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19 rows where experiment.library_layout = "PAIRED", technology = "unknown" and tissue_curation = "Spinal Cord"

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experiment.platform 3

experiment.library_selection 2

tissue_curation_coarse 1

tissue_curation 1

  • Spinal Cord · 19 ✖

technology 1

  • unknown · 19 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_layout 1

  • PAIRED · 19 ✖

devstage_curation_coarse 1

devstage_curation 1

Link 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
44 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. 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.   pubmed:40278963 Zebrafish 2 weeks post spinal cord injury replicate 3 Zebrafish 2wpi 3 SAMD00799623   sample name:Zebrafish 2wpi 3|biological replicate:3|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University|collection date:2023 04 25|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord                 DNBSEQ G400 paired end sequencing of SAMD00799623 DRX648352 RNA seq of spinal cord in zebrafish at 2wpi injured 3 1 Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   DRP012880 DNBSEQ G400 paired end sequencing of SAMD00799623       14782516800.0 73912584.0 DRR668250 0:100 1:100 A:4058090278;C:3335994894;G:3323563782;T:4062467903;N:2399943 100 100     4058090278 3335994894 3323563782 4062467903 2399943 DRX648352 DRS458865 DRA020617 Osaka University Osaka University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2025-05-12 Adult Adult Spinal Cord Nervous System
45 45 DRR668249 DRX648351 DRS458864 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. 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.   pubmed:40278963 Zebrafish 2 weeks post spinal cord injury replicate 2 Zebrafish 2wpi 2 SAMD00799622   sample name:Zebrafish 2wpi 2|biological replicate:2|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University|collection date:2023 04 14|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord                 DNBSEQ G400 paired end sequencing of SAMD00799622 DRX648351 RNA seq of spinal cord in zebrafish at 2wpi injured 2 1 Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   DRP012880 DNBSEQ G400 paired end sequencing of SAMD00799622       13687641800.0 68438209.0 DRR668249 0:100 1:100 A:3759784620;C:3087398782;G:3083881581;T:3754378915;N:2197902 100 100     3759784620 3087398782 3083881581 3754378915 2197902 DRX648351 DRS458864 DRA020617 Osaka University Osaka University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2025-05-12 Adult Adult Spinal Cord Nervous System
46 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. 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.   pubmed:40278963 Zebrafish 2 weeks post spinal cord injury replicate 1 Zebrafish 2wpi 1 SAMD00799621   sample name:Zebrafish 2wpi 1|biological replicate:1|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University|collection date:2023 04 14|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord                 DNBSEQ G400 paired end sequencing of SAMD00799621 DRX648350 RNA seq of spinal cord in zebrafish at 2wpi injured 1 1 Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   DRP012880 DNBSEQ G400 paired end sequencing of SAMD00799621       16376197200.0 81880986.0 DRR668248 0:100 1:100 A:4485868844;C:3700974430;G:3710833937;T:4475827800;N:2692189 100 100     4485868844 3700974430 3710833937 4475827800 2692189 DRX648350 DRS458863 DRA020617 Osaka University Osaka University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2025-05-12 Adult Adult Spinal Cord Nervous System
47 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. 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.   pubmed:40278963 Zebrafish Intact biological replicate 3 Zebrafish Control 3 SAMD00799620   sample name:Zebrafish Control 3|biological replicate:3|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University|collection date:2023 04 21|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord                 DNBSEQ G400 paired end sequencing of SAMD00799620 DRX648349 RNA seq of spinal cord in zebrafish at 0wpi control 3 1 Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   DRP012880 DNBSEQ G400 paired end sequencing of SAMD00799620       13377538600.0 66887693.0 DRR668247 0:100 1:100 A:3725064764;C:2973653932;G:2980883214;T:3695767890;N:2168800 100 100     3725064764 2973653932 2980883214 3695767890 2168800 DRX648349 DRS458862 DRA020617 Osaka University Osaka University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2025-05-12 Adult Adult Spinal Cord Nervous System
48 48 DRR668246 DRX648348 DRS458861 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. 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.   pubmed:40278963 Zebrafish Intact biological replicate 2 Zebrafish Control 2 SAMD00799619   sample name:Zebrafish Control 2|biological replicate:2|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University|collection date:2023 04 21|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord                 DNBSEQ G400 paired end sequencing of SAMD00799619 DRX648348 RNA seq of spinal cord in zebrafish at 0wpi control 2 1 Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   DRP012880 DNBSEQ G400 paired end sequencing of SAMD00799619       14971411400.0 74857057.0 DRR668246 0:100 1:100 A:4160326445;C:3329083037;G:3329123314;T:4150453700;N:2424904 100 100     4160326445 3329083037 3329123314 4150453700 2424904 DRX648348 DRS458861 DRA020617 Osaka University Osaka University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2025-05-12 Adult Adult Spinal Cord Nervous System
49 49 DRR668245 DRX648347 DRS458860 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. 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.   pubmed:40278963 Zebrafish Intact biological replicate 1 Zebrafish Control 1 SAMD00799618   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                 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. Libraries were constructed from the amplified total RNA.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   DRP012880 DNBSEQ G400 paired end sequencing of SAMD00799618       13912523800.0 69562619.0 DRR668245 0:100 1:100 A:3888902049;C:3079617959;G:3075111814;T:3866655202;N:2236776 100 100     3888902049 3079617959 3075111814 3866655202 2236776 DRX648347 DRS458860 DRA020617 Osaka University Osaka University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2025-05-12 Adult Adult Spinal Cord Nervous System
55972 55972 SRR10895875 SRX7564604 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. 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.   pubmed:33545088;pubmed:12470943     Zebrafish 009   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                 RNA Seq of Danio rerio : adult CL100103178 L01 9 CL100103178 L01 9       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L01_567_1.fq.gz CL100103178_L01_567_2.fq.gz fastq fastq 7926659000.0 79266590.0 CL100103178 L01 567 1.fq.gz 0:100 1:100 A:2177233520;C:1750763335;G:1793690428;T:2195598681;N:9373036 100 100     2177233520 1750763335 1793690428 2195598681 9373036 SRX7564604 SRS6001805 SRA1026516 BGI|BGI-Research BGI 1 0.90731   0.11069   0.70548   0.53521   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Spinal Cord Nervous System
55973 55973 SRR10895876 SRX7564603 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. 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.   pubmed:33545088;pubmed:12470943     Zebrafish 009   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                 RNA Seq of Danio rerio : adult CL100103178 L01 8 CL100103178 L01 8       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L01_563_1.fq.gz CL100103178_L01_563_2.fq.gz fastq fastq 9981278800.0 99812788.0 CL100103178 L01 563 1.fq.gz 0:100 1:100 A:2753622693;C:2192952746;G:2243702494;T:2779006876;N:11993991 100 100     2753622693 2192952746 2243702494 2779006876 11993991 SRX7564603 SRS6001805 SRA1026516 BGI|BGI-Research BGI 1 0.90715   0.11372   0.71467   0.5089   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Spinal Cord Nervous System
55974 55974 SRR10895877 SRX7564602 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. 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.   pubmed:33545088;pubmed:12470943     Zebrafish 009   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                 RNA Seq of Danio rerio : adult CL100103178 L01 7 CL100103178 L01 7       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     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     2418167382 1969456035 2015821568 2442764114 11343701 SRX7564602 SRS6001805 SRA1026516 BGI|BGI-Research BGI 1 0.90895   0.10978   0.71336   0.50272   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Spinal Cord Nervous System
55975 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. 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.   pubmed:33545088;pubmed:12470943     Zebrafish 009   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                 RNA Seq of Danio rerio : adult CL100103178 L01 6 CL100103178 L01 6       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L01_564_1.fq.gz CL100103178_L01_564_2.fq.gz fastq fastq 7468499200.0 74684992.0 CL100103178 L01 564 1.fq.gz 0:100 1:100 A:2052720985;C:1649448011;G:1690698471;T:2068073830;N:7557903 100 100     2052720985 1649448011 1690698471 2068073830 7557903 SRX7564601 SRS6001805 SRA1026516 BGI|BGI-Research BGI 1 0.90905   0.10883   0.69578   0.54193   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Spinal Cord Nervous System
55976 55976 SRR10895881 SRX7564598 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. 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.   pubmed:33545088;pubmed:12470943     Zebrafish 009   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                 RNA Seq of Danio rerio : adult CL100103178 L01 5 CL100103178 L01 5       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L01_561_1.fq.gz CL100103178_L01_561_2.fq.gz fastq fastq 9173572800.0 91735728.0 CL100103178 L01 561 1.fq.gz 0:100 1:100 A:2527132650;C:2020739240;G:2066720461;T:2548747865;N:10232584 100 100     2527132650 2020739240 2066720461 2548747865 10232584 SRX7564598 SRS6001805 SRA1026516 BGI|BGI-Research BGI 1 0.91539   0.11063   0.71427   0.48162   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Spinal Cord Nervous System
66008 66008 SRR15783460 SRX12076342 SRS10057008 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.   pubmed:36417881   SC mstnb mutant Uninjured replicate 2 GSM5566279   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 ≥ 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   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   SRP336073   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     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   United States 2021-09-07 Adult Adult Spinal Cord Nervous System
66009 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.   pubmed:36417881   SC mstnb mutant Uninjured replicate 1 GSM5566278   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 ≥ 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   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   SRP336073   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     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   United States 2021-09-07 Adult Adult Spinal Cord Nervous System
66010 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.   pubmed:36417881   SC mstnb wildtype Uninjured replicate 2 GSM5566277   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 ≥ 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   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   SRP336073   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     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   United States 2021-09-07 Adult Adult Spinal Cord Nervous System
66011 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.   pubmed:36417881   SC mstnb wildtype Uninjured replicate 1 GSM5566276   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 ≥ 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   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   SRP336073   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     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   United States 2021-09-07 Adult Adult Spinal Cord Nervous System
66012 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.   pubmed:36417881   SC mstnb mutant 1 wpi replicate 2 GSM5566275   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 ≥ 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   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   SRP336073   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     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   United States 2021-09-07 Adult Adult Spinal Cord Nervous System
66013 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.   pubmed:36417881   SC mstnb mutant 1 wpi replicate 1 GSM5566274   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 ≥ 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   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   SRP336073   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     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   United States 2021-09-07 Adult Adult Spinal Cord Nervous System
66014 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.   pubmed:36417881   SC mstnb wildtype 1 wpi replicate 2 GSM5566273   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 ≥ 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 GSM5566273 GSM5566273: SC mstnb wildtype 1 wpi replicate 2; Danio rerio; RNA Seq GSM5566273   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:GSM5566273 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP336073   loader:fastq load.py b3-mstnb-wt-1wpi-3.CGAATGGTAA-GCCGTTGAAG.CGAATGGTAA-GCCGTTGAAG_S53_L003_R1_001.fastq.gz b3-mstnb-wt-1wpi-3.CGAATGGTAA-GCCGTTGAAG.CGAATGGTAA-GCCGTTGAAG_S53_L003_R2_001.fastq.gz fastq fastq 14482193466.0 47954283.0 GSM5566273 r1 0:151 1:151 A:4100543408;C:3089308480;G:3430244810;T:3861934913;N:161855 151 151     4100543408 3089308480 3430244810 3861934913 161855 SRX12076330 SRS10056998 SRA1289934 GEO Developmental Biology, Washington University in St. Louis 2 0.91623 0.92213 0.16999 0.17638 0.71098 0.72216 0.52445 0.52788 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2021-09-07 Adult Adult Spinal Cord Nervous System
66015 66015 SRR15783453 SRX12076328 SRS10056997 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.   pubmed:36417881   SC mstnb wildtype 1 wpi replicate 1 GSM5566272   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 ≥ 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   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:GSM5566272 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP336073   loader:fastq load.py b1-mstnb-wt-1wpi-1.TGCACTAGGC-ACCAGAAGTA.TGCACTAGGC-ACCAGAAGTA_S83_L003_R1_001.fastq.gz b1-mstnb-wt-1wpi-1.TGCACTAGGC-ACCAGAAGTA.TGCACTAGGC-ACCAGAAGTA_S83_L003_R2_001.fastq.gz fastq fastq 13011457090.0 43084295.0 GSM5566272 r1 0:151 1:151 A:3677087058;C:2775903100;G:3064396339;T:3493922901;N:147692 151 151     3677087058 2775903100 3064396339 3493922901 147692 SRX12076328 SRS10056997 SRA1289934 GEO Developmental Biology, Washington University in St. Louis 2 0.92358 0.92964 0.1313 0.13299 0.71745 0.72772 0.52678 0.52632 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2021-09-07 Adult Adult Spinal Cord Nervous System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;