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 68121,SRR17606004,SRX13774802,SRS11654800,SRP354915,PRJNA796975,Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish,GSE193630,Transcriptome Analysis,In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;,,pubmed:35513710,,CEN Homo Kidney RNAseq rep3,GSM5815265,,source name:Kidney|strain:EK|tissue:Kidney|genotype:CEN homozygous knockout|treatment:cardiomyocyte ablation,CEN Homo Kidney RNAseq rep3,RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,Kidney,animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.,strain:EK|tissue:Kidney|genotype:CEN homozygous knockout|treatment:cardiomyocyte ablation,GSM5815265,GSM5815265: CEN Homo Kidney RNAseq rep3; Danio rerio; RNA Seq,GSM5815265 r1,GSM5815265,1,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP354915,,,CENHOMO3_2.fq.gz CENHOMO3_1.fq.gz,fastq fastq,7215517200.0,72155172.0,GSM5815265 r1,0:100 1:100,A:1927134950;C:1661322135;G:1683841967;T:1943218148;N:0,100,100,,,1927134950,1661322135,1683841967,1943218148,0,SRX13774802,SRS11654800,SRA1356624,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.94062,,0.07183,,0.72596,,0.55426,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-13,Larval,Larval,Kidney,Renal System 68122,SRR17606005,SRX13774801,SRS11654799,SRP354915,PRJNA796975,Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish,GSE193630,Transcriptome Analysis,In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;,,pubmed:35513710,,CEN Homo Kidney RNAseq rep2,GSM5815264,,source name:Kidney|strain:EK|tissue:Kidney|genotype:CEN homozygous knockout|treatment:cardiomyocyte ablation,CEN Homo Kidney RNAseq rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,Kidney,animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.,strain:EK|tissue:Kidney|genotype:CEN homozygous knockout|treatment:cardiomyocyte ablation,GSM5815264,GSM5815264: CEN Homo Kidney RNAseq rep2; Danio rerio; RNA Seq,GSM5815264 r1,GSM5815264,1,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP354915,,,CENHOMO2_2.fq.gz CENHOMO2_1.fq.gz,fastq fastq,7207596800.0,72075968.0,GSM5815264 r1,0:100 1:100,A:1913835378;C:1670319627;G:1686651138;T:1936790657;N:0,100,100,,,1913835378,1670319627,1686651138,1936790657,0,SRX13774801,SRS11654799,SRA1356624,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.94306,,0.06924,,0.72376,,0.56145,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-13,Larval,Larval,Kidney,Renal System 68123,SRR17606006,SRX13774800,SRS11654798,SRP354915,PRJNA796975,Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish,GSE193630,Transcriptome Analysis,In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;,,pubmed:35513710,,CEN Homo Kidney RNAseq rep1,GSM5815263,,source name:Kidney|strain:EK|tissue:Kidney|genotype:CEN homozygous knockout|treatment:cardiomyocyte ablation,CEN Homo Kidney RNAseq rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,Kidney,animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.,strain:EK|tissue:Kidney|genotype:CEN homozygous knockout|treatment:cardiomyocyte ablation,GSM5815263,GSM5815263: CEN Homo Kidney RNAseq rep1; Danio rerio; RNA Seq,GSM5815263 r1,GSM5815263,1,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP354915,,,CENHOMO1_1.fq.gz CENHOMO1_2.fq.gz,fastq fastq,7204062600.0,72040626.0,GSM5815263 r1,0:100 1:100,A:1902216192;C:1680493255;G:1696367176;T:1924985977;N:0,100,100,,,1902216192,1680493255,1696367176,1924985977,0,SRX13774800,SRS11654798,SRA1356624,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.9408,,0.06772,,0.71545,,0.53936,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-13,Larval,Larval,Kidney,Renal System 68124,SRR17606007,SRX13774799,SRS11654797,SRP354915,PRJNA796975,Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish,GSE193630,Transcriptome Analysis,In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;,,pubmed:35513710,,CEN WT Kidney RNAseq rep3,GSM5815262,,source name:Kidney|strain:EK|tissue:Kidney|genotype:Wild type|treatment:cardiomyocyte ablation,CEN WT Kidney RNAseq rep3,RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,Kidney,animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.,strain:EK|tissue:Kidney|genotype:Wild type|treatment:cardiomyocyte ablation,GSM5815262,GSM5815262: CEN WT Kidney RNAseq rep3; Danio rerio; RNA Seq,GSM5815262 r1,GSM5815262,1,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP354915,,,CENWT3_2.fq.gz CENWT3_1.fq.gz,fastq fastq,7205589000.0,72055890.0,GSM5815262 r1,0:100 1:100,A:1892937448;C:1690826558;G:1711136694;T:1910688300;N:0,100,100,,,1892937448,1690826558,1711136694,1910688300,0,SRX13774799,SRS11654797,SRA1356624,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.94358,,0.06548,,0.72336,,0.54655,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-13,Larval,Larval,Kidney,Renal System 68125,SRR17606008,SRX13774798,SRS11654796,SRP354915,PRJNA796975,Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish,GSE193630,Transcriptome Analysis,In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;,,pubmed:35513710,,CEN WT Kidney RNAseq rep2,GSM5815261,,source name:Kidney|strain:EK|tissue:Kidney|genotype:Wild type|treatment:cardiomyocyte ablation,CEN WT Kidney RNAseq rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,Kidney,animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.,strain:EK|tissue:Kidney|genotype:Wild type|treatment:cardiomyocyte ablation,GSM5815261,GSM5815261: CEN WT Kidney RNAseq rep2; Danio rerio; RNA Seq,GSM5815261 r1,GSM5815261,1,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP354915,,,CENWT2_1.fq.gz CENWT2_2.fq.gz,fastq fastq,7219678800.0,72196788.0,GSM5815261 r1,0:100 1:100,A:1908750065;C:1680876268;G:1700533938;T:1929518529;N:0,100,100,,,1908750065,1680876268,1700533938,1929518529,0,SRX13774798,SRS11654796,SRA1356624,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.94561,,0.06821,,0.71792,,0.54803,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-13,Larval,Larval,Kidney,Renal System 68126,SRR17606009,SRX13774797,SRS11654795,SRP354915,PRJNA796975,Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish,GSE193630,Transcriptome Analysis,In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;,,pubmed:35513710,,CEN WT Kidney RNAseq rep1,GSM5815260,,source name:Kidney|strain:EK|tissue:Kidney|genotype:Wild type|treatment:cardiomyocyte ablation,CEN WT Kidney RNAseq rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,Kidney,animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.,strain:EK|tissue:Kidney|genotype:Wild type|treatment:cardiomyocyte ablation,GSM5815260,GSM5815260: CEN WT Kidney RNAseq rep1; Danio rerio; RNA Seq,GSM5815260 r1,GSM5815260,1,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP354915,,,CENWT1_1.fq.gz CENWT1_2.fq.gz,fastq fastq,7213577400.0,72135774.0,GSM5815260 r1,0:100 1:100,A:1899760333;C:1688268609;G:1705140400;T:1920408058;N:0,100,100,,,1899760333,1688268609,1705140400,1920408058,0,SRX13774797,SRS11654795,SRA1356624,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.94364,,0.06593,,0.71796,,0.55315,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-13,Larval,Larval,Kidney,Renal System 68127,SRR17606010,SRX13774796,SRS11654794,SRP354915,PRJNA796975,Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish,GSE193630,Transcriptome Analysis,In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;,,pubmed:35513710,,cebpd Homo Kidney RNAseq rep3,GSM5815259,,source name:Kidney|strain:EK|tissue:Kidney|genotype:cebpd homozygous knockout|treatment:cardiomyocyte ablation,cebpd Homo Kidney RNAseq rep3,RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,Kidney,animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.,strain:EK|tissue:Kidney|genotype:cebpd homozygous knockout|treatment:cardiomyocyte ablation,GSM5815259,GSM5815259: cebpd Homo Kidney RNAseq rep3; Danio rerio; RNA Seq,GSM5815259 r1,GSM5815259,1,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP354915,,,cebpdHomo3_1.fq.gz cebpdHomo3_2.fq.gz,fastq fastq,7279069400.0,72790694.0,GSM5815259 r1,0:100 1:100,A:1930406096;C:1690658505;G:1705808112;T:1952196687;N:0,100,100,,,1930406096,1690658505,1705808112,1952196687,0,SRX13774796,SRS11654794,SRA1356624,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.94225,,0.05895,,0.74353,,0.55835,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-13,Larval,Larval,Kidney,Renal System 68128,SRR17606011,SRX13774795,SRS11654793,SRP354915,PRJNA796975,Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish,GSE193630,Transcriptome Analysis,In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;,,pubmed:35513710,,cebpd Homo Kidney RNAseq rep2,GSM5815258,,source name:Kidney|strain:EK|tissue:Kidney|genotype:cebpd homozygous knockout|treatment:cardiomyocyte ablation,cebpd Homo Kidney RNAseq rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,Kidney,animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.,strain:EK|tissue:Kidney|genotype:cebpd homozygous knockout|treatment:cardiomyocyte ablation,GSM5815258,GSM5815258: cebpd Homo Kidney RNAseq rep2; Danio rerio; RNA Seq,GSM5815258 r1,GSM5815258,1,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP354915,,,cebpdHomo2_2.fq.gz cebpdHomo2_1.fq.gz,fastq fastq,7264240800.0,72642408.0,GSM5815258 r1,0:100 1:100,A:1907893057;C:1703728991;G:1717658793;T:1934959959;N:0,100,100,,,1907893057,1703728991,1717658793,1934959959,0,SRX13774795,SRS11654793,SRA1356624,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.94566,,0.06391,,0.72417,,0.5235,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-13,Larval,Larval,Kidney,Renal System 68129,SRR17606012,SRX13774794,SRS11654791,SRP354915,PRJNA796975,Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish,GSE193630,Transcriptome Analysis,In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;,,pubmed:35513710,,cebpd Homo Kidney RNAseq rep1,GSM5815257,,source name:Kidney|strain:EK|tissue:Kidney|genotype:cebpd homozygous knockout|treatment:cardiomyocyte ablation,cebpd Homo Kidney RNAseq rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,Kidney,animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.,strain:EK|tissue:Kidney|genotype:cebpd homozygous knockout|treatment:cardiomyocyte ablation,GSM5815257,GSM5815257: cebpd Homo Kidney RNAseq rep1; Danio rerio; RNA Seq,GSM5815257 r1,GSM5815257,1,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP354915,,,cebpdHomo1_2.fq.gz cebpdHomo1_1.fq.gz,fastq fastq,7192873200.0,71928732.0,GSM5815257 r1,0:100 1:100,A:1905599298;C:1665589905;G:1707980534;T:1913703463;N:0,100,100,,,1905599298,1665589905,1707980534,1913703463,0,SRX13774794,SRS11654791,SRA1356624,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.92744,,0.062,,0.72393,,0.55384,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-13,Larval,Larval,Kidney,Renal System 68130,SRR17606013,SRX13774793,SRS11654792,SRP354915,PRJNA796975,Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish,GSE193630,Transcriptome Analysis,In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;,,pubmed:35513710,,cebpd WT Kidney RNAseq rep3,GSM5815256,,source name:Kidney|strain:EK|tissue:Kidney|genotype:Wild type|treatment:cardiomyocyte ablation,cebpd WT Kidney RNAseq rep3,RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,Kidney,animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.,strain:EK|tissue:Kidney|genotype:Wild type|treatment:cardiomyocyte ablation,GSM5815256,GSM5815256: cebpd WT Kidney RNAseq rep3; Danio rerio; RNA Seq,GSM5815256 r1,GSM5815256,1,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP354915,,,cebpdWT3_1.fq.gz cebpdWT3_2.fq.gz,fastq fastq,7280350400.0,72803504.0,GSM5815256 r1,0:100 1:100,A:1925119485;C:1698344141;G:1714885029;T:1942001745;N:0,100,100,,,1925119485,1698344141,1714885029,1942001745,0,SRX13774793,SRS11654792,SRA1356624,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.94212,,0.05877,,0.73446,,0.54431,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-13,Larval,Larval,Kidney,Renal System 68131,SRR17606014,SRX13774792,SRS11654802,SRP354915,PRJNA796975,Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish,GSE193630,Transcriptome Analysis,In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;,,pubmed:35513710,,cebpd WT Kidney RNAseq rep2,GSM5815255,,source name:Kidney|strain:EK|tissue:Kidney|genotype:Wild type|treatment:cardiomyocyte ablation,cebpd WT Kidney RNAseq rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,Kidney,animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.,strain:EK|tissue:Kidney|genotype:Wild type|treatment:cardiomyocyte ablation,GSM5815255,GSM5815255: cebpd WT Kidney RNAseq rep2; Danio rerio; RNA Seq,GSM5815255 r1,GSM5815255,1,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP354915,,,cebpdWT2_1.fq.gz cebpdWT2_2.fq.gz,fastq fastq,7264980400.0,72649804.0,GSM5815255 r1,0:100 1:100,A:1953740321;C:1658035501;G:1681062257;T:1972142321;N:0,100,100,,,1953740321,1658035501,1681062257,1972142321,0,SRX13774792,SRS11654802,SRA1356624,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.93531,,0.06698,,0.73499,,0.56385,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-13,Larval,Larval,Kidney,Renal System 68132,SRR17606015,SRX13774791,SRS11654790,SRP354915,PRJNA796975,Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish,GSE193630,Transcriptome Analysis,In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;,,pubmed:35513710,,cebpd WT Kidney RNAseq rep1,GSM5815254,,source name:Kidney|strain:EK|tissue:Kidney|genotype:Wild type|treatment:cardiomyocyte ablation,cebpd WT Kidney RNAseq rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,Kidney,animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.,strain:EK|tissue:Kidney|genotype:Wild type|treatment:cardiomyocyte ablation,GSM5815254,GSM5815254: cebpd WT Kidney RNAseq rep1; Danio rerio; RNA Seq,GSM5815254 r1,GSM5815254,1,Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP354915,,,cebpdWT1_1.fq.gz cebpdWT1_2.fq.gz,fastq fastq,7256843800.0,72568438.0,GSM5815254 r1,0:100 1:100,A:1920544243;C:1687420610;G:1707252526;T:1941626421;N:0,100,100,,,1920544243,1687420610,1707252526,1941626421,0,SRX13774791,SRS11654790,SRA1356624,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.94388,,0.06494,,0.7265,,0.54419,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-01-13,Larval,Larval,Kidney,Renal 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