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 24854,SRR25519420,SRX21249697,SRS18503946,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish AR42 TFA 4 3dpf,GSM7681266,,source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish AR42 TFA 4 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae with TFA modeling,GSM7681266,GSM7681266: zebrafish AR42 TFA 4 3dpf; Danio rerio; RNA Seq,GSM7681266 r1,GSM7681266,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_TFA_4.R1.fq.gz AR42_TFA_4.R2.fq.gz,fastq fastq,9896772900.0,32989243.0,GSM7681266 r1,0:150 1:150,A:2382403653;C:2457377213;G:2470646159;T:2586345875;N:0,150,150,,,2382403653,2457377213,2470646159,2586345875,0,SRX21249697,SRS18503946,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70537,0.88934,0.03159,0.04209,0.78013,0.75416,0.50713,0.45138,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24855,SRR25519421,SRX21249696,SRS18503945,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish AR42 TFA 3 3dpf,GSM7681265,,source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish AR42 TFA 3 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae with TFA modeling,GSM7681265,GSM7681265: zebrafish AR42 TFA 3 3dpf; Danio rerio; RNA Seq,GSM7681265 r1,GSM7681265,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_TFA_3.R1.fq.gz AR42_TFA_3.R2.fq.gz,fastq fastq,10265927100.0,34219757.0,GSM7681265 r1,0:150 1:150,A:2473552302;C:2548535087;G:2562873160;T:2680966551;N:0,150,150,,,2473552302,2548535087,2562873160,2680966551,0,SRX21249696,SRS18503945,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70516,0.88765,0.03163,0.04168,0.7782,0.75083,0.50851,0.45305,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24856,SRR25519422,SRX21249695,SRS18503944,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish AR42 TFA 2 3dpf,GSM7681264,,source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish AR42 TFA 2 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae with TFA modeling,GSM7681264,GSM7681264: zebrafish AR42 TFA 2 3dpf; Danio rerio; RNA Seq,GSM7681264 r1,GSM7681264,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_TFA_2.R2.fq.gz AR42_TFA_2.R1.fq.gz,fastq fastq,10003398900.0,33344663.0,GSM7681264 r1,0:150 1:150,A:2409580340;C:2483650756;G:2497057051;T:2613110753;N:0,150,150,,,2409580340,2483650756,2497057051,2613110753,0,SRX21249695,SRS18503944,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70787,0.89158,0.03203,0.04194,0.77851,0.75108,0.5072,0.45508,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24857,SRR25519423,SRX21249694,SRS18503943,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish AR42 TFA 1 3dpf,GSM7681263,,source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish AR42 TFA 1 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae with TFA modeling,GSM7681263,GSM7681263: zebrafish AR42 TFA 1 3dpf; Danio rerio; RNA Seq,GSM7681263 r1,GSM7681263,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_TFA_1.R1.fq.gz AR42_TFA_1.R2.fq.gz,fastq fastq,7420308900.0,24734363.0,GSM7681263 r1,0:150 1:150,A:1791092728;C:1841012408;G:1852583633;T:1935620131;N:0,150,150,,,1791092728,1841012408,1852583633,1935620131,0,SRX21249694,SRS18503943,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.69668,0.87862,0.03153,0.04215,0.77463,0.74949,0.50657,0.45971,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24858,SRR25519424,SRX21249693,SRS18503942,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish DMSO TFA 4 3dpf,GSM7681262,,source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish DMSO TFA 4 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae with TFA modeling,GSM7681262,GSM7681262: zebrafish DMSO TFA 4 3dpf; Danio rerio; RNA Seq,GSM7681262 r1,GSM7681262,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_TFA_4.R1.fq.gz DMSO_TFA_4.R2.fq.gz,fastq fastq,10178474100.0,33928247.0,GSM7681262 r1,0:150 1:150,A:2452172460;C:2526571372;G:2532799116;T:2666931152;N:0,150,150,,,2452172460,2526571372,2532799116,2666931152,0,SRX21249693,SRS18503942,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.72132,0.91072,0.03161,0.04366,0.77709,0.75016,0.516,0.45312,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24859,SRR25519425,SRX21249692,SRS18503941,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish DMSO TFA 3 3dpf,GSM7681261,,source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish DMSO TFA 3 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae with TFA modeling,GSM7681261,GSM7681261: zebrafish DMSO TFA 3 3dpf; Danio rerio; RNA Seq,GSM7681261 r1,GSM7681261,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_TFA_3.R1.fq.gz DMSO_TFA_3.R2.fq.gz,fastq fastq,9483201300.0,31610671.0,GSM7681261 r1,0:150 1:150,A:2282797855;C:2354211318;G:2361918927;T:2484273200;N:0,150,150,,,2282797855,2354211318,2361918927,2484273200,0,SRX21249692,SRS18503941,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.71779,0.90757,0.03224,0.04329,0.77853,0.74862,0.51128,0.44891,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24860,SRR25519426,SRX21249691,SRS18503940,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish DMSO TFA 2 3dpf,GSM7681260,,source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish DMSO TFA 2 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae with TFA modeling,GSM7681260,GSM7681260: zebrafish DMSO TFA 2 3dpf; Danio rerio; RNA Seq,GSM7681260 r1,GSM7681260,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_TFA_2.R1.fq.gz DMSO_TFA_2.R2.fq.gz,fastq fastq,9372641700.0,31242139.0,GSM7681260 r1,0:150 1:150,A:2255045813;C:2327185536;G:2333956274;T:2456454077;N:0,150,150,,,2255045813,2327185536,2333956274,2456454077,0,SRX21249691,SRS18503940,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.71913,0.91061,0.0318,0.04251,0.7778,0.74907,0.51295,0.45006,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24861,SRR25519427,SRX21249690,SRS18503939,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish DMSO TFA 1 3dpf,GSM7681259,,source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing,zebrafish DMSO TFA 1 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae with TFA modeling,GSM7681259,GSM7681259: zebrafish DMSO TFA 1 3dpf; Danio rerio; RNA Seq,GSM7681259 r1,GSM7681259,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_TFA_1.R1.fq.gz DMSO_TFA_1.R2.fq.gz,fastq fastq,8665981200.0,28886604.0,GSM7681259 r1,0:150 1:150,A:2086560929;C:2153111953;G:2157203992;T:2269104326;N:0,150,150,,,2086560929,2153111953,2157203992,2269104326,0,SRX21249690,SRS18503939,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.71996,0.90816,0.03211,0.04297,0.77739,0.75097,0.5122,0.452,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24862,SRR25519428,SRX21249689,SRS18503938,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish AR42 4 3dpf,GSM7681258,,source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish AR42 4 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae without xxx modeling,GSM7681258,GSM7681258: zebrafish AR42 4 3dpf; Danio rerio; RNA Seq,GSM7681258 r1,GSM7681258,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_4.R1.fq.gz AR42_4.R2.fq.gz,fastq fastq,10199154900.0,33997183.0,GSM7681258 r1,0:150 1:150,A:2461755295;C:2524481077;G:2536143078;T:2676775450;N:0,150,150,,,2461755295,2524481077,2536143078,2676775450,0,SRX21249689,SRS18503938,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70676,0.89456,0.031,0.04108,0.77508,0.747,0.44642,0.47521,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24863,SRR25519429,SRX21249688,SRS18503937,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish AR42 3 3dpf,GSM7681257,,source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish AR42 3 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae without xxx modeling,GSM7681257,GSM7681257: zebrafish AR42 3 3dpf; Danio rerio; RNA Seq,GSM7681257 r1,GSM7681257,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_3.R1.fq.gz AR42_3.R2.fq.gz,fastq fastq,9953498100.0,33178327.0,GSM7681257 r1,0:150 1:150,A:2400858967;C:2463285586;G:2477369817;T:2611983730;N:0,150,150,,,2400858967,2463285586,2477369817,2611983730,0,SRX21249688,SRS18503937,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70865,0.89517,0.03101,0.04127,0.77325,0.74679,0.50253,0.50409,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24864,SRR25519430,SRX21249687,SRS18503936,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish AR42 2 3dpf,GSM7681256,,source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish AR42 2 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae without xxx modeling,GSM7681256,GSM7681256: zebrafish AR42 2 3dpf; Danio rerio; RNA Seq,GSM7681256 r1,GSM7681256,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_2.R1.fq.gz AR42_2.R2.fq.gz,fastq fastq,10005489000.0,33351630.0,GSM7681256 r1,0:150 1:150,A:2413672248;C:2477611702;G:2491304598;T:2622900452;N:0,150,150,,,2413672248,2477611702,2491304598,2622900452,0,SRX21249687,SRS18503936,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70639,0.89204,0.03035,0.04087,0.77502,0.74955,0.50558,0.50545,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24865,SRR25519431,SRX21249686,SRS18503935,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish AR42 1 3dpf,GSM7681255,,source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish AR42 1 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:AR 42 treated larvae without xxx modeling,GSM7681255,GSM7681255: zebrafish AR42 1 3dpf; Danio rerio; RNA Seq,GSM7681255 r1,GSM7681255,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,AR42_1.R1.fq.gz AR42_1.R2.fq.gz,fastq fastq,9698587800.0,32328626.0,GSM7681255 r1,0:150 1:150,A:2337968859;C:2400315331;G:2416067610;T:2544236000;N:0,150,150,,,2337968859,2400315331,2416067610,2544236000,0,SRX21249686,SRS18503935,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70903,0.89448,0.02976,0.04032,0.77583,0.74935,0.50747,0.5081,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24866,SRR25519432,SRX21249685,SRS18503934,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish DMSO 4 3dpf,GSM7681254,,source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish DMSO 4 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae without xxx modeling,GSM7681254,GSM7681254: zebrafish DMSO 4 3dpf; Danio rerio; RNA Seq,GSM7681254 r1,GSM7681254,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_4.R1.fq.gz DMSO_4.R2.fq.gz,fastq fastq,9083670000.0,30278900.0,GSM7681254 r1,0:150 1:150,A:2191941100;C:2247936730;G:2258913579;T:2384878591;N:0,150,150,,,2191941100,2247936730,2258913579,2384878591,0,SRX21249685,SRS18503934,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.71071,0.90457,0.03362,0.04688,0.77106,0.74357,0.50842,0.50975,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24867,SRR25519433,SRX21249684,SRS18503933,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish DMSO 3 3dpf,GSM7681253,,source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish DMSO 3 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae without xxx modeling,GSM7681253,GSM7681253: zebrafish DMSO 3 3dpf; Danio rerio; RNA Seq,GSM7681253 r1,GSM7681253,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_3.R2.fq.gz DMSO_3.R1.fq.gz,fastq fastq,9394455000.0,31314850.0,GSM7681253 r1,0:150 1:150,A:2266296733;C:2324081714;G:2335347043;T:2468729510;N:0,150,150,,,2266296733,2324081714,2335347043,2468729510,0,SRX21249684,SRS18503933,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70975,0.90445,0.03329,0.04594,0.77005,0.7417,0.51188,0.5163,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24868,SRR25519434,SRX21249683,SRS18503932,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish DMSO 2 3dpf,GSM7681252,,source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish DMSO 2 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae without xxx modeling,GSM7681252,GSM7681252: zebrafish DMSO 2 3dpf; Danio rerio; RNA Seq,GSM7681252 r1,GSM7681252,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_2.R1.fq.gz DMSO_2.R2.fq.gz,fastq fastq,9157453500.0,30524845.0,GSM7681252 r1,0:150 1:150,A:2209331568;C:2266614182;G:2273923578;T:2407584172;N:0,150,150,,,2209331568,2266614182,2273923578,2407584172,0,SRX21249683,SRS18503932,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.70922,0.90538,0.03379,0.04616,0.7723,0.74213,0.50839,0.50803,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 24869,SRR25519435,SRX21249682,SRS18503931,SRP453374,PRJNA1002260,Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model,GSE240080,Transcriptome Analysis,We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.,,pubmed:37728477,,zebrafish DMSO 1 3dpf,GSM7681251,,source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing,zebrafish DMSO 1 3dpf,Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample,tail,,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.,,tissue:tail|treatment:DMSO treated larvae without xxx modeling,GSM7681251,GSM7681251: zebrafish DMSO 1 3dpf; Danio rerio; RNA Seq,GSM7681251 r1,GSM7681251,1,RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP453374,,,DMSO_1.R2.fq.gz DMSO_1.R1.fq.gz,fastq fastq,8769040200.0,29230134.0,GSM7681251 r1,0:150 1:150,A:2114427483;C:2170929931;G:2179906163;T:2303776623;N:0,150,150,,,2114427483,2170929931,2179906163,2303776623,0,SRX21249682,SRS18503931,SRA1687041,Chongqing medical university,Chongqing medical university,2,0.71002,0.9037,0.0335,0.04604,0.77155,0.74308,0.51339,0.50801,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-08-04,Larval,Larval,Tail,Multi-system 30204,SRR27715729,SRX23381950,SRS20243484,SRP485714,PRJNA1068542,The effects of HSP60 chaperone deficiency on zebrafish larvae,GSE254091,Transcriptome Analysis,To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.,,pubmed:39147275,,Ko 3,GSM8033238,,source name:embryo|tissue:embryo|cell line:5 dpf|genotype:hspd1 / |treatment:hspd1 knockout|geo loc name:missing|collection date:missing,Ko 3,Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample,embryo,,The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.,Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.,tissue:embryo|cell line:5 dpf|genotype:hspd1 / |treatment:hspd1 knockout,GSM8033238,GSM8033238: Ko 3; Danio rerio; RNA Seq,GSM8033238 r1,GSM8033238,1,The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP485714,,,15_1.fq.gz 15_2.fq.gz,fastq fastq,5020450600.0,25102253.0,GSM8033238 r1,0:100 1:100,A:1371660785;C:1125396855;G:1130384333;T:1393008627;N:0,100,100,,,1371660785,1125396855,1130384333,1393008627,0,SRX23381950,SRS20243484,SRA1791378,"Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital","Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital",2,0.9229,0.92453,0.12667,0.12674,0.65143,0.65232,0.48379,0.48431,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Denmark,2024-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures 30205,SRR27715730,SRX23381949,SRS20243483,SRP485714,PRJNA1068542,The effects of HSP60 chaperone deficiency on zebrafish larvae,GSE254091,Transcriptome Analysis,To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.,,pubmed:39147275,,control 3,GSM8033237,,source name:embryo|tissue:embryo|cell line:5 dpf|genotype:hspd1+/+|treatment:control|geo loc name:missing|collection date:missing,control 3,Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample,embryo,,The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.,Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.,tissue:embryo|cell line:5 dpf|genotype:hspd1+/+|treatment:control,GSM8033237,GSM8033237: control 3; Danio rerio; RNA Seq,GSM8033237 r1,GSM8033237,1,The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP485714,,,14_1.fq.gz 14_2.fq.gz,fastq fastq,5020525200.0,25102626.0,GSM8033237 r1,0:100 1:100,A:1366975716;C:1129522599;G:1135845277;T:1388181608;N:0,100,100,,,1366975716,1129522599,1135845277,1388181608,0,SRX23381949,SRS20243483,SRA1791378,"Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital","Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital",2,0.92923,0.93091,0.11899,0.11908,0.65117,0.651,0.48861,0.48085,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Denmark,2024-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures 30206,SRR27715731,SRX23381948,SRS20243485,SRP485714,PRJNA1068542,The effects of HSP60 chaperone deficiency on zebrafish larvae,GSE254091,Transcriptome Analysis,To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.,,pubmed:39147275,,Ko 2,GSM8033236,,source name:embryo|tissue:embryo|cell line:5 dpf|genotype:hspd1 / |treatment:hspd1 knockout|geo loc name:missing|collection date:missing,Ko 2,Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample,embryo,,The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.,Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.,tissue:embryo|cell line:5 dpf|genotype:hspd1 / |treatment:hspd1 knockout,GSM8033236,GSM8033236: Ko 2; Danio rerio; RNA Seq,GSM8033236 r1,GSM8033236,1,The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP485714,,,13_1.fq.gz 13_2.fq.gz,fastq fastq,5016980000.0,25084900.0,GSM8033236 r1,0:100 1:100,A:1362095542;C:1131485761;G:1140659655;T:1382739042;N:0,100,100,,,1362095542,1131485761,1140659655,1382739042,0,SRX23381948,SRS20243485,SRA1791378,"Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital","Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital",2,0.92867,0.92952,0.12009,0.11989,0.64989,0.65129,0.48735,0.48822,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Denmark,2024-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures 30207,SRR27715732,SRX23381947,SRS20243482,SRP485714,PRJNA1068542,The effects of HSP60 chaperone deficiency on zebrafish larvae,GSE254091,Transcriptome Analysis,To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.,,pubmed:39147275,,control 2,GSM8033235,,source name:embryo|tissue:embryo|cell line:5 dpf|genotype:hspd1+/+|treatment:control|geo loc name:missing|collection date:missing,control 2,Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample,embryo,,The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.,Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.,tissue:embryo|cell line:5 dpf|genotype:hspd1+/+|treatment:control,GSM8033235,GSM8033235: control 2; Danio rerio; RNA Seq,GSM8033235 r1,GSM8033235,1,The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP485714,,,12_1.fq.gz 12_2.fq.gz,fastq fastq,5014043600.0,25070218.0,GSM8033235 r1,0:100 1:100,A:1365729811;C:1126481057;G:1137205154;T:1384627578;N:0,100,100,,,1365729811,1126481057,1137205154,1384627578,0,SRX23381947,SRS20243482,SRA1791378,"Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital","Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital",2,0.92582,0.92658,0.11419,0.11406,0.65173,0.65257,0.48606,0.48533,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Denmark,2024-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures 30208,SRR27715733,SRX23381946,SRS20243480,SRP485714,PRJNA1068542,The effects of HSP60 chaperone deficiency on zebrafish larvae,GSE254091,Transcriptome Analysis,To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.,,pubmed:39147275,,Ko 1,GSM8033234,,source name:embryo|tissue:embryo|cell line:5 dpf|genotype:hspd1 / |treatment:hspd1 knockout|geo loc name:missing|collection date:missing,Ko 1,Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample,embryo,,The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.,Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.,tissue:embryo|cell line:5 dpf|genotype:hspd1 / |treatment:hspd1 knockout,GSM8033234,GSM8033234: Ko 1; Danio rerio; RNA Seq,GSM8033234 r1,GSM8033234,1,The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP485714,,,11_1.fq.gz 11_2.fq.gz,fastq fastq,5245066800.0,26225334.0,GSM8033234 r1,0:100 1:100,A:1440549629;C:1168536590;G:1175698878;T:1460281703;N:0,100,100,,,1440549629,1168536590,1175698878,1460281703,0,SRX23381946,SRS20243480,SRA1791378,"Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital","Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital",2,0.92279,0.92105,0.13454,0.13464,0.65238,0.65291,0.47828,0.48217,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Denmark,2024-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures 30209,SRR27715734,SRX23381945,SRS20243481,SRP485714,PRJNA1068542,The effects of HSP60 chaperone deficiency on zebrafish larvae,GSE254091,Transcriptome Analysis,To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.,,pubmed:39147275,,control 1,GSM8033233,,source name:embryo|tissue:embryo|cell line:5 dpf|genotype:hspd1+/+|treatment:control|geo loc name:missing|collection date:missing,control 1,Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample,embryo,,The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.,Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.,tissue:embryo|cell line:5 dpf|genotype:hspd1+/+|treatment:control,GSM8033233,GSM8033233: control 1; Danio rerio; RNA Seq,GSM8033233 r1,GSM8033233,1,The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP485714,,,10_1.fq.gz 10_2.fq.gz,fastq fastq,5460961000.0,27304805.0,GSM8033233 r1,0:100 1:100,A:1485370839;C:1228940953;G:1237868479;T:1508780729;N:0,100,100,,,1485370839,1228940953,1237868479,1508780729,0,SRX23381945,SRS20243481,SRA1791378,"Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital","Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital",2,0.92598,0.92555,0.12074,0.12035,0.65731,0.6577,0.46497,0.47306,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Denmark,2024-01-24,Larval,Larval,Embryo Imprecise,All anatomical structures 32865,SRR29488925,SRX24999628,SRS21700588,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,DKO5,GSM8343040,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO|geo loc name:missing|collection date:missing,DKO5,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO,GSM8343040,GSM8343040: DKO5; Danio rerio; RNA Seq,GSM8343040 r1,GSM8343040,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,DKO5_1.fq.gz DKO5_2.fq.gz,fastq fastq,4813408600.0,24067043.0,GSM8343040 r1,0:100 1:100,A:1302917202;C:1105312585;G:1123058369;T:1282120444;N:0,100,100,,,1302917202,1105312585,1123058369,1282120444,0,SRX24999628,SRS21700588,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32866,SRR29488926,SRX24999627,SRS21700587,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,DKO4,GSM8343039,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO|geo loc name:missing|collection date:missing,DKO4,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO,GSM8343039,GSM8343039: DKO4; Danio rerio; RNA Seq,GSM8343039 r1,GSM8343039,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,DKO4_1.fq.gz DKO4_2.fq.gz,fastq fastq,4825860200.0,24129301.0,GSM8343039 r1,0:100 1:100,A:1303584214;C:1108617528;G:1131675283;T:1281983175;N:0,100,100,,,1303584214,1108617528,1131675283,1281983175,0,SRX24999627,SRS21700587,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32867,SRR29488927,SRX24999626,SRS21700586,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,DKO3,GSM8343038,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO|geo loc name:missing|collection date:missing,DKO3,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO,GSM8343038,GSM8343038: DKO3; Danio rerio; RNA Seq,GSM8343038 r1,GSM8343038,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,DKO3_1.fq.gz DKO3_2.fq.gz,fastq fastq,4806754400.0,24033772.0,GSM8343038 r1,0:100 1:100,A:1289902978;C:1113397086;G:1131727783;T:1271726553;N:0,100,100,,,1289902978,1113397086,1131727783,1271726553,0,SRX24999626,SRS21700586,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32868,SRR29488928,SRX24999625,SRS21700585,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,DKO2,GSM8343037,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO|geo loc name:missing|collection date:missing,DKO2,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO,GSM8343037,GSM8343037: DKO2; Danio rerio; RNA Seq,GSM8343037 r1,GSM8343037,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,DKO2_1.fq.gz DKO2_2.fq.gz,fastq fastq,4805757800.0,24028789.0,GSM8343037 r1,0:100 1:100,A:1299804990;C:1103101159;G:1124220106;T:1278631545;N:0,100,100,,,1299804990,1103101159,1124220106,1278631545,0,SRX24999625,SRS21700585,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32869,SRR29488929,SRX24999624,SRS21700584,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,DKO1,GSM8343036,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO|geo loc name:missing|collection date:missing,DKO1,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO,GSM8343036,GSM8343036: DKO1; Danio rerio; RNA Seq,GSM8343036 r1,GSM8343036,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,DKO1_1.fq.gz DKO1_2.fq.gz,fastq fastq,4819172400.0,24095862.0,GSM8343036 r1,0:100 1:100,A:1296017748;C:1112321357;G:1133115185;T:1277718110;N:0,100,100,,,1296017748,1112321357,1133115185,1277718110,0,SRX24999624,SRS21700584,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32870,SRR29488930,SRX24999623,SRS21700583,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,GLO1KO5,GSM8343035,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO|geo loc name:missing|collection date:missing,GLO1KO5,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO,GSM8343035,GSM8343035: GLO1KO5; Danio rerio; RNA Seq,GSM8343035 r1,GSM8343035,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,GLO1KO5_1.fq.gz GLO1KO5_2.fq.gz,fastq fastq,4813614800.0,24068074.0,GSM8343035 r1,0:100 1:100,A:1289774342;C:1116099072;G:1136080400;T:1271660986;N:0,100,100,,,1289774342,1116099072,1136080400,1271660986,0,SRX24999623,SRS21700583,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32871,SRR29488931,SRX24999622,SRS21700582,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,GLO1KO4,GSM8343034,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO|geo loc name:missing|collection date:missing,GLO1KO4,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO,GSM8343034,GSM8343034: GLO1KO4; Danio rerio; RNA Seq,GSM8343034 r1,GSM8343034,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,GLO1KO4_1.fq.gz GLO1KO4_2.fq.gz,fastq fastq,4805954200.0,24029771.0,GSM8343034 r1,0:100 1:100,A:1288997011;C:1113616764;G:1132409574;T:1270930851;N:0,100,100,,,1288997011,1113616764,1132409574,1270930851,0,SRX24999622,SRS21700582,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32872,SRR29488932,SRX24999621,SRS21700581,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,GLO1KO3,GSM8343033,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO|geo loc name:missing|collection date:missing,GLO1KO3,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO,GSM8343033,GSM8343033: GLO1KO3; Danio rerio; RNA Seq,GSM8343033 r1,GSM8343033,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,GLO1KO3_1.fq.gz GLO1KO3_2.fq.gz,fastq fastq,4817965600.0,24089828.0,GSM8343033 r1,0:100 1:100,A:1290593290;C:1118086028;G:1134064137;T:1275222145;N:0,100,100,,,1290593290,1118086028,1134064137,1275222145,0,SRX24999621,SRS21700581,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32873,SRR29488933,SRX24999620,SRS21700580,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,GLO1KO2,GSM8343032,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO|geo loc name:missing|collection date:missing,GLO1KO2,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO,GSM8343032,GSM8343032: GLO1KO2; Danio rerio; RNA Seq,GSM8343032 r1,GSM8343032,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,GLO1KO2_1.fq.gz GLO1KO2_2.fq.gz,fastq fastq,4805999000.0,24029995.0,GSM8343032 r1,0:100 1:100,A:1293609489;C:1109265811;G:1128786421;T:1274337279;N:0,100,100,,,1293609489,1109265811,1128786421,1274337279,0,SRX24999620,SRS21700580,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32874,SRR29488934,SRX24999619,SRS21700579,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,GLO1KO1,GSM8343031,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO|geo loc name:missing|collection date:missing,GLO1KO1,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO,GSM8343031,GSM8343031: GLO1KO1; Danio rerio; RNA Seq,GSM8343031 r1,GSM8343031,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,GLO1KO1_1.fq.gz GLO1KO1_2.fq.gz,fastq fastq,4806768400.0,24033842.0,GSM8343031 r1,0:100 1:100,A:1286467027;C:1115478546;G:1135313631;T:1269509196;N:0,100,100,,,1286467027,1115478546,1135313631,1269509196,0,SRX24999619,SRS21700579,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32875,SRR29488935,SRX24999618,SRS21700578,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,ALDH3A1KO5,GSM8343030,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO|geo loc name:missing|collection date:missing,ALDH3A1KO5,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO,GSM8343030,GSM8343030: ALDH3A1KO5; Danio rerio; RNA Seq,GSM8343030 r1,GSM8343030,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,ALDH3A1KO5_1.fq.gz ALDH3A1KO5_2.fq.gz,fastq fastq,4811331000.0,24056655.0,GSM8343030 r1,0:100 1:100,A:1314568654;C:1091419677;G:1111494171;T:1293848498;N:0,100,100,,,1314568654,1091419677,1111494171,1293848498,0,SRX24999618,SRS21700578,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32876,SRR29488936,SRX24999617,SRS21700577,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,ALDH3A1KO4,GSM8343029,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO|geo loc name:missing|collection date:missing,ALDH3A1KO4,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO,GSM8343029,GSM8343029: ALDH3A1KO4; Danio rerio; RNA Seq,GSM8343029 r1,GSM8343029,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,ALDH3A1KO4_1.fq.gz ALDH3A1KO4_2.fq.gz,fastq fastq,4816993800.0,24084969.0,GSM8343029 r1,0:100 1:100,A:1320840277;C:1087361823;G:1108886472;T:1299905228;N:0,100,100,,,1320840277,1087361823,1108886472,1299905228,0,SRX24999617,SRS21700577,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32877,SRR29488937,SRX24999616,SRS21700576,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,ALDH3A1KO3,GSM8343028,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO|geo loc name:missing|collection date:missing,ALDH3A1KO3,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO,GSM8343028,GSM8343028: ALDH3A1KO3; Danio rerio; RNA Seq,GSM8343028 r1,GSM8343028,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,ALDH3A1KO3_1.fq.gz ALDH3A1KO3_2.fq.gz,fastq fastq,4828261200.0,24141306.0,GSM8343028 r1,0:100 1:100,A:1325980327;C:1088988247;G:1107987702;T:1305304924;N:0,100,100,,,1325980327,1088988247,1107987702,1305304924,0,SRX24999616,SRS21700576,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32878,SRR29488938,SRX24999615,SRS21700575,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,ALDH3A1KO2,GSM8343027,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO|geo loc name:missing|collection date:missing,ALDH3A1KO2,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO,GSM8343027,GSM8343027: ALDH3A1KO2; Danio rerio; RNA Seq,GSM8343027 r1,GSM8343027,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,ALDH3A1KO2_1.fq.gz ALDH3A1KO2_2.fq.gz,fastq fastq,4806790400.0,24033952.0,GSM8343027 r1,0:100 1:100,A:1296924744;C:1110667292;G:1117161162;T:1282037202;N:0,100,100,,,1296924744,1110667292,1117161162,1282037202,0,SRX24999615,SRS21700575,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32879,SRR29488939,SRX24999614,SRS21700574,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,ALDH3A1KO1,GSM8343026,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO|geo loc name:missing|collection date:missing,ALDH3A1KO1,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO,GSM8343026,GSM8343026: ALDH3A1KO1; Danio rerio; RNA Seq,GSM8343026 r1,GSM8343026,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,ALDH3A1KO1_1.fq.gz ALDH3A1KO1_2.fq.gz,fastq fastq,4801013600.0,24005068.0,GSM8343026 r1,0:100 1:100,A:1307355551;C:1094613295;G:1111765622;T:1287279132;N:0,100,100,,,1307355551,1094613295,1111765622,1287279132,0,SRX24999614,SRS21700574,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32880,SRR29488940,SRX24999613,SRS21700573,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,WT5,GSM8343025,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT|geo loc name:missing|collection date:missing,WT5,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT,GSM8343025,GSM8343025: WT5; Danio rerio; RNA Seq,GSM8343025 r1,GSM8343025,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,WT5_1.fq.gz WT5_2.fq.gz,fastq fastq,4820580400.0,24102902.0,GSM8343025 r1,0:100 1:100,A:1288306977;C:1120287477;G:1138943028;T:1273042918;N:0,100,100,,,1288306977,1120287477,1138943028,1273042918,0,SRX24999613,SRS21700573,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32881,SRR29488941,SRX24999612,SRS21700572,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,WT4,GSM8343024,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT|geo loc name:missing|collection date:missing,WT4,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT,GSM8343024,GSM8343024: WT4; Danio rerio; RNA Seq,GSM8343024 r1,GSM8343024,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,WT4_1.fq.gz WT4_2.fq.gz,fastq fastq,4821144600.0,24105723.0,GSM8343024 r1,0:100 1:100,A:1275218149;C:1133748961;G:1151831603;T:1260345887;N:0,100,100,,,1275218149,1133748961,1151831603,1260345887,0,SRX24999612,SRS21700572,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32882,SRR29488942,SRX24999611,SRS21700571,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,WT3,GSM8343023,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT|geo loc name:missing|collection date:missing,WT3,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT,GSM8343023,GSM8343023: WT3; Danio rerio; RNA Seq,GSM8343023 r1,GSM8343023,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,WT3_1.fq.gz WT3_2.fq.gz,fastq fastq,4826072600.0,24130363.0,GSM8343023 r1,0:100 1:100,A:1278424901;C:1132200743;G:1150406212;T:1265040744;N:0,100,100,,,1278424901,1132200743,1150406212,1265040744,0,SRX24999611,SRS21700571,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32883,SRR29488943,SRX24999610,SRS21700570,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,WT2,GSM8343022,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT|geo loc name:missing|collection date:missing,WT2,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT,GSM8343022,GSM8343022: WT2; Danio rerio; RNA Seq,GSM8343022 r1,GSM8343022,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,WT2_1.fq.gz WT2_2.fq.gz,fastq fastq,4801181000.0,24005905.0,GSM8343022 r1,0:100 1:100,A:1271169177;C:1127438892;G:1145437659;T:1257135272;N:0,100,100,,,1271169177,1127438892,1145437659,1257135272,0,SRX24999610,SRS21700570,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 32884,SRR29488944,SRX24999609,SRS21700569,SRP515253,PRJNA1126644,Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity,GSE270442,Transcriptome Analysis,Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.,,,,WT1,GSM8343021,,source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT|geo loc name:missing|collection date:missing,WT1,Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.,larvae,,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT,GSM8343021,GSM8343021: WT1; Danio rerio; RNA Seq,GSM8343021 r1,GSM8343021,1,Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP515253,,,WT1_1.fq.gz WT1_2.fq.gz,fastq fastq,4802502800.0,24012514.0,GSM8343021 r1,0:100 1:100,A:1263416018;C:1135581393;G:1152700487;T:1250804902;N:0,100,100,,,1263416018,1135581393,1152700487,1250804902,0,SRX24999609,SRS21700569,SRA1904686,ECAS,ECAS,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-06-21,Larval,Larval,Cell Line,Cell Line 33934,SRR30947094,SRX26349630,SRS22874784,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 / and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart tak1+/+ wild type replicate #3,GSM8565205,,source name:Whole heart 3 dpf|tissue:Whole heart 3 dpf|genotype:tak1+/+|geo loc name:missing|collection date:missing,whole heart tak1+/+ wild type replicate #3,post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart 3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart 3 dpf|genotype:tak1+/+,GSM8565205,GSM8565205: whole heart tak1+/+ wild type replicate #3; Danio rerio; RNA Seq,GSM8565205 r1,GSM8565205,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,WT_3_1.fq.gz WT_3_2.fq.gz,fastq fastq,4449566200.0,22247831.0,GSM8565205 r1,0:100 1:100,A:1179341017;C:1046638560;G:1046356098;T:1177230525;N:0,100,100,,,1179341017,1046638560,1046356098,1177230525,0,SRX26349630,SRS22874784,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System 33935,SRR30947095,SRX26349629,SRS22874783,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 / and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart tak1+/+ wild type replicate #2,GSM8565204,,source name:Whole heart 3 dpf|tissue:Whole heart 3 dpf|genotype:tak1+/+|geo loc name:missing|collection date:missing,whole heart tak1+/+ wild type replicate #2,post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart 3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart 3 dpf|genotype:tak1+/+,GSM8565204,GSM8565204: whole heart tak1+/+ wild type replicate #2; Danio rerio; RNA Seq,GSM8565204 r1,GSM8565204,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,WT_2_1.fq.gz WT_2_2.fq.gz,fastq fastq,4519627600.0,22598138.0,GSM8565204 r1,0:100 1:100,A:1207344552;C:1055139553;G:1056806709;T:1200336786;N:0,100,100,,,1207344552,1055139553,1056806709,1200336786,0,SRX26349629,SRS22874783,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System 33936,SRR30947096,SRX26349628,SRS22874781,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 / and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart tak1+/+ wild type replicate #1,GSM8565203,,source name:Whole heart 3 dpf|tissue:Whole heart 3 dpf|genotype:tak1+/+|geo loc name:missing|collection date:missing,whole heart tak1+/+ wild type replicate #1,post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart 3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart 3 dpf|genotype:tak1+/+,GSM8565203,GSM8565203: whole heart tak1+/+ wild type replicate #1; Danio rerio; RNA Seq,GSM8565203 r1,GSM8565203,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,WT_1_1.fq.gz WT_1_2.fq.gz,fastq fastq,4496601200.0,22483006.0,GSM8565203 r1,0:100 1:100,A:1201390946;C:1050348674;G:1051355386;T:1193506194;N:0,100,100,,,1201390946,1050348674,1051355386,1193506194,0,SRX26349628,SRS22874781,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System 33937,SRR30947097,SRX26349627,SRS22874780,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 / and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart tak1 / mutant replicate #3,GSM8565202,,source name:Whole heart 3 dpf|tissue:Whole heart 3 dpf|genotype:tak1 / |geo loc name:missing|collection date:missing,whole heart tak1 / mutant replicate #3,post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart 3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart 3 dpf|genotype:tak1 / ,GSM8565202,GSM8565202: whole heart tak1 / mutant replicate #3; Danio rerio; RNA Seq,GSM8565202 r1,GSM8565202,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,mut_3_1.fq.gz mut_3_2.fq.gz,fastq fastq,4451759600.0,22258798.0,GSM8565202 r1,0:100 1:100,A:1167798041;C:1064608876;G:1066460994;T:1152891689;N:0,100,100,,,1167798041,1064608876,1066460994,1152891689,0,SRX26349627,SRS22874780,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System 33938,SRR30947098,SRX26349626,SRS22874782,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 / and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart tak1 / mutant replicate #2,GSM8565201,,source name:Whole heart 3 dpf|tissue:Whole heart 3 dpf|genotype:tak1 / |geo loc name:missing|collection date:missing,whole heart tak1 / mutant replicate #2,post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart 3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart 3 dpf|genotype:tak1 / ,GSM8565201,GSM8565201: whole heart tak1 / mutant replicate #2; Danio rerio; RNA Seq,GSM8565201 r1,GSM8565201,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,mut_2_1.fq.gz mut_2_2.fq.gz,fastq fastq,4534495200.0,22672476.0,GSM8565201 r1,,,,,,,,,,,,SRX26349626,SRS22874782,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System 33939,SRR30947099,SRX26349625,SRS22874779,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 / and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart tak1 / mutant replicate #1,GSM8565200,,source name:Whole heart 3 dpf|tissue:Whole heart 3 dpf|genotype:tak1 / |geo loc name:missing|collection date:missing,whole heart tak1 / mutant replicate #1,post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart 3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart 3 dpf|genotype:tak1 / ,GSM8565200,GSM8565200: whole heart tak1 / mutant replicate #1; Danio rerio; RNA Seq,GSM8565200 r1,GSM8565200,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,mut_1_1.fq.gz mut_1_2.fq.gz,fastq fastq,4425052600.0,22125263.0,GSM8565200 r1,0:100 1:100,A:1161989932;C:1055452567;G:1055912540;T:1151697561;N:0,100,100,,,1161989932,1055452567,1055912540,1151697561,0,SRX26349625,SRS22874779,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System 35452,SRR32815440,SRX28098911,SRS24455832,SRP572346,PRJNA1240620,The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes,PRJNA1240620,Other,,,,,,T4Danio rerio,,strain:T4|age:96hpf|collection date:2023 12 20|geo loc name:China: Xiangyang|sex:missing|tissue:Tissue of juvenile fish|replicate:T4|BioSampleModel:Model organism or animal,,,,,,,,,T4,T4,T4,T4,,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP572346,,,T4_1.fq.gz T4_2.fq.gz,fastq fastq,6608651700.0,22028839.0,T4 1.fq.gz,0:150 1:150,A:1815401801;C:1489859310;G:1499379699;T:1804010890;N:0,150,150,,,1815401801,1489859310,1499379699,1804010890,0,SRX28098911,SRS24455832,SRA2098321,Wuhan University of Science and Technology|School of Medicine,Wuhan University of Science and Technology,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-03-22,Larval,Larval,Undetermined,Undetermined 35453,SRR32815441,SRX28098910,SRS24455831,SRP572346,PRJNA1240620,The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes,PRJNA1240620,Other,,,,,,T3Danio rerio,,strain:T3|age:96hpf|collection date:2023 12 20|geo loc name:China: Xiangyang|sex:missing|tissue:Tissue of juvenile fish|replicate:T3|BioSampleModel:Model organism or animal,,,,,,,,,T3,T3,T3,T3,,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP572346,,,T3_1.fq.gz T3_2.fq.gz,fastq fastq,6656167200.0,22187224.0,T3 1.fq.gz,0:150 1:150,A:1840552276;C:1489247530;G:1499297584;T:1827069810;N:0,150,150,,,1840552276,1489247530,1499297584,1827069810,0,SRX28098910,SRS24455831,SRA2098321,Wuhan University of Science and Technology|School of Medicine,Wuhan University of Science and Technology,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-03-22,Larval,Larval,Undetermined,Undetermined 35454,SRR32815442,SRX28098909,SRS24455830,SRP572346,PRJNA1240620,The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes,PRJNA1240620,Other,,,,,,T2Danio rerio,,strain:T2|age:96hpf|collection date:2023 12 20|geo loc name:China: Xiangyang|sex:missing|tissue:Tissue of juvenile fish|replicate:T2|BioSampleModel:Model organism or animal,,,,,,,,,T2,T2,T2,T2,,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP572346,,,T2_1.fq.gz T2_2.fq.gz,fastq fastq,6622204800.0,22074016.0,T2 1.fq.gz,0:150 1:150,A:1834396150;C:1480094606;G:1490046882;T:1817667162;N:0,150,150,,,1834396150,1480094606,1490046882,1817667162,0,SRX28098909,SRS24455830,SRA2098321,Wuhan University of Science and Technology|School of Medicine,Wuhan University of Science and Technology,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-03-22,Larval,Larval,Undetermined,Undetermined 35455,SRR32815443,SRX28098908,SRS24455829,SRP572346,PRJNA1240620,The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes,PRJNA1240620,Other,,,,,,T1Danio rerio,,strain:T1|age:96hpf|collection date:2023 12 20|geo loc name:China: Xiangyang|sex:missing|tissue:Tissue of juvenile fish|replicate:T1|BioSampleModel:Model organism or animal,,,,,,,,,T1,T1,T1,T1,,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP572346,,,T1_1.fq.gz T1_2.fq.gz,fastq fastq,6626122500.0,22087075.0,T1 1.fq.gz,0:150 1:150,A:1833541012;C:1481665295;G:1491851279;T:1819064914;N:0,150,150,,,1833541012,1481665295,1491851279,1819064914,0,SRX28098908,SRS24455829,SRA2098321,Wuhan University of Science and Technology|School of Medicine,Wuhan University of Science and Technology,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-03-22,Larval,Larval,Undetermined,Undetermined 35456,SRR32815444,SRX28098907,SRS24455828,SRP572346,PRJNA1240620,The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes,PRJNA1240620,Other,,,,,,Q4Danio rerio,,strain:Q4|age:96hpf|collection date:2023 12 20|geo loc name:China: Xiangyang|sex:missing|tissue:Tissue of juvenile fish|replicate:Q4|BioSampleModel:Model organism or animal,,,,,,,,,Q4,Q4,Q4,Q4,,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP572346,,,Q4_1.fq.gz Q4_2.fq.gz,fastq fastq,6646083600.0,22153612.0,Q4 1.fq.gz,0:150 1:150,A:1823086981;C:1499930776;G:1510718905;T:1812346938;N:0,150,150,,,1823086981,1499930776,1510718905,1812346938,0,SRX28098907,SRS24455828,SRA2098321,Wuhan University of Science and Technology|School of Medicine,Wuhan University of Science and Technology,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-03-22,Larval,Larval,Undetermined,Undetermined 35457,SRR32815445,SRX28098906,SRS24455827,SRP572346,PRJNA1240620,The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes,PRJNA1240620,Other,,,,,,Q3Danio rerio,,strain:Q3|age:96hpf|collection date:2023 12 20|geo loc name:China: Xiangyang|sex:missing|tissue:Tissue of juvenile fish|replicate:Q3|BioSampleModel:Model organism or animal,,,,,,,,,Q3,Q3,Q3,Q3,,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP572346,,,Q3_1.fq.gz Q3_2.fq.gz,fastq fastq,6683275200.0,22277584.0,Q3 1.fq.gz,0:150 1:150,A:1838068171;C:1503920885;G:1514577234;T:1826708910;N:0,150,150,,,1838068171,1503920885,1514577234,1826708910,0,SRX28098906,SRS24455827,SRA2098321,Wuhan University of Science and Technology|School of Medicine,Wuhan University of Science and Technology,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-03-22,Larval,Larval,Undetermined,Undetermined 35458,SRR32815446,SRX28098905,SRS24455826,SRP572346,PRJNA1240620,The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes,PRJNA1240620,Other,,,,,,Q2Danio rerio,,strain:Q2|age:96hpf|collection date:2023 12 20|geo loc name:China: Xiangyang|sex:missing|tissue:Tissue of juvenile fish|replicate:Q2|BioSampleModel:Model organism or animal,,,,,,,,,Q2,Q2,Q2,Q2,,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP572346,,,Q2_1.fq.gz Q2_2.fq.gz,fastq fastq,6612253800.0,22040846.0,Q2 1.fq.gz,0:150 1:150,A:1821750297;C:1484945478;G:1495582042;T:1809975983;N:0,150,150,,,1821750297,1484945478,1495582042,1809975983,0,SRX28098905,SRS24455826,SRA2098321,Wuhan University of Science and Technology|School of Medicine,Wuhan University of Science and Technology,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-03-22,Larval,Larval,Undetermined,Undetermined 35459,SRR32815447,SRX28098904,SRS24455825,SRP572346,PRJNA1240620,The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes,PRJNA1240620,Other,,,,,,Q1Danio rerio,,strain:Q1|age:96hpf|collection date:2023 12 20|geo loc name:China: Xiangyang|sex:missing|tissue:Tissue of juvenile fish|replicate:Q1|BioSampleModel:Model organism or animal,,,,,,,,,Q1,Q1,Q1,Q1,,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP572346,,,Q1_1.fq.gz Q1_2.fq.gz,fastq fastq,6725919900.0,22419733.0,Q1 1.fq.gz,0:150 1:150,A:1845653740;C:1518697545;G:1530630124;T:1830938491;N:0,150,150,,,1845653740,1518697545,1530630124,1830938491,0,SRX28098904,SRS24455825,SRA2098321,Wuhan University of Science and Technology|School of Medicine,Wuhan University of Science and Technology,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-03-22,Larval,Larval,Undetermined,Undetermined 36214,SRR33581822,SRX28811683,SRS25048556,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,Rg1 L3,,strain:Not collected|isolate:Rg1 L3|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:9|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Treatment,Rg1 L3,Rg1 L3,Treatment,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,D4_1.fq.gz D4_2.fq.gz,fastq fastq,6696495000.0,22321650.0,D4 1.fq.gz,0:150 1:150,A:1846856660;C:1513002602;G:1504866522;T:1831769216;N:0,150,150,,,1846856660,1513002602,1504866522,1831769216,0,SRX28811683,SRS25048556,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined 36215,SRR33581823,SRX28811682,SRS25048555,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,Rg1 L7,,strain:Not collected|isolate:Rg1 L7|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:8|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Treatment,Rg1 L7,Rg1 L7,Treatment,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,D2_1.fq.gz D2_2.fq.gz,fastq fastq,6666041700.0,22220139.0,D2 1.fq.gz,0:150 1:150,A:1845276816;C:1500512488;G:1492917547;T:1827334849;N:0,150,150,,,1845276816,1500512488,1492917547,1827334849,0,SRX28811682,SRS25048555,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined 36216,SRR33581824,SRX28811681,SRS25048554,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,Rg1 L5,,strain:Not collected|isolate:Rg1 L5|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:7|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Treatment,Rg1 L5,Rg1 L5,Treatment,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,D1_1.fq.gz D1_2.fq.gz,fastq fastq,6698296200.0,22327654.0,D1 1.fq.gz,0:150 1:150,A:1843962508;C:1518208646;G:1509450148;T:1826674898;N:0,150,150,,,1843962508,1518208646,1509450148,1826674898,0,SRX28811681,SRS25048554,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined 36217,SRR33581825,SRX28811680,SRS25048553,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,PN L7,,strain:Not collected|isolate:PN L7|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:6|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Model,PN L7,PN L7,Model,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,B3_1.fq.gz B3_2.fq.gz,fastq fastq,6611023200.0,22036744.0,B3 1.fq.gz,0:150 1:150,A:1823488173;C:1492231000;G:1485521400;T:1809782627;N:0,150,150,,,1823488173,1492231000,1485521400,1809782627,0,SRX28811680,SRS25048553,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined 36218,SRR33581826,SRX28811679,SRS25048552,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,PN L2,,strain:Not collected|isolate:PN L2|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:5|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Model,PN L2,PN L2,Model,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,B2_1.fq.gz B2_2.fq.gz,fastq fastq,6673419600.0,22244732.0,B2 1.fq.gz,0:150 1:150,A:1853555661;C:1496204062;G:1487686506;T:1835973371;N:0,150,150,,,1853555661,1496204062,1487686506,1835973371,0,SRX28811679,SRS25048552,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined 36219,SRR33581827,SRX28811678,SRS25048551,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,PN L4,,strain:Not collected|isolate:PN L4|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:4|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Model,PN L4,PN L4,Model,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,B1_1.fq.gz B1_2.fq.gz,fastq fastq,6654915300.0,22183051.0,B1 1.fq.gz,0:150 1:150,A:1864666474;C:1477163584;G:1469026869;T:1844058373;N:0,150,150,,,1864666474,1477163584,1469026869,1844058373,0,SRX28811678,SRS25048551,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined 36220,SRR33581828,SRX28811677,SRS25048550,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,Con L1,,strain:Not collected|isolate:Con L1|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Control,Con L1,Con L1,Control,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,A3_1.fq.gz A3_2.fq.gz,fastq fastq,6805948200.0,22686494.0,A3 1.fq.gz,0:150 1:150,A:1865806598;C:1548653255;G:1540767459;T:1850720888;N:0,150,150,,,1865806598,1548653255,1540767459,1850720888,0,SRX28811677,SRS25048550,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined 36221,SRR33581829,SRX28811676,SRS25048549,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,Con Lb,,strain:Not collected|isolate:Con Lb|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Control,Con Lb,Con Lb,Control,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,A2_1.fq.gz A2_2.fq.gz,fastq fastq,6807123600.0,22690412.0,A2 1.fq.gz,0:150 1:150,A:1868554012;C:1546467202;G:1539322143;T:1852780243;N:0,150,150,,,1868554012,1546467202,1539322143,1852780243,0,SRX28811676,SRS25048549,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined 36222,SRR33581830,SRX28811675,SRS25048548,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,Con La,,strain:Not collected|isolate:Con La|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Control,Con La,Con La,,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,A1_1.fq.gz A1_2.fq.gz,fastq fastq,6782914200.0,22609714.0,A1 1.fq.gz,0:150 1:150,A:1857557307;C:1544915899;G:1537431564;T:1843009430;N:0,150,150,,,1857557307,1544915899,1537431564,1843009430,0,SRX28811675,SRS25048548,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined 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 64515,SRR17137061,SRX13321491,SRS11229252,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 COL103,GSM5718327,,source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 72hpf COL103,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,GSM5718327,GSM5718327: Microwell seq datasets of Zebrafish 72hpf COL103; Danio rerio; RNA Seq,GSM5718327,,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_COL103.bam,bam,97437769842.0,559987183.0,GSM5718327 r1,0:24 1:150,A:28425257606;C:21026057575;G:22210354179;T:25724166722;N:51933760,24,150,,,28425257606,21026057575,22210354179,25724166722,51933760,SRX13321491,SRS11229252,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00232,0.76296,0.00214,0.09247,0.99975,0.7963,0.58333,0.50975,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-05,Larval,Larval,Whole Organism,All anatomical structures 64516,SRR17137060,SRX13321490,SRS11229251,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 COL102,GSM5718326,,source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 72hpf COL102,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,GSM5718326,GSM5718326: Microwell seq datasets of Zebrafish 72hpf COL102; Danio rerio; RNA Seq,GSM5718326,,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_COL102.bam,bam,99647119878.0,572684597.0,GSM5718326 r1,0:24 1:150,A:29163675513;C:21410312143;G:22841561495;T:26179135838;N:52434889,24,150,,,29163675513,21410312143,22841561495,26179135838,52434889,SRX13321490,SRS11229251,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00211,0.75462,0.00197,0.08783,0.99979,0.79614,0.6,0.48777,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-05,Larval,Larval,Whole Organism,All anatomical structures 64517,SRR17137059,SRX13321489,SRS11229250,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 COL101,GSM5718325,,source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 72hpf COL101,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,GSM5718325,GSM5718325: Microwell seq datasets of Zebrafish 72hpf COL101; Danio rerio; RNA Seq,GSM5718325,,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_COL101.bam,bam,103850532360.0,596842140.0,GSM5718325 r1,0:24 1:150,A:30253504994;C:22208170461;G:23486370057;T:27846281411;N:56205437,24,150,,,30253504994,22208170461,23486370057,27846281411,56205437,SRX13321489,SRS11229250,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00248,0.76955,0.00238,0.09242,0.99985,0.78549,0.0,0.48332,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-05,Larval,Larval,Whole Organism,All anatomical structures 64518,SRR17137058,SRX13321488,SRS11229249,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 COL100,GSM5718324,,source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 72hpf COL100,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,GSM5718324,GSM5718324: Microwell seq datasets of Zebrafish 72hpf COL100; Danio rerio; RNA Seq,GSM5718324,,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_COL100.bam,bam,79732033224.0,458230076.0,GSM5718324 r1,0:24 1:150,A:23142121477;C:17273443279;G:18152994838;T:21124595570;N:38878060,24,150,,,23142121477,17273443279,18152994838,21124595570,38878060,SRX13321488,SRS11229249,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.0019,0.78954,0.00176,0.1,0.99977,0.79302,0.45454,0.53183,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-05,Larval,Larval,Whole Organism,All anatomical structures 64519,SRR17137057,SRX13321487,SRS11229248,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 COL99,GSM5718323,,source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 72hpf COL99,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,GSM5718323,GSM5718323: Microwell seq datasets of Zebrafish 72hpf COL99; Danio rerio; RNA Seq,GSM5718323,,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_COL99.bam,bam,57905355774.0,332789401.0,GSM5718323 r1,0:24 1:150,A:16732054497;C:12484254815;G:13099812159;T:15561038953;N:28195350,24,150,,,16732054497,12484254815,13099812159,15561038953,28195350,SRX13321487,SRS11229248,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.0023,0.79516,0.00213,0.10777,0.99977,0.79413,0.5,0.52425,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-05,Larval,Larval,Whole Organism,All anatomical structures 64520,SRR17137056,SRX13321486,SRS11229247,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 COL98,GSM5718322,,source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 72hpf COL98,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,GSM5718322,GSM5718322: Microwell seq datasets of Zebrafish 72hpf COL98; Danio rerio; RNA Seq,GSM5718322,,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_COL98.bam,bam,133922399388.0,769668962.0,GSM5718322 r1,0:24 1:150,A:39157671234;C:28685783001;G:30222645162;T:35787052837;N:69247154,24,150,,,39157671234,28685783001,30222645162,35787052837,69247154,SRX13321486,SRS11229247,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00205,0.77779,0.00189,0.10045,0.99977,0.7903,0.36363,0.52076,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-05,Larval,Larval,Whole Organism,All anatomical structures 64521,SRR17137055,SRX13321485,SRS11229246,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 COL97,GSM5718321,,source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 72hpf COL97,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,GSM5718321,GSM5718321: Microwell seq datasets of Zebrafish 72hpf COL97; Danio rerio; RNA Seq,GSM5718321,,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_COL97.bam,bam,102882979782.0,591281493.0,GSM5718321 r1,0:24 1:150,A:30066107926;C:21991309044;G:23041144876;T:27728508333;N:55909603,24,150,,,30066107926,21991309044,23041144876,27728508333,55909603,SRX13321485,SRS11229246,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00231,0.78387,0.00216,0.09479,0.99977,0.78638,0.63636,0.48401,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-12-05,Larval,Larval,Whole Organism,All anatomical structures 64522,SRR17075126,SRX13263481,SRS11185248,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,,Micorwell seq datasets of Zebrafish 72hpf COL92,GSM5709061,,source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL92,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 sample2,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5709061,GSM5709061: Micorwell seq datasets of Zebrafish 72hpf COL92; Danio rerio; RNA Seq,GSM5709061,,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_COL92.bam,bam,93305697882.0,536239643.0,GSM5709061 r1,0:24 1:150,A:27107741517;C:19830183542;G:20994123402;T:25327971257;N:45678164,24,150,,,27107741517,19830183542,20994123402,25327971257,45678164,SRX13263481,SRS11185248,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00194,0.78236,0.00179,0.10164,0.99975,0.78618,0.75,0.48898,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-30,Larval,Larval,Whole Organism,All anatomical structures 64523,SRR17075125,SRX13263480,SRS11185247,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,,Micorwell seq datasets of Zebrafish 72hpf COL91,GSM5709060,,source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL91,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 sample2,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5709060,GSM5709060: Micorwell seq datasets of Zebrafish 72hpf COL91; Danio rerio; RNA Seq,GSM5709060,,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_COL91.bam,bam,96227810904.0,553033396.0,GSM5709060 r1,0:24 1:150,A:27923073482;C:20564137902;G:21719882675;T:25970776374;N:49940471,24,150,,,27923073482,20564137902,21719882675,25970776374,49940471,SRX13263480,SRS11185247,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.0019,0.78115,0.00184,0.10758,0.99989,0.78725,0.4,0.49305,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-30,Larval,Larval,Whole Organism,All anatomical structures 64524,SRR17075124,SRX13263479,SRS11185246,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,,Micorwell seq datasets of Zebrafish 72hpf COL90,GSM5709059,,source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL90,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 sample2,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5709059,GSM5709059: Micorwell seq datasets of Zebrafish 72hpf COL90; Danio rerio; RNA Seq,GSM5709059,,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_COL90.bam,bam,101004540858.0,580485867.0,GSM5709059 r1,0:24 1:150,A:29424345909;C:21610893920;G:22734702528;T:27180463498;N:54135003,24,150,,,29424345909,21610893920,22734702528,27180463498,54135003,SRX13263479,SRS11185246,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00188,0.78353,0.00176,0.10575,0.99981,0.78699,0.55555,0.50829,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-30,Larval,Larval,Whole Organism,All anatomical structures 64525,SRR17075123,SRX13263478,SRS11185245,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,,Micorwell seq datasets of Zebrafish 72hpf COL89,GSM5709058,,source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL89,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 sample2,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5709058,GSM5709058: Micorwell seq datasets of Zebrafish 72hpf COL89; Danio rerio; RNA Seq,GSM5709058,,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_COL89.bam,bam,103228879080.0,593269420.0,GSM5709058 r1,0:24 1:150,A:30122538038;C:21933106979;G:23172314020;T:27949125385;N:51794658,24,150,,,30122538038,21933106979,23172314020,27949125385,51794658,SRX13263478,SRS11185245,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00229,0.78058,0.00208,0.11813,0.99967,0.78642,0.4375,0.51666,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-30,Larval,Larval,Whole Organism,All anatomical structures 64526,SRR17075130,SRX13263477,SRS11185244,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,,Micorwell seq datasets of Zebrafish 72hpf COL96,GSM5709065,,source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL96,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 sample2,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5709065,GSM5709065: Micorwell seq datasets of Zebrafish 72hpf COL96; Danio rerio; RNA Seq,GSM5709065,,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_COL96.bam,bam,72161390838.0,414720637.0,GSM5709065 r1,0:24 1:150,A:20858972054;C:15631755598;G:16378791674;T:19256108785;N:35762727,24,150,,,20858972054,15631755598,16378791674,19256108785,35762727,SRX13263477,SRS11185244,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.0024,0.78585,0.00221,0.10389,0.99971,0.79099,0.64285,0.51929,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-30,Larval,Larval,Whole Organism,All anatomical structures 64527,SRR17075129,SRX13263476,SRS11185243,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,,Micorwell seq datasets of Zebrafish 72hpf COL95,GSM5709064,,source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL95,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 sample2,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5709064,GSM5709064: Micorwell seq datasets of Zebrafish 72hpf COL95; Danio rerio; RNA Seq,GSM5709064,,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_COL95.bam,bam,116725350900.0,670835350.0,GSM5709064 r1,0:24 1:150,A:33766055210;C:25258192198;G:26422558801;T:31219012086;N:59532605,24,150,,,33766055210,25258192198,26422558801,31219012086,59532605,SRX13263476,SRS11185243,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00223,0.78242,0.00205,0.10222,0.99973,0.7948,0.76923,0.51107,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-30,Larval,Larval,Whole Organism,All anatomical structures 64528,SRR17075128,SRX13263475,SRS11185241,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,,Micorwell seq datasets of Zebrafish 72hpf COL94,GSM5709063,,source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL94,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 sample2,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5709063,GSM5709063: Micorwell seq datasets of Zebrafish 72hpf COL94; Danio rerio; RNA Seq,GSM5709063,,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_COL94.bam,bam,115204393758.0,662094217.0,GSM5709063 r1,0:24 1:150,A:33385976074;C:24728619684;G:25999313932;T:31027995525;N:62488543,24,150,,,33385976074,24728619684,25999313932,31027995525,62488543,SRX13263475,SRS11185241,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00227,0.78471,0.00206,0.10458,0.99967,0.78591,0.4375,0.50275,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-30,Larval,Larval,Whole Organism,All anatomical structures 64529,SRR17075127,SRX13263474,SRS11185242,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,,Micorwell seq datasets of Zebrafish 72hpf COL93,GSM5709062,,source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL93,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 sample2,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5709062,GSM5709062: Micorwell seq datasets of Zebrafish 72hpf COL93; Danio rerio; RNA Seq,GSM5709062,,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_COL93.bam,bam,109890007632.0,631551768.0,GSM5709062 r1,0:24 1:150,A:31784495967;C:23590735781;G:24835459995;T:29625393694;N:53922195,24,150,,,31784495967,23590735781,24835459995,29625393694,53922195,SRX13263474,SRS11185242,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00221,0.77545,0.002,0.11238,0.99969,0.78879,0.4375,0.50979,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-30,Larval,Larval,Whole Organism,All anatomical structures 64530,SRR17010806,SRX13200959,SRS11127611,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,,Micorwell seq datasets of Zebrafish 72hpf COL88,GSM5699934,,source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL88,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 sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5699934,GSM5699934: Micorwell seq datasets of Zebrafish 72hpf COL88; Danio rerio; RNA Seq,GSM5699934,,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:Danio rerio reference genome GRCz11|intentional duplicate,Zebrafish_72hpf_COL88.bam,bam,105325546890.0,605319235.0,GSM5699934 r1,0:24 1:150,A:30618141170;C:22639431941;G:23832910711;T:28175599693;N:59463375,24,150,,,30618141170,22639431941,23832910711,28175599693,59463375,SRX13200959,SRS11127611,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00204,0.77653,0.00184,0.1038,0.99969,0.78896,0.4,0.49664,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-22,Larval,Larval,Whole Organism,All anatomical structures 64531,SRR17010805,SRX13200958,SRS11127610,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,,Micorwell seq datasets of Zebrafish 72hpf COL87,GSM5699933,,source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL87,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 sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5699933,GSM5699933: Micorwell seq datasets of Zebrafish 72hpf COL87; Danio rerio; RNA Seq,GSM5699933,,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:Danio rerio reference genome GRCz11|intentional duplicate,Zebrafish_72hpf_COL87.bam,bam,104410657848.0,600061252.0,GSM5699933 r1,0:24 1:150,A:30448105235;C:22372529466;G:23651054417;T:27884763811;N:54204919,24,150,,,30448105235,22372529466,23651054417,27884763811,54204919,SRX13200958,SRS11127610,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00239,0.76912,0.00221,0.11084,0.99971,0.78847,0.5,0.51741,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-22,Larval,Larval,Whole Organism,All anatomical structures 64532,SRR17010804,SRX13200957,SRS11127609,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,,Micorwell seq datasets of Zebrafish 72hpf COL86,GSM5699932,,source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL86,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 sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5699932,GSM5699932: Micorwell seq datasets of Zebrafish 72hpf COL86; Danio rerio; RNA Seq,GSM5699932,,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:Danio rerio reference genome GRCz11|intentional duplicate,Zebrafish_72hpf_COL86.bam,bam,85539017526.0,491603549.0,GSM5699932 r1,0:24 1:150,A:24891444353;C:18382714837;G:19465935988;T:22755762595;N:43159753,24,150,,,24891444353,18382714837,19465935988,22755762595,43159753,SRX13200957,SRS11127609,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00186,0.7737,0.00168,0.10503,0.99973,0.78553,0.35714,0.52806,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-22,Larval,Larval,Whole Organism,All anatomical structures 64533,SRR17010803,SRX13200956,SRS11127608,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,,Micorwell seq datasets of Zebrafish 72hpf COL85,GSM5699931,,source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL85,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 sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5699931,GSM5699931: Micorwell seq datasets of Zebrafish 72hpf COL85; Danio rerio; RNA Seq,GSM5699931,,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:Danio rerio reference genome GRCz11|intentional duplicate,Zebrafish_72hpf_COL85.bam,bam,96579499182.0,555054593.0,GSM5699931 r1,0:24 1:150,A:28258999810;C:20566647022;G:21776511096;T:25928948228;N:48393026,24,150,,,28258999810,20566647022,21776511096,25928948228,48393026,SRX13200956,SRS11127608,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00215,0.77075,0.00203,0.09684,0.99981,0.78348,0.44444,0.50291,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-22,Larval,Larval,Whole Organism,All anatomical structures 64534,SRR17010802,SRX13200955,SRS11127607,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,,Micorwell seq datasets of Zebrafish 72hpf COL84,GSM5699930,,source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL84,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 sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5699930,GSM5699930: Micorwell seq datasets of Zebrafish 72hpf COL84; Danio rerio; RNA Seq,GSM5699930,,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:Danio rerio reference genome GRCz11|intentional duplicate,Zebrafish_72hpf_COL84.bam,bam,95402087292.0,548287858.0,GSM5699930 r1,0:24 1:150,A:27920812951;C:20371734068;G:21595614980;T:25463535654;N:50389639,24,150,,,27920812951,20371734068,21595614980,25463535654,50389639,SRX13200955,SRS11127607,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00199,0.76291,0.00186,0.09597,0.99981,0.79001,0.3,0.50069,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-22,Larval,Larval,Whole Organism,All anatomical structures 64535,SRR17010801,SRX13200954,SRS11127606,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,,Micorwell seq datasets of Zebrafish 72hpf COL83,GSM5699929,,source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL83,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 sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5699929,GSM5699929: Micorwell seq datasets of Zebrafish 72hpf COL83; Danio rerio; RNA Seq,GSM5699929,,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:Danio rerio reference genome GRCz11|intentional duplicate,Zebrafish_72hpf_COL83.bam,bam,94589605254.0,543618421.0,GSM5699929 r1,0:24 1:150,A:27596905697;C:20243328527;G:21378738112;T:25321573995;N:49058923,24,150,,,27596905697,20243328527,21378738112,25321573995,49058923,SRX13200954,SRS11127606,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00216,0.77625,0.00202,0.09982,0.99979,0.78831,0.36363,0.51012,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-22,Larval,Larval,Whole Organism,All anatomical structures 64536,SRR17010800,SRX13200953,SRS11127605,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,,Micorwell seq datasets of Zebrafish 72hpf COL82,GSM5699928,,source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL82,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 sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5699928,GSM5699928: Micorwell seq datasets of Zebrafish 72hpf COL82; Danio rerio; RNA Seq,GSM5699928,,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:Danio rerio reference genome GRCz11|intentional duplicate,Zebrafish_72hpf_COL82.bam,bam,89062661598.0,511854377.0,GSM5699928 r1,0:24 1:150,A:26102790989;C:19094974289;G:20282271482;T:23541508213;N:41116625,24,150,,,26102790989,19094974289,20282271482,23541508213,41116625,SRX13200953,SRS11127605,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00227,0.76728,0.00206,0.10248,0.99969,0.79196,0.29411,0.53203,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-22,Larval,Larval,Whole Organism,All anatomical structures 64537,SRR17010799,SRX13200952,SRS11127604,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,,Micorwell seq datasets of Zebrafish 72hpf COL81,GSM5699927,,source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism,Micorwell seq datasets of Zebrafish 72hpf COL81,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 sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5699927,GSM5699927: Micorwell seq datasets of Zebrafish 72hpf COL81; Danio rerio; RNA Seq,GSM5699927,,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:Danio rerio reference genome GRCz11|intentional duplicate,Zebrafish_72hpf_COL81.bam,bam,97306386444.0,559232106.0,GSM5699927 r1,0:24 1:150,A:28504741466;C:20782464199;G:21987624297;T:25985173510;N:46382972,24,150,,,28504741466,20782464199,21987624297,25985173510,46382972,SRX13200952,SRS11127604,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00232,0.76473,0.00224,0.09727,0.99987,0.79153,0.66666,0.51198,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2021-11-22,Larval,Larval,Whole Organism,All anatomical structures 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