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run_metadata

27 rows where experiment.library_strategy = "RNA-Seq", experiment.platform = "DNBSEQ" and technology = "10x"

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tissue_curation 4

experiment.library_source 2

devstage_curation_coarse 2

devstage_curation 2

technology 1

  • 10x · 27 ✖

experiment.platform 1

  • DNBSEQ · 27 ✖

experiment.library_strategy 1

  • RNA-Seq · 27 ✖

experiment.library_selection 1

experiment.library_layout 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
34517 34517 SRR32044795 SRX27393953 SRS23824014 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 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 gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr+VC 3 I   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:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 3|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Cr+VC 3 Cr+VC 3 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295     Cr+VC-3.R1.raw.fastq.gz Cr+VC-3.R2.raw.fastq.gz fastq fastq 6773536558.0 22428929.0 Cr+VC 3.R1.raw.fastq.gz 0:151 1:151 A:1792253952;C:1581454013;G:1629330621;T:1770470694;N:27278 151 151     1792253952 1581454013 1629330621 1770470694 27278 SRX27393953 SRS23824014 SRA2054568 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 2025-01-19 Adult Adult Gut Digestive System
34518 34518 SRR32044796 SRX27393952 SRS23824013 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 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 gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr+VC 2 H   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:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 2|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Cr+VC 2 Cr+VC 2 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295     Cr+VC-2.R1.raw.fastq.gz Cr+VC-2.R2.raw.fastq.gz fastq fastq 7449518862.0 24667281.0 Cr+VC 2.R1.raw.fastq.gz 0:151 1:151 A:1969693675;C:1748150730;G:1771267240;T:1960378098;N:29119 151 151     1969693675 1748150730 1771267240 1960378098 29119 SRX27393952 SRS23824013 SRA2054568 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 2025-01-19 Adult Adult Gut Digestive System
34519 34519 SRR32044797 SRX27393951 SRS23824012 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 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 gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr+VC 1 G   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:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 1|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Cr+VC 1 Cr+VC 1 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295   loader:fastq load.py|options: doNotUseSharq Cr+VC-1.R1.raw.fastq Cr+VC-1.R2.raw.fastq fastq fastq 6865491179.0 45466829.0 Cr+VC 1.R1.raw.fastq.gz 0:151 A:1830069736;C:1600281531;G:1626303427;T:1808809011;N:27474 151       1830069736 1600281531 1626303427 1808809011 27474 SRX27393951 SRS23824012 SRA2054568 Hainan University|School of Life and Health Sciences Hainan University                       B   usable mapping rate bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-19 Adult Adult Gut Digestive System
34520 34520 SRR32044798 SRX27393950 SRS23824011 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 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 gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr 3 F   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:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 3|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Cr 3 Cr 3 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295     Cr-3.R1.raw.fastq.gz Cr-3.R2.raw.fastq.gz fastq fastq 6069804078.0 20098689.0 Cr 3.R1.raw.fastq.gz 0:151 1:151 A:1603886661;C:1431213970;G:1440806224;T:1593873144;N:24079 151 151     1603886661 1431213970 1440806224 1593873144 24079 SRX27393950 SRS23824011 SRA2054568 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 2025-01-19 Adult Adult Gut Digestive System
34521 34521 SRR32044799 SRX27393949 SRS23824010 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 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 gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr 2 E   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:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 2|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Cr 2 Cr 2 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295   loader:fastq load.py|options: doNotUseSharq Cr-2.R1.raw.fastq Cr-2.R2.raw.fastq fastq fastq 8327156985.0 55146735.0 Cr 2.R1.raw.fastq.gz 0:151 A:2181317777;C:1974793526;G:2003240106;T:2167771431;N:34145 151       2181317777 1974793526 2003240106 2167771431 34145 SRX27393949 SRS23824010 SRA2054568 Hainan University|School of Life and Health Sciences Hainan University                       B   usable mapping rate bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2025-01-19 Adult Adult Gut Digestive System
34522 34522 SRR32044800 SRX27393948 SRS23824009 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 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 gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Cr 1 D   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:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 1|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Cr 1 Cr 1 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295     Cr-1.R1.raw.fastq.gz Cr-1.R2.raw.fastq.gz fastq fastq 7322067614.0 24245257.0 Cr 1.R1.raw.fastq.gz 0:151 1:151 A:1927213281;C:1727973559;G:1748866497;T:1917985720;N:28557 151 151     1927213281 1727973559 1748866497 1917985720 28557 SRX27393948 SRS23824009 SRA2054568 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 2025-01-19 Adult Adult Gut Digestive System
34523 34523 SRR32044801 SRX27393947 SRS23824008 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 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 gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Con 3 C   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:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 3|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Con 3 Con 3 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295     Con-3.R1.raw.fastq.gz Con-3.R2.raw.fastq.gz fastq fastq 10329187314.0 34202607.0 Con 3.R1.raw.fastq.gz 0:151 1:151 A:2805764955;C:2343400161;G:2421657823;T:2758323021;N:41354 151 151     2805764955 2343400161 2421657823 2758323021 41354 SRX27393947 SRS23824008 SRA2054568 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 2025-01-19 Adult Adult Gut Digestive System
34524 34524 SRR32044802 SRX27393946 SRS23824007 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 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 gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Con 2 B   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:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 2|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Con 2 Con 2 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295     Con-2.R1.raw.fastq.gz Con-2.R2.raw.fastq.gz fastq fastq 10789961398.0 35728349.0 Con 2.R1.raw.fastq.gz 0:151 1:151 A:2983305704;C:2396592872;G:2488165589;T:2921853880;N:43353 151 151     2983305704 2396592872 2488165589 2921853880 43353 SRX27393946 SRS23824007 SRA2054568 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 2025-01-19 Adult Adult Gut Digestive System
34525 34525 SRR32044803 SRX27393945 SRS23824006 SRP558295 PRJNA1212482 vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish PRJNA1212482 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 gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.       Con 1 A   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:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 1|BioSampleModel:Model organism or animal                 RNA Seq of brian:Adult female and male zebrafish Con 1 Con 1 normal     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP558295     Con-1.R1.raw.fastq.gz Con-1.R2.raw.fastq.gz fastq fastq 7118179260.0 23570130.0 Con 1.R1.raw.fastq.gz 0:151 1:151 A:1874284939;C:1673861890;G:1718740497;T:1851263659;N:28275 151 151     1874284939 1673861890 1718740497 1851263659 28275 SRX27393945 SRS23824006 SRA2054568 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 2025-01-19 Adult Adult Gut Digestive System
64514 64514 SRR17137062 SRX13321492 SRS11229253 SRP324000 PRJNA737474 Construction the larval and adult zebrafish cell atlas at single cell resolution GSE178150 Transcriptome Analysis Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. parent bioproject:PRJNA737471 pubmed:36229673   Microwell seq datasets of Zebrafish 72hpf COL104 GSM5718328   source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism Microwell seq datasets of Zebrafish 72hpf COL104 Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. Zebrafish 72hpf sample3   Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol   strain:AB|age:72 hours|tissue:whole organism GSM5718328 GSM5718328: Microwell seq datasets of Zebrafish 72hpf COL104; Danio rerio; RNA Seq GSM5718328   1 Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP324000   assembly:GRCz11|intentional duplicate Zebrafish_72hpf_COL104.bam 10X Genomics bam file 90497447328.0 520100272.0 GSM5718328 r1 0:24 1:150 A:26568037621;C:19526761960;G:20762820842;T:23593883403;N:45943502 24 150     26568037621 19526761960 20762820842 23593883403 45943502 SRX13321492 SRS11229253 SRA1244752 GEO Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine 2 0.00219 0.7651 0.00205 0.0914 0.99981 0.79953 0.5 0.51979 24 150 T B sc-like readlen bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2021-12-05 Larval Larval Whole Organism All anatomical structures
69032 69032 SRR18915949 SRX14993867 SRS12743200 SRP363983 PRJNA816047 Mapping the zebrafish developmental and aging atlas by single cell mRNA seq GSE198571 Transcriptome Analysis Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate. parent bioproject:PRJNA817101 pubmed:35929025   Micorwell seq datasets of Zebrafish 21d COL79 GSM6065255   source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism Micorwell seq datasets of Zebrafish 21d COL79 Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. Zebrafish 21d sample1   Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol   strain:AB|age:21 day|tissue:whole organism GSM6065255 GSM6065255: Micorwell seq datasets of Zebrafish 21d COL79; Danio rerio; RNA Seq GSM6065255 r1 GSM6065255 1 Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP363983   assembly:GRCz11|intentional duplicate Zebrafish_21d_COL79.bam 10X Genomics bam file 141397811748.0 812631102.0 GSM6065255 r1 0:24 1:150 A:42419601578;C:30491813752;G:32301586155;T:36094049456;N:90760807 24 150     42419601578 30491813752 32301586155 36094049456 90760807 SRX14993867 SRS12743200 SRA1409755 Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine 2 0.00187 0.69179 0.00172 0.07347 0.99975 0.82231 0.33333 0.52514 24 150 T B sc-like readlen bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2022-04-25 Larval Larval Whole Organism All anatomical structures
69035 69035 SRR18915952 SRX14993864 SRS12743197 SRP363983 PRJNA816047 Mapping the zebrafish developmental and aging atlas by single cell mRNA seq GSE198571 Transcriptome Analysis Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate. parent bioproject:PRJNA817101 pubmed:35929025   Micorwell seq datasets of Zebrafish 21d COL76 GSM6065252   source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism Micorwell seq datasets of Zebrafish 21d COL76 Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. Zebrafish 21d sample1   Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol   strain:AB|age:21 day|tissue:whole organism GSM6065252 GSM6065252: Micorwell seq datasets of Zebrafish 21d COL76; Danio rerio; RNA Seq GSM6065252 r1 GSM6065252 1 Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP363983   assembly:GRCz11|intentional duplicate Zebrafish_21d_COL76.bam 10X Genomics bam file 111633243510.0 641570365.0 GSM6065252 r1 0:24 1:150 A:33972927532;C:23914299609;G:25579933876;T:28104989997;N:61092496 24 150     33972927532 23914299609 25579933876 28104989997 61092496 SRX14993864 SRS12743197 SRA1409755 Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine 2 0.00193 0.6842 0.00182 0.07841 0.99983 0.82059 0.375 0.55944 24 150 T B sc-like readlen bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2022-04-25 Larval Larval Whole Organism All anatomical structures
69038 69038 SRR18642995 SRX14746259 SRS12507764 SRP363983 PRJNA816047 Mapping the zebrafish developmental and aging atlas by single cell mRNA seq GSE198571 Transcriptome Analysis Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate. parent bioproject:PRJNA817101 pubmed:35929025   Micorwell seq datasets of Zebrafish 21d COL73 GSM6019658   source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism Micorwell seq datasets of Zebrafish 21d COL73 Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. Zebrafish 21d sample1   Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol   strain:AB|age:21 day|tissue:whole organism GSM6019658 GSM6019658: Micorwell seq datasets of Zebrafish 21d COL73; Danio rerio; RNA Seq GSM6019658 r1 GSM6019658 1 Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP363983   assembly:GRCz11|intentional duplicate Zebrafish_21d_COL73.bam 10X Genomics bam file 94495251666.0 543076159.0 GSM6019658 r1 0:24 1:150 A:28813859102;C:20196407259;G:21422570931;T:24009240216;N:53174158 24 150     28813859102 20196407259 21422570931 24009240216 53174158 SRX14746259 SRS12507764 SRA1398049 Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine 2 0.002 0.68935 0.00186 0.07467 0.99977 0.82392 0.45454 0.54871 24 150 T B sc-like readlen bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2022-04-05 Larval Larval Whole Organism All anatomical structures
69040 69040 SRR18642997 SRX14746257 SRS12507765 SRP363983 PRJNA816047 Mapping the zebrafish developmental and aging atlas by single cell mRNA seq GSE198571 Transcriptome Analysis Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate. parent bioproject:PRJNA817101 pubmed:35929025   Micorwell seq datasets of Zebrafish 21d COL71 GSM6019656   source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism Micorwell seq datasets of Zebrafish 21d COL71 Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. Zebrafish 21d sample1   Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol   strain:AB|age:21 day|tissue:whole organism GSM6019656 GSM6019656: Micorwell seq datasets of Zebrafish 21d COL71; Danio rerio; RNA Seq GSM6019656 r1 GSM6019656 1 Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP363983   assembly:GRCz11|intentional duplicate Zebrafish_21d_COL71.bam 10X Genomics bam file 141830365482.0 815117043.0 GSM6019656 r1 0:24 1:150 A:43213881758;C:30298104199;G:32190676130;T:36046592777;N:81110618 24 150     43213881758 30298104199 32190676130 36046592777 81110618 SRX14746257 SRS12507765 SRA1398049 Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine 2 0.00172 0.68841 0.00159 0.06954 0.99977 0.82351 0.54545 0.55717 24 150 T B sc-like readlen bgi bgi unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2022-04-05 Larval Larval Whole Organism All anatomical structures
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");;