{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", experiment.platform = \"DNBSEQ\" 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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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. 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 SAMD00799618", null, null, null, 13912523800.0, 69562619.0, "DRR668245", "0:100 1:100", "A:3888902049;C:3079617959;G:3075111814;T:3866655202;N:2236776", 100, 100, null, null, 3888902049, 3079617959, 3075111814, 3866655202, 2236776, "DRX648347", "DRS458860", "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"], [71409, "SRR21590947", "SRX17592668", "SRS15130333", "SRP397443", "PRJNA880627", "Single cell sequencing of WT and hb egfaKO zebrafish spinal cord  at 1 week post sham or transection injury.", "GSE213435", "Transcriptome Analysis", "We identified hb egfa as a secreted factor necessary and sufficient for spinal cord regeneration in zebrafish. To elucidate the Hb egfa mechanism of action  we perforemd single cell sequencing of WT and hb egfaKO zebrafish spinal cord. Overall design: Adult zebrafish were subjected to spinal cord transection. 2 mm rostral and caudal to the transection site were collected at 1 xxx post injury. Spinal cord of sham injured animals was collected as control. Samples were and subjected to the 10X Genomics pipeline for single cell sequencing 4 samples in total  WT 1 wpi  WT sham  hb egfaKO 1 wpi  hb egfaKO sham.", null, "pubmed:37567873", null, "danRer11 WT 7dpi", "GSM6586115", null, "source name:spinal cord|genotype:WT|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:7dpi|geo loc name:missing|collection date:missing", "danRer11 WT 7dpi", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danRer11 Supplementary files format and content: h5 files for count table", "spinal cord", null, "Samples were processed following the 10X Chromium platform following the manufacturer\u2019s guidelines  using 10X Single Cell 3\u2019 v3 chemistry 10X Genomics  Pleasanton  USA.", null, "genotype:WT|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:7dpi", "GSM6586115", "GSM6586115: danRer11 WT 7dpi; Danio rerio; RNA Seq", "GSM6586115 r1", "GSM6586115", "1", "Samples were processed following the 10X Chromium platform following the manufacturer's guidelines  using 10X Single Cell three prime v3 chemistry 10X Genomics  Pleasanton  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP397443", null, null, "KP_VC_sample4_S1_L001_R2_001.fastq.gz KP_VC_sample4_S1_L001_R1_001.fastq.gz", "fastq fastq", 50454681480.0, 423988920.0, "GSM6586115 r1", "0:28 1:91", "A:14159328348;C:10820572193;G:11486998159;T:13985883249;N:1899531", 28, 91, null, null, 14159328348, 10820572193, 11486998159, 13985883249, 1899531, "SRX17592668", "SRS15130333", "SRA1500311", "Cell biology, Duke University", "Poss, Cell Biology, Duke University", 2, 0.00753, 0.88935, 0.00224, 0.18283, 0.98528, 0.77656, 0.24704, 0.5609, 28, 91, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-09-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [71410, "SRR21590948", "SRX17592667", "SRS15130332", "SRP397443", "PRJNA880627", "Single cell sequencing of WT and hb egfaKO zebrafish spinal cord  at 1 week post sham or transection injury.", "GSE213435", "Transcriptome Analysis", "We identified hb egfa as a secreted factor necessary and sufficient for spinal cord regeneration in zebrafish. To elucidate the Hb egfa mechanism of action  we perforemd single cell sequencing of WT and hb egfaKO zebrafish spinal cord. Overall design: Adult zebrafish were subjected to spinal cord transection. 2 mm rostral and caudal to the transection site were collected at 1 xxx post injury. Spinal cord of sham injured animals was collected as control. Samples were and subjected to the 10X Genomics pipeline for single cell sequencing 4 samples in total  WT 1 wpi  WT sham  hb egfaKO 1 wpi  hb egfaKO sham.", null, "pubmed:37567873", null, "danRer11 WT sham", "GSM6586114", null, "source name:spinal cord|genotype:WT|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:sham|geo loc name:missing|collection date:missing", "danRer11 WT sham", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danRer11 Supplementary files format and content: h5 files for count table", "spinal cord", null, "Samples were processed following the 10X Chromium platform following the manufacturer\u2019s guidelines  using 10X Single Cell 3\u2019 v3 chemistry 10X Genomics  Pleasanton  USA.", null, "genotype:WT|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:sham", "GSM6586114", "GSM6586114: danRer11 WT sham; Danio rerio; RNA Seq", "GSM6586114 r1", "GSM6586114", "1", "Samples were processed following the 10X Chromium platform following the manufacturer's guidelines  using 10X Single Cell three prime v3 chemistry 10X Genomics  Pleasanton  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP397443", null, null, "KP_VC_sample3_S1_L001_R1_001.fastq.gz KP_VC_sample3_S1_L001_R2_001.fastq.gz", "fastq fastq", 49434606578.0, 415416862.0, "GSM6586114 r1", "0:28 1:91", "A:13689985840;C:10750469002;G:11165716773;T:13825714788;N:2720175", 28, 91, null, null, 13689985840, 10750469002, 11165716773, 13825714788, 2720175, "SRX17592667", "SRS15130332", "SRA1500311", "Cell biology, Duke University", "Poss, Cell Biology, Duke University", 2, 0.01019, 0.90181, 0.00309, 0.16838, 0.98522, 0.78459, 0.27523, 0.51926, 28, 91, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-09-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [71411, "SRR21590949", "SRX17592666", "SRS15130331", "SRP397443", "PRJNA880627", "Single cell sequencing of WT and hb egfaKO zebrafish spinal cord  at 1 week post sham or transection injury.", "GSE213435", "Transcriptome Analysis", "We identified hb egfa as a secreted factor necessary and sufficient for spinal cord regeneration in zebrafish. To elucidate the Hb egfa mechanism of action  we perforemd single cell sequencing of WT and hb egfaKO zebrafish spinal cord. Overall design: Adult zebrafish were subjected to spinal cord transection. 2 mm rostral and caudal to the transection site were collected at 1 xxx post injury. Spinal cord of sham injured animals was collected as control. Samples were and subjected to the 10X Genomics pipeline for single cell sequencing 4 samples in total  WT 1 wpi  WT sham  hb egfaKO 1 wpi  hb egfaKO sham.", null, "pubmed:37567873", null, "danRer11 hbegfaKO 7dpi", "GSM6586113", null, "source name:spinal cord|genotype:hbegfaKO|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:7dpi|geo loc name:missing|collection date:missing", "danRer11 hbegfaKO 7dpi", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danRer11 Supplementary files format and content: h5 files for count table", "spinal cord", null, "Samples were processed following the 10X Chromium platform following the manufacturer\u2019s guidelines  using 10X Single Cell 3\u2019 v3 chemistry 10X Genomics  Pleasanton  USA.", null, "genotype:hbegfaKO|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:7dpi", "GSM6586113", "GSM6586113: danRer11 hbegfaKO 7dpi; Danio rerio; RNA Seq", "GSM6586113 r1", "GSM6586113", "1", "Samples were processed following the 10X Chromium platform following the manufacturer's guidelines  using 10X Single Cell three prime v3 chemistry 10X Genomics  Pleasanton  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP397443", null, null, "KP_VC_sample2_S1_L001_R1_001.fastq.gz KP_VC_sample2_S1_L001_R2_001.fastq.gz", "fastq fastq", 48346471411.0, 406272869.0, "GSM6586113 r1", "0:28 1:91", "A:13278513523;C:10826562396;G:11318717473;T:12918171753;N:4506266", 28, 91, null, null, 13278513523, 10826562396, 11318717473, 12918171753, 4506266, "SRX17592666", "SRS15130331", "SRA1500311", "Cell biology, Duke University", "Poss, Cell Biology, Duke University", 2, 0.01379, 0.89003, 0.00446, 0.1909, 0.97808, 0.78415, 0.32888, 0.6007, 28, 91, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-09-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [71412, "SRR21590950", "SRX17592665", "SRS15130330", "SRP397443", "PRJNA880627", "Single cell sequencing of WT and hb egfaKO zebrafish spinal cord  at 1 week post sham or transection injury.", "GSE213435", "Transcriptome Analysis", "We identified hb egfa as a secreted factor necessary and sufficient for spinal cord regeneration in zebrafish. To elucidate the Hb egfa mechanism of action  we perforemd single cell sequencing of WT and hb egfaKO zebrafish spinal cord. Overall design: Adult zebrafish were subjected to spinal cord transection. 2 mm rostral and caudal to the transection site were collected at 1 xxx post injury. Spinal cord of sham injured animals was collected as control. Samples were and subjected to the 10X Genomics pipeline for single cell sequencing 4 samples in total  WT 1 wpi  WT sham  hb egfaKO 1 wpi  hb egfaKO sham.", null, "pubmed:37567873", null, "danRer11 hbegfaKO sham", "GSM6586112", null, "source name:spinal cord|genotype:hbegfaKO|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:sham|geo loc name:missing|collection date:missing", "danRer11 hbegfaKO sham", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danRer11 Supplementary files format and content: h5 files for count table", "spinal cord", null, "Samples were processed following the 10X Chromium platform following the manufacturer\u2019s guidelines  using 10X Single Cell 3\u2019 v3 chemistry 10X Genomics  Pleasanton  USA.", null, "genotype:hbegfaKO|tissue:spinal cord|strain:Ekkwill EK|age:6 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