Spinal Cord", "Nervous System"], [46, "DRR668248", "DRX648350", "DRS458863", "DRP012880", "PRJDB18466", "Comparison of spinal cord regeneration capacity in zebrafish and medaka", "PRJDB18466", "Other", "Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. 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Libraries were constructed from the amplified total RNA.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "DRP012880", "DNBSEQ G400 paired end sequencing of SAMD00799621", null, null, null, 16376197200.0, 81880986.0, "DRR668248", "0:100 1:100", "A:4485868844;C:3700974430;G:3710833937;T:4475827800;N:2692189", 100, 100, null, null, 4485868844, 3700974430, 3710833937, 4475827800, 2692189, "DRX648350", "DRS458863", "DRA020617", "Osaka University", "Osaka University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2025-05-12", "Adult", "Adult", "Spinal Cord", "Nervous System"], [47, "DRR668247", "DRX648349", "DRS458862", "DRP012880", "PRJDB18466", "Comparison of spinal cord regeneration capacity in zebrafish and medaka", "PRJDB18466", "Other", "Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. 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Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. 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Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.", null, "pubmed:40278963", "Zebrafish Intact biological replicate 1", "Zebrafish Control 1", "SAMD00799618", null, "sample name:Zebrafish Control 1|biological replicate:1|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2024 05 04|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord", null, null, null, null, null, null, null, null, "DNBSEQ G400 paired end sequencing of SAMD00799618", "DRX648347", "RNA seq of spinal cord in zebrafish at 0wpi control 1", "1", "Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. 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Although they belong to fish  their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates  we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.", null, "pubmed:33545088;pubmed:12470943", null, null, "Zebrafish 009", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Spinal cord|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : adult", "CL100103178 L01 7", "CL100103178 L01 7", null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP241982", null, null, "CL100103178_L01_562_1.fq.gz CL100103178_L01_562_2.fq.gz", "fastq fastq", 8857552800.0, 88575528.0, "CL100103178 L01 562 1.fq.gz", "0:100 1:100", "A:2418167382;C:1969456035;G:2015821568;T:2442764114;N:11343701", 100, 100, null, null, 2418167382, 1969456035, 2015821568, 2442764114, 11343701, "SRX7564602", "SRS6001805", "SRA1026516", "BGI|BGI-Research", "BGI", 1, 0.90895, null, 0.10978, null, 0.71336, null, 0.50272, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [55975, "SRR10895878", "SRX7564601", "SRS6001805", "SRP241982", "PRJNA599026", "Project of basal ray finned fishes", "PRJNA599026", "Other", "The project is to study the oldest fish lineages in the ray finned fishes. 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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 mutant   Uninjured   replicate 2", "GSM5566279", null, "source name:Spinal cord|tissue:Spinal cord|experiment:Uninjured|time:Control|genotype:mstnb mutant  / ", "SC  mstnb mutant   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:mstnb mutant  / ", "GSM5566279", "GSM5566279: SC  mstnb mutant   Uninjured   replicate 2; Danio rerio; RNA Seq", "GSM5566279", 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:GSM5566279", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP336073", null, "loader:fastq load.py", "b9-mstnb-mut-uninj-2.ACTTCTCGTA-AGTCCAGCGT.ACTTCTCGTA-AGTCCAGCGT_S16_L003_R1_001.fastq.gz b9-mstnb-mut-uninj-2.ACTTCTCGTA-AGTCCAGCGT.ACTTCTCGTA-AGTCCAGCGT_S16_L003_R2_001.fastq.gz", "fastq fastq", 18561707616.0, 61462608.0, "GSM5566279 r1", "0:151 1:151", "A:5376008692;C:3846947319;G:4240142329;T:5098398439;N:210837", 151, 151, null, null, 5376008692, 3846947319, 4240142329, 5098398439, 210837, "SRX12076342", "SRS10057008", "SRA1289934", "GEO", "Developmental Biology, Washington University in St. Louis", 2, 0.90875, 0.91227, 0.22236, 0.22895, 0.71729, 0.72571, 0.53799, 0.53913, 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"], [66009, "SRR15783459", "SRX12076340", "SRS10057005", "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 mutant   Uninjured   replicate 1", "GSM5566278", null, "source name:Spinal cord|tissue:Spinal cord|experiment:Uninjured|time:Control|genotype:mstnb mutant  / ", "SC  mstnb mutant   Uninjured   replicate 1", "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:mstnb mutant  / ", "GSM5566278", "GSM5566278: SC  mstnb mutant   Uninjured   replicate 1; Danio rerio; RNA Seq", "GSM5566278", 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:GSM5566278", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP336073", null, "loader:fastq load.py", "b8-mstnb-mut-uninj-1.TCTGGATAAG-GAAGGAGCCT.TCTGGATAAG-GAAGGAGCCT_S80_L003_R1_001.fastq.gz b8-mstnb-mut-uninj-1.TCTGGATAAG-GAAGGAGCCT.TCTGGATAAG-GAAGGAGCCT_S80_L003_R2_001.fastq.gz", "fastq fastq", 19751058512.0, 65400856.0, "GSM5566278 r1", "0:151 1:151", "A:5608025200;C:4101762755;G:4708073935;T:5332976769;N:219853", 151, 151, null, null, 5608025200, 4101762755, 4708073935, 5332976769, 219853, "SRX12076340", "SRS10057005", "SRA1289934", "GEO", "Developmental Biology, Washington University in St. Louis", 2, 0.93136, 0.93887, 0.10405, 0.10774, 0.75282, 0.76416, 0.57913, 0.54405, 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"], [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"], [66011, "SRR15783457", "SRX12076336", "SRS10057001", "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 1", "GSM5566276", null, "source name:Spinal cord|tissue:Spinal cord|experiment:Uninjured|time:Control|genotype:wildtype", "SC  mstnb wildtype   Uninjured   replicate 1", "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", "GSM5566276", "GSM5566276: SC  mstnb wildtype   Uninjured   replicate 1; Danio rerio; RNA Seq", "GSM5566276", 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:GSM5566276", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP336073", null, "loader:fastq load.py", "b6-mstnb-wt-uninj-1.GTCGGTTCAC-ATCCTCGAGT.GTCGGTTCAC-ATCCTCGAGT_S72_L003_R1_001.fastq.gz b6-mstnb-wt-uninj-1.GTCGGTTCAC-ATCCTCGAGT.GTCGGTTCAC-ATCCTCGAGT_S72_L003_R2_001.fastq.gz", "fastq fastq", 20288059208.0, 67179004.0, "GSM5566276 r1", "0:151 1:151", "A:6194227425;C:3762932453;G:4520501753;T:5810174695;N:222882", 151, 151, null, null, 6194227425, 3762932453, 4520501753, 5810174695, 222882, "SRX12076336", "SRS10057001", "SRA1289934", "GEO", "Developmental Biology, Washington University in St. Louis", 2, 0.85748, 0.88273, 0.16029, 0.16517, 0.74862, 0.76213, 0.53814, 0.52267, 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"], [66012, "SRR15783456", "SRX12076334", "SRS10057000", "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 mutant   1 wpi   replicate 2", "GSM5566275", null, "source name:Spinal cord|tissue:Spinal cord|experiment:Spinal cord SC injury|time:1 xxx post injury|genotype:mstnb mutant  / ", "SC  mstnb mutant   1 wpi   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:Spinal cord SC injury|time:1 xxx post injury|genotype:mstnb mutant  / ", "GSM5566275", "GSM5566275: SC  mstnb mutant   1 wpi   replicate 2; Danio rerio; RNA Seq", "GSM5566275", 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:GSM5566275", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP336073", null, "loader:fastq load.py", "b5-mstnb-mut-1wpi-2.TCATACTGTC-GACGGTAACA.TCATACTGTC-GACGGTAACA_S76_L003_R1_001.fastq.gz b5-mstnb-mut-1wpi-2.TCATACTGTC-GACGGTAACA.TCATACTGTC-GACGGTAACA_S76_L003_R2_001.fastq.gz", "fastq fastq", 14646143226.0, 48497163.0, "GSM5566275 r1", "0:151 1:151", "A:4126803891;C:3109100967;G:3456339137;T:3953737070;N:162161", 151, 151, null, null, 4126803891, 3109100967, 3456339137, 3953737070, 162161, "SRX12076334", "SRS10057000", "SRA1289934", "GEO", "Developmental Biology, Washington University in St. Louis", 2, 0.91954, 0.92658, 0.15759, 0.16283, 0.70767, 0.71843, 0.53151, 0.52744, 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"], [66013, "SRR15783455", "SRX12076332", "SRS10056999", "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 mutant   1 wpi   replicate 1", "GSM5566274", null, "source name:Spinal cord|tissue:Spinal cord|experiment:Spinal cord SC injury|time:1 xxx post injury|genotype:mstnb mutant  / ", "SC  mstnb mutant   1 wpi   replicate 1", "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:Spinal cord SC injury|time:1 xxx post injury|genotype:mstnb mutant  / ", "GSM5566274", "GSM5566274: SC  mstnb mutant   1 wpi   replicate 1; Danio rerio; RNA Seq", "GSM5566274", 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:GSM5566274", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP336073", null, "loader:fastq load.py", "b4-mstnb-mut-1wpi-1.CGACTTATGC-CTCTCCAACG.CGACTTATGC-CTCTCCAACG_S55_L003_R1_001.fastq.gz b4-mstnb-mut-1wpi-1.CGACTTATGC-CTCTCCAACG.CGACTTATGC-CTCTCCAACG_S55_L003_R2_001.fastq.gz", "fastq fastq", 14196618642.0, 47008671.0, "GSM5566274 r1", "0:151 1:151", "A:3947758941;C:3098646858;G:3422183464;T:3727869800;N:159579", 151, 151, null, null, 3947758941, 3098646858, 3422183464, 3727869800, 159579, "SRX12076332", "SRS10056999", "SRA1289934", "GEO", "Developmental Biology, Washington University in St. Louis", 2, 0.92795, 0.9335, 0.13646, 0.14167, 0.71104, 0.72062, 0.45975, 0.53033, 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"], [66014, "SRR15783454", "SRX12076330", "SRS10056998", "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   1 wpi   replicate 2", "GSM5566273", null, "source name:Spinal cord|tissue:Spinal cord|experiment:Spinal cord SC injury|time:1 xxx post injury|genotype:wildtype", "SC  mstnb wildtype   1 wpi   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. 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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   1 wpi   replicate 1", "GSM5566272", null, "source name:Spinal cord|tissue:Spinal cord|experiment:Spinal cord SC injury|time:1 xxx post injury|genotype:wildtype", "SC  mstnb wildtype   1 wpi   replicate 1", "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:Spinal cord SC injury|time:1 xxx post injury|genotype:wildtype", "GSM5566272", "GSM5566272: SC  mstnb wildtype   1 wpi   replicate 1; Danio rerio; RNA Seq", "GSM5566272", 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. 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