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13 rows where experiment.platform = "DNBSEQ", technology = "10x" and tissue_curation_coarse = "Nervous System"

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tissue_curation 2

experiment.library_source 2

tissue_curation_coarse 1

  • Nervous System · 13 ✖

technology 1

  • 10x · 13 ✖

experiment.platform 1

  • DNBSEQ · 13 ✖

experiment.library_strategy 1

experiment.library_selection 1

experiment.library_layout 1

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
34508 34508 SRR32041235 SRX27390499 SRS23823272 SRP558202 PRJNA1212333 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212333 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr[VI]+VC 3 group Cr+VC 3   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 14|health state:health|sample type:tissue|lep:Cr+VC 3|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish EHK0300476 EHK0300476 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558202     Cr+VC-3.R1.raw.fastq.gz Cr+VC-3.R2.raw.fastq.gz fastq fastq 6579236402.0 21785551.0 Cr+VC 3.R1.raw.fastq.gz 0:151 1:151 A:1950296368;C:1342383640;G:1373591474;T:1912893257;N:71663 151 151     1950296368 1342383640 1373591474 1912893257 71663 SRX27390499 SRS23823272 SRA2054545 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-18 Adult Adult Brain Nervous System
34509 34509 SRR32041236 SRX27390498 SRS23823271 SRP558202 PRJNA1212333 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212333 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr[VI]+VC 2 group Cr+VC 2   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 14|health state:health|sample type:tissue|lep:Cr+VC 2|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish EHK0300475 EHK0300475 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558202     Cr+VC-2.R1.raw.fastq.gz Cr+VC-2.R2.raw.fastq.gz fastq fastq 7431192898.0 24606599.0 Cr+VC 2.R1.raw.fastq.gz 0:151 1:151 A:2185434880;C:1533450452;G:1567401090;T:2144825061;N:81415 151 151     2185434880 1533450452 1567401090 2144825061 81415 SRX27390498 SRS23823271 SRA2054545 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-18 Adult Adult Brain Nervous System
34510 34510 SRR32041237 SRX27390497 SRS23823270 SRP558202 PRJNA1212333 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212333 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr[VI]+VC 1 group Cr+VC 1   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 14|health state:health|sample type:tissue|lep:Cr+VC 1|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish EHK0300474 EHK0300474 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558202     Cr+VC-1.R1.raw.fastq.gz Cr+VC-1.R2.raw.fastq.gz fastq fastq 6385666180.0 21144590.0 Cr+VC 1.R1.raw.fastq.gz 0:151 1:151 A:1864936934;C:1329491594;G:1363211111;T:1827956599;N:69942 151 151     1864936934 1329491594 1363211111 1827956599 69942 SRX27390497 SRS23823270 SRA2054545 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-18 Adult Adult Brain Nervous System
34511 34511 SRR32041238 SRX27390496 SRS23823269 SRP558202 PRJNA1212333 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212333 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr[VI] 3 group Cr 3   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 13|health state:health|sample type:tissue|lep:Cr 3|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish EHK0300473 EHK0300473 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558202     Cr-3.R1.raw.fastq.gz Cr-3.R2.raw.fastq.gz fastq fastq 6339933716.0 20993158.0 Cr 3.R1.raw.fastq.gz 0:151 1:151 A:1873178321;C:1296125569;G:1333622723;T:1836939106;N:67997 151 151     1873178321 1296125569 1333622723 1836939106 67997 SRX27390496 SRS23823269 SRA2054545 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-18 Adult Adult Brain Nervous System
34512 34512 SRR32041239 SRX27390495 SRS23823268 SRP558202 PRJNA1212333 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212333 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr[VI] 2 group Cr 2   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 13|health state:health|sample type:tissue|lep:Cr 2|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish EHK0300472 EHK0300472 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558202     Cr-2.R1.raw.fastq.gz Cr-2.R2.raw.fastq.gz fastq fastq 6461518010.0 21395755.0 Cr 2.R1.raw.fastq.gz 0:151 1:151 A:1878799067;C:1352321588;G:1386809443;T:1843520259;N:67653 151 151     1878799067 1352321588 1386809443 1843520259 67653 SRX27390495 SRS23823268 SRA2054545 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-18 Adult Adult Brain Nervous System
34513 34513 SRR32041240 SRX27390494 SRS23823267 SRP558202 PRJNA1212333 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212333 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr[VI] 1 group Cr 1   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 13|health state:health|sample type:tissue|lep:Cr 1|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish EHK0300471 EHK0300471 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558202     Cr-1.R1.raw.fastq.gz Cr-1.R2.raw.fastq.gz fastq fastq 7143701582.0 23654641.0 Cr 1.R1.raw.fastq.gz 0:151 1:151 A:1955056767;C:1615392059;G:1650478323;T:1922695182;N:79251 151 151     1955056767 1615392059 1650478323 1922695182 79251 SRX27390494 SRS23823267 SRA2054545 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-18 Adult Adult Brain Nervous System
34514 34514 SRR32041241 SRX27390493 SRS23823266 SRP558202 PRJNA1212333 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212333 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       control 3 group Con 3   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 12|health state:health|sample type:tissue|lep:Con 3|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish EHK0300470 EHK0300470 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558202     Con-3.R1.raw.fastq.gz Con-3.R2.raw.fastq.gz fastq fastq 6474159730.0 21437615.0 Con 3.R1.raw.fastq.gz 0:151 1:151 A:1937289968;C:1298659806;G:1337603954;T:1900535989;N:70013 151 151     1937289968 1298659806 1337603954 1900535989 70013 SRX27390493 SRS23823266 SRA2054545 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-18 Adult Adult Brain Nervous System
34515 34515 SRR32041242 SRX27390492 SRS23823265 SRP558202 PRJNA1212333 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212333 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       control 2 group Con 2   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 12|health state:health|sample type:tissue|lep:Con 2|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish EHK0300469 EHK0300469 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558202     Con-2.R1.raw.fastq.gz Con-2.R2.raw.fastq.gz fastq fastq 8372440828.0 27723314.0 Con 2.R1.raw.fastq.gz 0:151 1:151 A:2235968446;C:1933538809;G:1977416201;T:2225425413;N:91959 151 151     2235968446 1933538809 1977416201 2225425413 91959 SRX27390492 SRS23823265 SRA2054545 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-18 Adult Adult Brain Nervous System
34516 34516 SRR32041243 SRX27390491 SRS23823264 SRP558202 PRJNA1212333 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212333 Other Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       control 1 group Con 1   ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 12|health state:health|sample type:tissue|lep:Con 1|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish EHK0300468 EHK0300468 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558202     Con-1.R1.raw.fastq.gz Con-1.R2.raw.fastq.gz fastq fastq 6527063486.0 21612793.0 Con 1.R1.raw.fastq.gz 0:151 1:151 A:1939230604;C:1326702799;G:1357063348;T:1903995450;N:71285 151 151     1939230604 1326702799 1357063348 1903995450 71285 SRX27390491 SRS23823264 SRA2054545 Hainan University|School of Life and Health Sciences Hainan University                       B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-18 Adult Adult Brain Nervous System
71409 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.   pubmed:37567873   danRer11 WT 7dpi GSM6586115   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   Samples were processed following the 10X Chromium platform following the manufacturer’s guidelines using 10X Single Cell 3’ v3 chemistry 10X Genomics Pleasanton USA.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP397443     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     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   United States 2022-09-15 Adult Adult Spinal Cord Nervous System
71410 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.   pubmed:37567873   danRer11 WT sham GSM6586114   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   Samples were processed following the 10X Chromium platform following the manufacturer’s guidelines using 10X Single Cell 3’ v3 chemistry 10X Genomics Pleasanton USA.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP397443     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     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   United States 2022-09-15 Adult Adult Spinal Cord Nervous System
71411 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.   pubmed:37567873   danRer11 hbegfaKO 7dpi GSM6586113   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   Samples were processed following the 10X Chromium platform following the manufacturer’s guidelines using 10X Single Cell 3’ v3 chemistry 10X Genomics Pleasanton USA.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP397443     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     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   United States 2022-09-15 Adult Adult Spinal Cord Nervous System
71412 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.   pubmed:37567873   danRer11 hbegfaKO sham GSM6586112   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   Samples were processed following the 10X Chromium platform following the manufacturer’s guidelines using 10X Single Cell 3’ v3 chemistry 10X Genomics Pleasanton USA.   genotype:hbegfaKO|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:sham GSM6586112 GSM6586112: danRer11 hbegfaKO sham; Danio rerio; RNA Seq GSM6586112 r1 GSM6586112 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP397443     KP_VC_sample1_S1_L001_R1_001.fastq.gz KP_VC_sample1_S1_L001_R2_001.fastq.gz fastq fastq 50009919813.0 420251427.0 GSM6586112 r1 0:28 1:91 A:13721824199;C:11296818044;G:11807686254;T:13179637678;N:3953638 28 91     13721824199 11296818044 11807686254 13179637678 3953638 SRX17592665 SRS15130330 SRA1500311 Cell biology, Duke University Poss, Cell Biology, Duke University 2 0.01254 0.83945 0.00371 0.16358 0.98378 0.80728 0.25895 0.57907 28 91 T B sc-like readlen bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-09-15 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");;