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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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 72561,SRR22722190,SRX18683720,SRS16126888,SRP412911,PRJNA911847,Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukaemia,PRJNA911847,Other,Isocitrate dehydrogenase 2 IDH2 mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia CN AML but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to maturity full blown leukemia ensued with multi lineage dysplasia increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in T cell development at embryonic and adult stage. Single cell transcriptomic analysis revealed increased myeloid skewing differentiation blockade and enrichment of leukemia associated gene signatures in both zebrafish models. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in interferon signals at adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion the zebrafish models of IDH2 mutated AML recapitulated the morphologic clinical functional and transcriptomic characteristics of human diseases and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening,,,,,Transgenic FLT3 ITD IDH2 R140Q,,strain:TU|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:8 month|dev stage:8 month|sex:pooled male and female|tissue:kidney marrow|genotype:Transgenic Runx1:FLT3ITDIDH2R140Q|BioSampleModel:Model organism or animal,,,,,,,,,Single cell RNA seq of Danio rerio: Transgenic FLT3 ITD IDH2 R140Q,ITD140Q,ITD140Q,Single cell RNA seq library.Single viable KM cells were collected from the transgenic double mutant n=3; pooled and WT n=3; pooled fish at 7 mpf into 0.9X PBS with 5% FBS. Their viability was examined by 0.4% Trypan blue staining under microscopy. The single cell library was constructed using the ChromiumTM Controller and ChromiumTM Next GEM Single Cell 3 Kit v3.1 10x Genomics Pleasanton CA. Complementary DNA cDNA was synthesized from the fragmentated RNAs using N6 random primers followed by end repair and ligation to BGISEQ sequencer compatible adapters. Quality control of the final library was performed by checking the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantification was performed by real time quantitative PCR using TaqMan probes. The final products were sequenced using the DNBSEQTM platform BGI HK China.,,,OTHER,TRANSCRIPTOMIC,other,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP412911,,loader:fastq load.py,ITD172KA_S1_L001_I1_001.fastq.gz ITD172KA_S1_L001_R1_001.fastq.gz ITD172KA_S1_L001_R2_001.fastq.gz,fastq fastq fastq,52149830422.0,410628586.0,ITD172KA S1 L001 I1 001.fastq.gz,0:8 1:28 2:91,A:10282953217;C:8459559201;G:8851285287;T:9772343870;N:1059751,8,28,91,,10282953217,8459559201,8851285287,9772343870,1059751,SRX18683720,SRS16126888,SRA1558824,The University of Hong Kong|Department of Medicine,The University of Hong Kong,1,0.88465,,0.13112,,0.81789,,0.55842,,91,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,China,2022-12-14,Adult,Adult,Kidney,Renal System 72562,SRR22722191,SRX18683719,SRS16126887,SRP412911,PRJNA911847,Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukaemia,PRJNA911847,Other,Isocitrate dehydrogenase 2 IDH2 mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia CN AML but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to maturity full blown leukemia ensued with multi lineage dysplasia increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in T cell development at embryonic and adult stage. Single cell transcriptomic analysis revealed increased myeloid skewing differentiation blockade and enrichment of leukemia associated gene signatures in both zebrafish models. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in interferon signals at adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion the zebrafish models of IDH2 mutated AML recapitulated the morphologic clinical functional and transcriptomic characteristics of human diseases and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening,,,,,Transgenic FLT3 ITD IDH2 R172K,,strain:TU|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:8 month|dev stage:8 month|sex:pooled male and female|tissue:kidney marrow|genotype:Transgenic Runx1:FLT3ITDIDH2R172K|BioSampleModel:Model organism or animal,,,,,,,,,Single cell RNA seq of Danio rerio: Transgenic FLT3 ITD IDH2 R172K,ITD172K,ITD172K,Single cell RNA seq library.Single viable KM cells were collected from the transgenic double mutant n=3; pooled and WT n=3; pooled fish at 7 mpf into 0.9X PBS with 5% FBS. Their viability was examined by 0.4% Trypan blue staining under microscopy. The single cell library was constructed using the ChromiumTM Controller and ChromiumTM Next GEM Single Cell 3 Kit v3.1 10x Genomics Pleasanton CA. Complementary DNA cDNA was synthesized from the fragmentated RNAs using N6 random primers followed by end repair and ligation to BGISEQ sequencer compatible adapters. Quality control of the final library was performed by checking the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantification was performed by real time quantitative PCR using TaqMan probes. The final products were sequenced using the DNBSEQTM platform BGI HK China.,,,OTHER,TRANSCRIPTOMIC,other,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP412911,,loader:fastq load.py,ITD140QA_S1_L004_I1_001.fastq.gz ITD140QA_S1_L004_R1_001.fastq.gz ITD140QA_S1_L004_R2_001.fastq.gz,fastq fastq fastq,28595025233.0,225157679.0,ITD140QA S1 L004 I1 001.fastq.gz,0:8 1:28 2:91,A:5628987577;C:4565848641;G:4959209904;T:5302394659;N:32908008,8,28,91,,5628987577,4565848641,4959209904,5302394659,32908008,SRX18683719,SRS16126887,SRA1558824,The University of Hong Kong|Department of Medicine,The University of Hong Kong,1,0.81404,,0.11315,,0.83327,,0.56222,,91,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,China,2022-12-13,Adult,Adult,Kidney,Renal System 72563,SRR22722192,SRX18683718,SRS16126886,SRP412911,PRJNA911847,Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukaemia,PRJNA911847,Other,Isocitrate dehydrogenase 2 IDH2 mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia CN AML but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to maturity full blown leukemia ensued with multi lineage dysplasia increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in T cell development at embryonic and adult stage. Single cell transcriptomic analysis revealed increased myeloid skewing differentiation blockade and enrichment of leukemia associated gene signatures in both zebrafish models. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in interferon signals at adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion the zebrafish models of IDH2 mutated AML recapitulated the morphologic clinical functional and transcriptomic characteristics of human diseases and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening,,,,,Wild type,,strain:TU|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:8 month|dev stage:8 month|sex:pooled male and female|tissue:kidney marrow|genotype:Wild type|BioSampleModel:Model organism or animal,,,,,,,,,Single cell RNA seq of Danio rerio: Wild type,Control,Control,Single cell RNA seq library.Single viable KM cells were collected from the transgenic double mutant n=3; pooled and WT n=3; pooled fish at 7 mpf into 0.9X PBS with 5% FBS. Their viability was examined by 0.4% Trypan blue staining under microscopy. The single cell library was constructed using the ChromiumTM Controller and ChromiumTM Next GEM Single Cell 3 Kit v3.1 10x Genomics Pleasanton CA. Complementary DNA cDNA was synthesized from the fragmentated RNAs using N6 random primers followed by end repair and ligation to BGISEQ sequencer compatible adapters. Quality control of the final library was performed by checking the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantification was performed by real time quantitative PCR using TaqMan probes. The final products were sequenced using the DNBSEQTM platform BGI HK China.,,,OTHER,TRANSCRIPTOMIC,other,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP412911,,loader:fastq load.py,ControlA_S1_L003_R2_001.fastq.gz ControlA_S1_L003_R1_001.fastq.gz ControlA_S1_L003_I1_001.fastq.gz,fastq fastq fastq,37892727491.0,298367933.0,ControlA S1 L003 I1 001.fastq.gz,0:8 1:28 2:91,A:7386602298;C:6174680460;G:6579652828;T:6955791213;N:54755104,8,28,91,,7386602298,6174680460,6579652828,6955791213,54755104,SRX18683718,SRS16126886,SRA1558824,The University of Hong Kong|Department of Medicine,The University of Hong Kong,1,0.81686,,0.11049,,0.84139,,0.46084,,91,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,China,2022-12-14,Adult,Adult,Kidney,Renal System