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
25297,SRR25764099,SRX21486772,SRS18719072,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,Adult itgb4+ basal cells,GSM7734879,,tissue:epidermal cells|cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing,Adult itgb4+ basal cells,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry,GSM7734879,GSM7734879: Adult itgb4+ basal cells; Danio rerio; RNA Seq,GSM7734879 r1,GSM7734879,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,Adult_itgb4mcherry_S230_R1_001.fastq.gz Adult_itgb4mcherry_S230_R2_001.fastq.gz,fastq fastq,5035430000.0,12588575.0,GSM7734879 r1,0:200 1:200,A:1339392170;C:1117195164;G:1254708952;T:1323174485;N:959229,200,200,,,1339392170,1117195164,1254708952,1323174485,959229,SRX21486772,SRS18719072,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01543,0.02468,0.00098,0.00102,0.99318,0.99387,0.47878,0.31718,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Adult,Adult,Skin,Surface Structure
25298,SRR25764100,SRX21486771,SRS18719071,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf itgb4+ embryonic basal precursors rep2,GSM7734878,,tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing,1 dpf itgb4+ embryonic basal precursors rep2,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry,GSM7734878,GSM7734878: 1 dpf itgb4+ embryonic basal precursors rep2; Danio rerio; RNA Seq,GSM7734878 r1,GSM7734878,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,itgb4mcherry_2_S229_R1_001.fastq.gz itgb4mcherry_2_S229_R2_001.fastq.gz,fastq fastq,6040245600.0,15100614.0,GSM7734878 r1,0:200 1:200,A:1588346322;C:1356558310;G:1524614760;T:1569583583;N:1142625,200,200,,,1588346322,1356558310,1524614760,1569583583,1142625,SRX21486771,SRS18719071,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.0156,0.0191,0.00074,0.00093,0.99024,0.99088,0.47058,0.47838,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
25299,SRR25764101,SRX21486770,SRS18719070,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf itgb4+ embryonic basal precursors rep1,GSM7734877,,tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing,1 dpf itgb4+ embryonic basal precursors rep1,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry,GSM7734877,GSM7734877: 1 dpf itgb4+ embryonic basal precursors rep1; Danio rerio; RNA Seq,GSM7734877 r1,GSM7734877,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,itgb4mcherry_1_S20_R1_001.fastq.gz itgb4mcherry_1_S20_R2_001.fastq.gz,fastq fastq,7055215600.0,17638039.0,GSM7734877 r1,0:200 1:200,A:1894635584;C:1556854856;G:1769420212;T:1825520802;N:8784146,200,200,,,1894635584,1556854856,1769420212,1825520802,8784146,SRX21486770,SRS18719070,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01135,0.01881,0.00043,0.00016,0.9932,0.99543,0.46234,0.43106,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
25300,SRR25764102,SRX21486769,SRS18719069,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf krt4+ embryonic periderm cells rep2,GSM7734876,,tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing,1 dpf krt4+ embryonic periderm cells rep2,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp,GSM7734876,GSM7734876: 1 dpf krt4+ embryonic periderm cells rep2; Danio rerio; RNA Seq,GSM7734876 r1,GSM7734876,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,krt4cre-gfp_2_S4_R2_001.fastq.gz krt4cre-gfp_2_S4_R1_001.fastq.gz,fastq fastq,9439207600.0,23598019.0,GSM7734876 r1,0:200 1:200,A:2499982675;C:2086665360;G:2395002073;T:2454282285;N:3275207,200,200,,,2499982675,2086665360,2395002073,2454282285,3275207,SRX21486769,SRS18719069,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.44931,0.01877,0.02236,0.00115,0.80012,0.99032,0.45473,0.49453,200,200,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
25301,SRR25764103,SRX21486768,SRS18719066,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf krt4+ embryonic periderm cells rep1,GSM7734875,,tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing,1 dpf krt4+ embryonic periderm cells rep1,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp,GSM7734875,GSM7734875: 1 dpf krt4+ embryonic periderm cells rep1; Danio rerio; RNA Seq,GSM7734875 r1,GSM7734875,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,krt4cre-gfp_1_S19_R2_001.fastq.gz krt4cre-gfp_1_S19_R1_001.fastq.gz,fastq fastq,6119547200.0,15298868.0,GSM7734875 r1,0:200 1:200,A:1642059769;C:1349462427;G:1535937964;T:1584527048;N:7559992,200,200,,,1642059769,1349462427,1535937964,1584527048,7559992,SRX21486768,SRS18719066,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01112,0.01017,0.0003,0.00014,0.9931,0.99586,0.43605,0.40821,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
29191,SRR27308233,SRX22985581,SRS19950789,SRP479308,PRJNA1055256,Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish,GSE251757,Transcriptome Analysis,Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.,,pubmed:38193362,,EGFP /sp7+  Osteoblast  rep2,GSM7987448,,source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing,EGFP /sp7+  Osteoblast  rep2,High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.,14 dpa adult caudal fin,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry,GSM7987448,GSM7987448: EGFP /sp7+  Osteoblast  rep2; Danio rerio; RNA Seq,GSM7987448 r1,GSM7987448,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP479308,,,Ob-GR2_S6_R2_001.fastq.gz Ob-GR2_S6_R1_001.fastq.gz,fastq fastq,6044999600.0,15112499.0,GSM7987448 r1,0:200 1:200,A:1547731745;C:1388120378;G:1581574912;T:1523597213;N:3975352,200,200,,,1547731745,1388120378,1581574912,1523597213,3975352,SRX22985581,SRS19950789,SRA1773396,"Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.36888,0.02272,0.01109,0.00038,0.86914,0.99328,0.46943,0.4982,200,200,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-12-20,Adult,Adult,Fin,Surface Structure
29192,SRR27308234,SRX22985580,SRS19950790,SRP479308,PRJNA1055256,Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish,GSE251757,Transcriptome Analysis,Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.,,pubmed:38193362,,EGFP /sp7+  Osteoblast  rep1,GSM7987447,,source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing,EGFP /sp7+  Osteoblast  rep1,High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.,14 dpa adult caudal fin,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry,GSM7987447,GSM7987447: EGFP /sp7+  Osteoblast  rep1; Danio rerio; RNA Seq,GSM7987447 r1,GSM7987447,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP479308,,,Ob-GR_S77_R1_001.fastq.gz Ob-GR_S77_R2_001.fastq.gz,fastq fastq,4847773600.0,12119434.0,GSM7987447 r1,0:200 1:200,A:1242312480;C:1120397684;G:1256425065;T:1226991694;N:1646677,200,200,,,1242312480,1120397684,1256425065,1226991694,1646677,SRX22985580,SRS19950790,SRA1773396,"Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.0146,0.02559,0.00038,0.00052,0.99397,0.99405,0.50471,0.47146,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-12-20,Adult,Adult,Fin,Surface Structure
29193,SRR27308235,SRX22985579,SRS19950788,SRP479308,PRJNA1055256,Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish,GSE251757,Transcriptome Analysis,Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.,,pubmed:38193362,,EGFP+/sp7+  OMP  rep2,GSM7987446,,source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing,EGFP+/sp7+  OMP  rep2,High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.,14 dpa adult caudal fin,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry,GSM7987446,GSM7987446: EGFP+/sp7+  OMP  rep2; Danio rerio; RNA Seq,GSM7987446 r1,GSM7987446,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP479308,,,Ob-G2_S5_R2_001.fastq.gz Ob-G2_S5_R1_001.fastq.gz,fastq fastq,6253558800.0,15633897.0,GSM7987446 r1,0:200 1:200,A:1638931864;C:1404420075;G:1600115132;T:1605939571;N:4152158,200,200,,,1638931864,1404420075,1600115132,1605939571,4152158,SRX22985579,SRS19950788,SRA1773396,"Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.41021,0.02334,0.01523,0.00074,0.83989,0.99099,0.52255,0.52173,200,200,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-12-20,Adult,Adult,Fin,Surface Structure
29194,SRR27308236,SRX22985578,SRS19950791,SRP479308,PRJNA1055256,Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish,GSE251757,Transcriptome Analysis,Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.,,pubmed:38193362,,EGFP+/sp7+  OMP  rep1,GSM7987445,,source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing,EGFP+/sp7+  OMP  rep1,High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.,14 dpa adult caudal fin,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry,GSM7987445,GSM7987445: EGFP+/sp7+  OMP  rep1; Danio rerio; RNA Seq,GSM7987445 r1,GSM7987445,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP479308,,,Ob-G_S28_R2_001.fastq.gz Ob-G_S28_R1_001.fastq.gz,fastq fastq,4832320400.0,12080801.0,GSM7987445 r1,0:200 1:200,A:1252095509;C:1107971153;G:1236349772;T:1233319775;N:2584191,200,200,,,1252095509,1107971153,1236349772,1233319775,2584191,SRX22985578,SRS19950791,SRA1773396,"Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01133,0.02895,0.00033,0.00043,0.99439,0.99297,0.50298,0.45574,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-12-20,Adult,Adult,Fin,Surface Structure
29195,SRR27308237,SRX22985577,SRS19950787,SRP479308,PRJNA1055256,Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish,GSE251757,Transcriptome Analysis,Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.,,pubmed:38193362,,EGFP+/sp7   CMP  rep2,GSM7987444,,source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing,EGFP+/sp7   CMP  rep2,High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.,14 dpa adult caudal fin,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry,GSM7987444,GSM7987444: EGFP+/sp7   CMP  rep2; Danio rerio; RNA Seq,GSM7987444 r1,GSM7987444,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP479308,,,Mes-G2_S4_R1_001.fastq.gz Mes-G2_S4_R2_001.fastq.gz,fastq fastq,5812163600.0,14530409.0,GSM7987444 r1,0:200 1:200,A:1538664561;C:1291748975;G:1473028809;T:1504905134;N:3816121,200,200,,,1538664561,1291748975,1473028809,1504905134,3816121,SRX22985577,SRS19950787,SRA1773396,"Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.40138,0.02482,0.0176,0.00091,0.83918,0.99099,0.47875,0.43124,200,200,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-12-20,Adult,Adult,Fin,Surface Structure
29196,SRR27308238,SRX22985576,SRS19950786,SRP479308,PRJNA1055256,Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish,GSE251757,Transcriptome Analysis,Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.,,pubmed:38193362,,EGFP+/sp7   CMP  rep1,GSM7987443,,source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing,EGFP+/sp7   CMP  rep1,High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.,14 dpa adult caudal fin,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry,GSM7987443,GSM7987443: EGFP+/sp7   CMP  rep1; Danio rerio; RNA Seq,GSM7987443 r1,GSM7987443,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP479308,,,Mes-G_S15_R1_001.fastq.gz Mes-G_S15_R2_001.fastq.gz,fastq fastq,5321588000.0,13303970.0,GSM7987443 r1,0:200 1:200,A:1405233304;C:1195662643;G:1342003810;T:1376732727;N:1955516,200,200,,,1405233304,1195662643,1342003810,1376732727,1955516,SRX22985576,SRS19950786,SRA1773396,"Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.00961,0.02419,0.00032,0.00052,0.9945,0.99324,0.51073,0.48429,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-12-20,Adult,Adult,Fin,Surface Structure
34053,SRR31034578,SRX26420033,SRS22939666,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,eif5a1/2 morpholino 3,GSM8579963,,source name:whole body|tissue:whole body|treatment:eif5a1/2 morpholino|geo loc name:missing|collection date:missing,eif5a1/2 morpholino 3,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:eif5a1/2 morpholino,GSM8579963,GSM8579963: eif5a1/2 morpholino 3; Danio rerio; RNA Seq,GSM8579963 r1,GSM8579963,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,eIF5AMO3_1.fq.gz eIF5AMO3_2.fq.gz,fastq fastq,6591810600.0,21972702.0,GSM8579963 r1,0:150 1:150,A:1735827111;C:1561621052;G:1576813159;T:1717549278;N:0,150,150,,,1735827111,1561621052,1576813159,1717549278,0,SRX26420033,SRS22939666,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34054,SRR31034579,SRX26420032,SRS22939665,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,eif5a1/2 morpholino 2,GSM8579962,,source name:whole body|tissue:whole body|treatment:eif5a1/2 morpholino|geo loc name:missing|collection date:missing,eif5a1/2 morpholino 2,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:eif5a1/2 morpholino,GSM8579962,GSM8579962: eif5a1/2 morpholino 2; Danio rerio; RNA Seq,GSM8579962 r1,GSM8579962,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,eIF5AMO2_1.fq.gz eIF5AMO2_2.fq.gz,fastq fastq,6615856500.0,22052855.0,GSM8579962 r1,0:150 1:150,A:1712890711;C:1594159797;G:1606364019;T:1702441973;N:0,150,150,,,1712890711,1594159797,1606364019,1702441973,0,SRX26420032,SRS22939665,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34055,SRR31034580,SRX26420031,SRS22939663,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,eif5a1/2 morpholino 1,GSM8579961,,source name:whole body|tissue:whole body|treatment:eif5a1/2 morpholino|geo loc name:missing|collection date:missing,eif5a1/2 morpholino 1,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:eif5a1/2 morpholino,GSM8579961,GSM8579961: eif5a1/2 morpholino 1; Danio rerio; RNA Seq,GSM8579961 r1,GSM8579961,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,eIF5AMO1_1.fq.gz eIF5AMO1_2.fq.gz,fastq fastq,6172597200.0,20575324.0,GSM8579961 r1,0:150 1:150,A:1612632964;C:1473173555;G:1490511736;T:1596278945;N:0,150,150,,,1612632964,1473173555,1490511736,1596278945,0,SRX26420031,SRS22939663,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34056,SRR31034581,SRX26420030,SRS22939664,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,dhps morpholino 3,GSM8579960,,source name:whole body|tissue:whole body|treatment:dhps morpholino|geo loc name:missing|collection date:missing,dhps morpholino 3,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:dhps morpholino,GSM8579960,GSM8579960: dhps morpholino 3; Danio rerio; RNA Seq,GSM8579960 r1,GSM8579960,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,DHPSMO3_1.fq.gz DHPSMO3_2.fq.gz,fastq fastq,6620802600.0,22069342.0,GSM8579960 r1,0:150 1:150,A:1736599369;C:1572800715;G:1587922794;T:1723479722;N:0,150,150,,,1736599369,1572800715,1587922794,1723479722,0,SRX26420030,SRS22939664,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34057,SRR31034582,SRX26420029,SRS22939659,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,dhps morpholino 2,GSM8579959,,source name:whole body|tissue:whole body|treatment:dhps morpholino|geo loc name:missing|collection date:missing,dhps morpholino 2,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:dhps morpholino,GSM8579959,GSM8579959: dhps morpholino 2; Danio rerio; RNA Seq,GSM8579959 r1,GSM8579959,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,DHPSMO2_1.fq.gz DHPSMO2_2.fq.gz,fastq fastq,6582483600.0,21941612.0,GSM8579959 r1,0:150 1:150,A:1720509810;C:1570278366;G:1585433293;T:1706262131;N:0,150,150,,,1720509810,1570278366,1585433293,1706262131,0,SRX26420029,SRS22939659,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34058,SRR31034583,SRX26420028,SRS22939662,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,dhps morpholino 1,GSM8579958,,source name:whole body|tissue:whole body|treatment:dhps morpholino|geo loc name:missing|collection date:missing,dhps morpholino 1,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:dhps morpholino,GSM8579958,GSM8579958: dhps morpholino 1; Danio rerio; RNA Seq,GSM8579958 r1,GSM8579958,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,DHPSMO1_1.fq.gz DHPSMO1_2.fq.gz,fastq fastq,6596391000.0,21987970.0,GSM8579958 r1,0:150 1:150,A:1725362753;C:1572510096;G:1586851982;T:1711666169;N:0,150,150,,,1725362753,1572510096,1586851982,1711666169,0,SRX26420028,SRS22939662,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34059,SRR31034584,SRX26420027,SRS22939661,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,Control morpholino 3,GSM8579957,,source name:whole body|tissue:whole body|treatment:Control morpholino|geo loc name:missing|collection date:missing,Control morpholino 3,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:Control morpholino,GSM8579957,GSM8579957: Control morpholino 3; Danio rerio; RNA Seq,GSM8579957 r1,GSM8579957,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,CtrlMO3_1.fq.gz CtrlMO3_2.fq.gz,fastq fastq,6625089300.0,22083631.0,GSM8579957 r1,0:150 1:150,A:1728439807;C:1584339137;G:1602988513;T:1709321843;N:0,150,150,,,1728439807,1584339137,1602988513,1709321843,0,SRX26420027,SRS22939661,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34060,SRR31034585,SRX26420026,SRS22939658,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,Control morpholino 2,GSM8579956,,source name:whole body|tissue:whole body|treatment:Control morpholino|geo loc name:missing|collection date:missing,Control morpholino 2,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:Control morpholino,GSM8579956,GSM8579956: Control morpholino 2; Danio rerio; RNA Seq,GSM8579956 r1,GSM8579956,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,CtrlMO2_1.fq.gz CtrlMO2_2.fq.gz,fastq fastq,6823000500.0,22743335.0,GSM8579956 r1,0:150 1:150,A:1777305843;C:1633379395;G:1649025317;T:1763289945;N:0,150,150,,,1777305843,1633379395,1649025317,1763289945,0,SRX26420026,SRS22939658,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
34061,SRR31034586,SRX26420025,SRS22939660,SRP539240,PRJNA1174234,Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A,GSE279773,Transcriptome Analysis,Prior to type 2 diabetes onset  ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS  which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation  it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A  we used the following animal and cell based models: transgenic zebrafish and inducible  ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although  those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented  these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly  following 4 weeks of high fat diet feeding and obesity  mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells  despite similar weight gain and insulin sensitivity. Taken together  our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function  inpart  from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control  dhps  or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.,,pubmed:39832654,,Control morpholino 1,GSM8579955,,source name:whole body|tissue:whole body|treatment:Control morpholino|geo loc name:missing|collection date:missing,Control morpholino 1,Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value,whole body,zebrafish were treated with morpholino and RNA was extracted 24 hours later,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,tissue:whole body|treatment:Control morpholino,GSM8579955,GSM8579955: Control morpholino 1; Danio rerio; RNA Seq,GSM8579955 r1,GSM8579955,1,RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer  followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated  with a protruding 'A' at the three prime end forming a blunt end  followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands  and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP539240,,,CtrlMO1_1.fq.gz CtrlMO1_2.fq.gz,fastq fastq,6625797900.0,22085993.0,GSM8579955 r1,0:150 1:150,A:1738695154;C:1575541452;G:1592240618;T:1719320676;N:0,150,150,,,1738695154,1575541452,1592240618,1719320676,0,SRX26420025,SRS22939660,SRA1993170,"Medicine, University of Chicago","Medicine, University of Chicago",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2024-10-17,Undetermined,Embryo,Trunk,Surface Structure
36227,SRR33613672,SRX28842027,SRS25072222,SRP586119,PRJNA1263917,Danio rerio Transcriptome or Gene expression,PRJNA1263917,Other,Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.,,,,Danio rerio,Danio rerio,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,HFD 3,HFD 3,Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP586119,,,HFD-3-1.fq.gz HFD-3-2.fq.gz,fastq fastq,6810755100.0,22702517.0,HFD 3 1.fq.gz,0:150 1:150,A:1804127778;C:1596175018;G:1609090701;T:1801361603;N:0,150,150,,,1804127778,1596175018,1609090701,1801361603,0,SRX28842027,SRS25072222,SRA2131918,Yibin University|Faculty of Quality Management and Inspection &amp; Qua,Yibin University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-18,Multi-stage,Multi-stage,Trunk,Surface Structure
36228,SRR33613673,SRX28842026,SRS25072222,SRP586119,PRJNA1263917,Danio rerio Transcriptome or Gene expression,PRJNA1263917,Other,Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.,,,,Danio rerio,Danio rerio,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,HFD 2,HFD 2,Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP586119,,,HFD-2-1.fq.gz HFD-2-2.fq.gz,fastq fastq,6826358400.0,22754528.0,HFD 2 1.fq.gz,0:150 1:150,A:1826465185;C:1582322712;G:1596188986;T:1821381517;N:0,150,150,,,1826465185,1582322712,1596188986,1821381517,0,SRX28842026,SRS25072222,SRA2131918,Yibin University|Faculty of Quality Management and Inspection &amp; Qua,Yibin University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-18,Multi-stage,Multi-stage,Trunk,Surface Structure
36229,SRR33613674,SRX28842025,SRS25072222,SRP586119,PRJNA1263917,Danio rerio Transcriptome or Gene expression,PRJNA1263917,Other,Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.,,,,Danio rerio,Danio rerio,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,HFD 1,HFD 1,Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP586119,,,HFD-1-1.fq.gz HFD-1-2.fq.gz,fastq fastq,6598410300.0,21994701.0,HFD 1 1.fq.gz,0:150 1:150,A:1765905584;C:1529581410;G:1542056821;T:1760866485;N:0,150,150,,,1765905584,1529581410,1542056821,1760866485,0,SRX28842025,SRS25072222,SRA2131918,Yibin University|Faculty of Quality Management and Inspection &amp; Qua,Yibin University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-18,Multi-stage,Multi-stage,Trunk,Surface Structure
36230,SRR33613675,SRX28842024,SRS25072222,SRP586119,PRJNA1263917,Danio rerio Transcriptome or Gene expression,PRJNA1263917,Other,Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.,,,,Danio rerio,Danio rerio,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,HFD10 3,HFD10 3,Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP586119,,,HFD10-3-1.fq.gz HFD10-3-2.fq.gz,fastq fastq,6609153300.0,22030511.0,HFD10 3 1.fq.gz,0:150 1:150,A:1780787716;C:1521027085;G:1532800826;T:1774537673;N:0,150,150,,,1780787716,1521027085,1532800826,1774537673,0,SRX28842024,SRS25072222,SRA2131918,Yibin University|Faculty of Quality Management and Inspection &amp; Qua,Yibin University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-18,Multi-stage,Multi-stage,Trunk,Surface Structure
36231,SRR33613676,SRX28842023,SRS25072222,SRP586119,PRJNA1263917,Danio rerio Transcriptome or Gene expression,PRJNA1263917,Other,Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.,,,,Danio rerio,Danio rerio,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,HFD10 2,HFD10 2,Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP586119,,,HFD10-2-1.fq.gz HFD10-2-2.fq.gz,fastq fastq,6605145900.0,22017153.0,HFD10 2 1.fq.gz,0:150 1:150,A:1765731508;C:1533254667;G:1545960098;T:1760199627;N:0,150,150,,,1765731508,1533254667,1545960098,1760199627,0,SRX28842023,SRS25072222,SRA2131918,Yibin University|Faculty of Quality Management and Inspection &amp; Qua,Yibin University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-18,Multi-stage,Multi-stage,Trunk,Surface Structure
36232,SRR33613677,SRX28842022,SRS25072222,SRP586119,PRJNA1263917,Danio rerio Transcriptome or Gene expression,PRJNA1263917,Other,Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.,,,,Danio rerio,Danio rerio,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,HFD10 1,HFD10 1,Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP586119,,,HFD10-1-1.fq.gz HFD10-1-2.fq.gz,fastq fastq,6780056700.0,22600189.0,HFD10 1 1.fq.gz,0:150 1:150,A:1819443100;C:1566081115;G:1580525465;T:1814007020;N:0,150,150,,,1819443100,1566081115,1580525465,1814007020,0,SRX28842022,SRS25072222,SRA2131918,Yibin University|Faculty of Quality Management and Inspection &amp; Qua,Yibin University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-18,Multi-stage,Multi-stage,Trunk,Surface Structure
36233,SRR33613678,SRX28842021,SRS25072222,SRP586119,PRJNA1263917,Danio rerio Transcriptome or Gene expression,PRJNA1263917,Other,Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.,,,,Danio rerio,Danio rerio,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,NFD 3,NFD 3,Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP586119,,,NFD-3-1.fq.gz NFD-3-2.fq.gz,fastq fastq,6677775900.0,22259253.0,NFD 3 1.fq.gz,0:150 1:150,A:1794821611;C:1541478212;G:1552820105;T:1788655972;N:0,150,150,,,1794821611,1541478212,1552820105,1788655972,0,SRX28842021,SRS25072222,SRA2131918,Yibin University|Faculty of Quality Management and Inspection &amp; Qua,Yibin University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-18,Multi-stage,Multi-stage,Trunk,Surface Structure
36234,SRR33613679,SRX28842020,SRS25072222,SRP586119,PRJNA1263917,Danio rerio Transcriptome or Gene expression,PRJNA1263917,Other,Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.,,,,Danio rerio,Danio rerio,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,NFD 2,NFD 2,Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP586119,,,NFD-2-1.fq.gz NFD-2-2.fq.gz,fastq fastq,6680197200.0,22267324.0,NFD 2 1.fq.gz,0:150 1:150,A:1810744167;C:1526383805;G:1539949310;T:1803119918;N:0,150,150,,,1810744167,1526383805,1539949310,1803119918,0,SRX28842020,SRS25072222,SRA2131918,Yibin University|Faculty of Quality Management and Inspection &amp; Qua,Yibin University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-18,Multi-stage,Multi-stage,Trunk,Surface Structure
36235,SRR33613680,SRX28842019,SRS25072222,SRP586119,PRJNA1263917,Danio rerio Transcriptome or Gene expression,PRJNA1263917,Other,Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.,,,,Danio rerio,Danio rerio,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,NFD 1,NFD 1,Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP586119,,,NFD-1-1.fq.gz NFD-1-2.fq.gz,fastq fastq,6587923800.0,21959746.0,NFD 1 1.fq.gz,0:150 1:150,A:1773646514;C:1516320091;G:1530275621;T:1767681574;N:0,150,150,,,1773646514,1516320091,1530275621,1767681574,0,SRX28842019,SRS25072222,SRA2131918,Yibin University|Faculty of Quality Management and Inspection &amp; Qua,Yibin University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-18,Multi-stage,Multi-stage,Trunk,Surface Structure