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
25320,SRR25810878,SRX21533024,SRS18745490,SRP457576,PRJNA1010780,Effect of egr3 knockout on gene expression of dissected zebrafish hearts,GSE241935,Transcriptome Analysis,To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype  we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf.  We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS.  Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12µl of RNase free water.   Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples.   1. Boezio  G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571,,pubmed:38748804,,egr3 wild type siblings 2,GSM7745909,,source name:Heart|tissue:Heart|genotype:bns577+/+|geo loc name:missing|collection date:missing,egr3 wild type siblings 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al.  Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts,Heart,,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,tissue:Heart|genotype:bns577+/+,GSM7745909,GSM7745909: egr3 wild type siblings 2; Danio rerio; RNA Seq,GSM7745909 r1,GSM7745909,1,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP457576,,loader:fastq load.py,E22_3626_Lib_Agatha_egr3_WT2_R1.fastq.gz,fastq,3473319384.0,49279465.0,GSM7745909 r1,0:70.48,A:943794847;C:792135324;G:792042625;T:945083925;N:262663,70,,,,943794847,792135324,792042625,945083925,262663,SRX21533024,SRS18745490,SRA1702458,MPI for heart and lung research,MPI for heart and lung research,1,0.68549,,0.04588,,0.76865,,0.44964,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2023-08-30,Undetermined,Undetermined,Heart,Cardiovascular System
25321,SRR25810879,SRX21533023,SRS18745489,SRP457576,PRJNA1010780,Effect of egr3 knockout on gene expression of dissected zebrafish hearts,GSE241935,Transcriptome Analysis,To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype  we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf.  We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS.  Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12µl of RNase free water.   Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples.   1. Boezio  G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571,,pubmed:38748804,,egr3 wild type siblings 1,GSM7745908,,source name:Heart|tissue:Heart|genotype:bns577+/+|geo loc name:missing|collection date:missing,egr3 wild type siblings 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al.  Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts,Heart,,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,tissue:Heart|genotype:bns577+/+,GSM7745908,GSM7745908: egr3 wild type siblings 1; Danio rerio; RNA Seq,GSM7745908 r1,GSM7745908,1,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP457576,,loader:fastq load.py,E22_3626_Lib_Agatha_egr3_WT1_R1.fastq.gz,fastq,3909248616.0,55045571.0,GSM7745908 r1,0:71.02,A:1048107387;C:905014546;G:907455489;T:1048528690;N:142504,71,,,,1048107387,905014546,907455489,1048528690,142504,SRX21533023,SRS18745489,SRA1702458,MPI for heart and lung research,MPI for heart and lung research,1,0.94958,,0.06298,,0.74819,,0.45762,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2023-08-30,Undetermined,Undetermined,Heart,Cardiovascular System
25322,SRR25810880,SRX21533022,SRS18745488,SRP457576,PRJNA1010780,Effect of egr3 knockout on gene expression of dissected zebrafish hearts,GSE241935,Transcriptome Analysis,To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype  we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf.  We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS.  Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12µl of RNase free water.   Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples.   1. Boezio  G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571,,pubmed:38748804,,egr3 mutants 2,GSM7745907,,source name:Heart|tissue:Heart|genotype:bns577 / |geo loc name:missing|collection date:missing,egr3 mutants 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al.  Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts,Heart,,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,tissue:Heart|genotype:bns577 / ,GSM7745907,GSM7745907: egr3 mutants 2; Danio rerio; RNA Seq,GSM7745907 r1,GSM7745907,1,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP457576,,loader:fastq load.py,E22_3626_Lib_Agatha_egr3_Mut2_R1.fastq.gz,fastq,3432675258.0,48483287.0,GSM7745907 r1,0:70.80,A:925832958;C:788551205;G:790129536;T:927993012;N:168547,70,,,,925832958,788551205,790129536,927993012,168547,SRX21533022,SRS18745488,SRA1702458,MPI for heart and lung research,MPI for heart and lung research,1,0.75652,,0.04046,,0.76455,,0.46333,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2023-08-30,Undetermined,Undetermined,Heart,Cardiovascular System
25323,SRR25810881,SRX21533021,SRS18745487,SRP457576,PRJNA1010780,Effect of egr3 knockout on gene expression of dissected zebrafish hearts,GSE241935,Transcriptome Analysis,To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype  we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf.  We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS.  Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12µl of RNase free water.   Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples.   1. Boezio  G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571,,pubmed:38748804,,egr3 mutants 1,GSM7745906,,source name:Heart|tissue:Heart|genotype:bns577 / |geo loc name:missing|collection date:missing,egr3 mutants 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al.  Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts,Heart,,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,tissue:Heart|genotype:bns577 / ,GSM7745906,GSM7745906: egr3 mutants 1; Danio rerio; RNA Seq,GSM7745906 r1,GSM7745906,1,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP457576,,loader:fastq load.py,E22_3626_Lib_Agatha_egr3_Mut1_R1.fastq.gz,fastq,3838969347.0,54545950.0,GSM7745906 r1,0:70.38,A:1016913415;C:902500250;G:903033204;T:1016194618;N:327860,70,,,,1016913415,902500250,903033204,1016194618,327860,SRX21533021,SRS18745487,SRA1702458,MPI for heart and lung research,MPI for heart and lung research,1,0.9511,,0.05017,,0.75341,,0.47152,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2023-08-30,Undetermined,Undetermined,Heart,Cardiovascular System
29201,SRR27319715,SRX22996941,SRS19961590,SRP479504,PRJNA1055557,Border zone cardiomyocytes and macrophages contribute to remodeling of the extracellular matrix to promote cardiomyocyte invasion during zebrafish cardiac regeneration,GSE251856,Other,Despite numerous advances in our understanding of zebrafish cardiac regeneration  an aspect that remains less studied is how newly proliferated cardiomyocytes invade  and eventually replace  the collagen containing fibrotic tissue following injury.  Here  we provide an in depth analysis of the process of cardiomyocyte invasion and migration using live imaging and histological approaches.  We observed a close interaction between protruding cardiomyocytes and macrophages at the wound border zone  and irf8 mutant zebrafish  which largely lack macrophages  exhibited defects in extracellular matrix ECM remodeling and cardiomyocyte protrusion into the injured area.  Using a resident macrophage ablation model  we show that defects in ECM remodeling at the border zone and subsequent cardiomyocyte protrusion can be partly attributed to a population of resident macrophages.  Single cell RNA sequencing analysis of cells at the wound border revealed a population of cardiomyocytes and macrophages with fibroblast like gene expression signatures  including the expression of genes encoding ECM structural proteins and ECM remodeling proteins.  The expression of mmp14b  which encodes a membrane anchored matrix metalloproteinase  was restricted to cells in the border zone and genetic deletion of mmp14b led to a decrease in 1 collagen degradation at the border zone  2 macrophage recruitment to the border zone  and 3 subsequent cardiomyocyte invasion.  Furthermore  cardiomyocyte specific overexpression of mmp14b was sufficient to enhance cardiomyocyte invasion both into the injured area and along the apical surface of the wound.  Altogether  our data shed important insights into the process of cardiomyocyte invasion of the collagen containing injured tissue during cardiac regeneration.  They further suggest that cardiomyocytes and resident macrophages contribute to ECM remodeling at the border zone to promote cardiomyocyte replenishment of the fibrotic injured tissue. Overall design: The border zone of regenerating wild type zebrafish hearts at 7 dpci was microdissected and subjected to scRNA seq,,pubmed:39962064;pubmed:40268967,,scRNA seq of wild type border z1 cells of regenerating hearts at 7 dpci,GSM7989198,,source name:Heart|tissue:Heart|genotype:Wild type|treatment:Hearts were cryoinjured and border z1 cells were microdissected at 7 dpci and pooled for scRNA seq|geo loc name:missing|collection date:missing,scRNA seq of wild type border z1 cells of regenerating hearts at 7 dpci,Reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 23 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 40%. Furthermore  we filtered 9874 genes if they were detected in less than 30 cells <0.01%. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA  retaining 50 principal components. Subsequent steps  like low dimensional UMAP embedding and cell clustering via community detection  were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: danRer11 Supplementary files format and content: starsolo outputs,Heart,Zebrafish hearts were cryoinjured and extracted at 7 dpci.,Border zone cells from 8 hearts were pooled and tissue dissociation was performed using the Pierce Primary Cardiomyocyte Isolation kit according to manufacturer's instructions.  Cells were resuspended in DMEM with 10% FBS and 1x glutamate. The cell suspensions were depleted for dead cells using LeviCell 1.0 device Levitas Bio counted with MOX Z cell counter and diluted according to manufacturer’s protocol to obtain 10.000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.,,tissue:Heart|genotype:Wild type|treatment:Hearts were cryoinjured and border z1 cells were microdissected at 7 dpci and pooled for scRNA seq,GSM7989198,GSM7989198: scRNA seq of wild type border z1 cells of regenerating hearts at 7 dpci; Danio rerio; RNA Seq,GSM7989198 r1,GSM7989198,1,Border zone cells from 8 hearts were pooled and tissue dissociation was performed using the Pierce Primary Cardiomyocyte Isolation kit according to manufacturer's instructions.  Cells were resuspended in DMEM with 10% FBS and 1x glutamate. The cell suspensions were depleted for dead cells using LeviCell 1.0 device Levitas Bio counted with MOX Z cell counter and diluted according to manufacturer's protocol to obtain 10.000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP479504,,,Arica_10x_Zebrafish_Borderzone_Lib_R2.fastq.gz Arica_10x_Zebrafish_Borderzone_Lib_R1.fastq.gz,fastq fastq,35579193737.0,447572139.0,GSM7989198 r1,0:28 1:51.49,A:9662436792;C:7884457111;G:8055970010;T:9787114480;N:189215344,28,51,,,9662436792,7884457111,8055970010,9787114480,189215344,SRX22996941,SRS19961590,SRA1774131,MPI for heart and lung research,MPI for heart and lung research,2,0.00237,0.94011,0.00086,0.09945,0.99571,0.81907,0.32746,0.60892,28,51,T,B,sc-like readlen,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-12-21,Undetermined,Undetermined,Heart,Cardiovascular System
31502,SRR28411462,SRX24015869,SRS20810998,SRP497025,PRJNA1090509,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139,GSE262169,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing,parent bioproject:PRJNA1090894,pubmed:39271818,,injured tissue  myd88+/+  24 hpci 2,GSM8159071,,source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,injured tissue  myd88+/+  24 hpci 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts,cardiac ventricles,untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.,,tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury,GSM8159071,GSM8159071: injured tissue  myd88+/+  24 hpci 2; Danio rerio; RNA Seq,GSM8159071 r1,GSM8159071,1,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP497025,,loader:fastq load.py,Pinelopi_WT2_24h_pci_R1.fastq.gz,fastq,2454645976.0,33159360.0,GSM8159071 r1,0:74.03,A:660213492;C:527347733;G:572126573;T:694765347;N:192831,74,,,,660213492,527347733,572126573,694765347,192831,SRX24015869,SRS20810998,SRA1830778,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Germany,2024-03-21,Undetermined,Undetermined,Heart,Cardiovascular System
31503,SRR28411463,SRX24015868,SRS20810997,SRP497025,PRJNA1090509,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139,GSE262169,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing,parent bioproject:PRJNA1090894,pubmed:39271818,,injured tissue  myd88+/+  1 hpci 2,GSM8159070,,source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,injured tissue  myd88+/+  1 hpci 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts,cardiac ventricles,untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.,,tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury,GSM8159070,GSM8159070: injured tissue  myd88+/+  1 hpci 2; Danio rerio; RNA Seq,GSM8159070 r1,GSM8159070,1,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP497025,,loader:fastq load.py,Pinelopi_WT2_1h_pci_R1.fastq.gz,fastq,2674654542.0,36003719.0,GSM8159070 r1,0:74.29,A:713621237;C:556223861;G:630990745;T:773686189;N:132510,74,,,,713621237,556223861,630990745,773686189,132510,SRX24015868,SRS20810997,SRA1830778,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Germany,2024-03-21,Undetermined,Undetermined,Heart,Cardiovascular System
31504,SRR28411464,SRX24015867,SRS20810996,SRP497025,PRJNA1090509,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139,GSE262169,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing,parent bioproject:PRJNA1090894,pubmed:39271818,,ventricle  myd88+/+  untouched 2,GSM8159069,,source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment: |geo loc name:missing|collection date:missing,ventricle  myd88+/+  untouched 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts,cardiac ventricles,untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.,,tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment: ,GSM8159069,GSM8159069: ventricle  myd88+/+  untouched 2; Danio rerio; RNA Seq,GSM8159069 r1,GSM8159069,1,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP497025,,loader:fastq load.py,Pinelopi_WT2_0h_pci_R1.fastq.gz,fastq,2092632406.0,28163739.0,GSM8159069 r1,0:74.30,A:560190602;C:446185315;G:485011548;T:601082958;N:161983,74,,,,560190602,446185315,485011548,601082958,161983,SRX24015867,SRS20810996,SRA1830778,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Germany,2024-03-21,Undetermined,Undetermined,Heart,Cardiovascular System
31505,SRR28411465,SRX24015866,SRS20810995,SRP497025,PRJNA1090509,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139,GSE262169,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing,parent bioproject:PRJNA1090894,pubmed:39271818,,injured tissue  myd88+/+  24 hpci 1,GSM8159068,,source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,injured tissue  myd88+/+  24 hpci 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts,cardiac ventricles,untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.,,tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury,GSM8159068,GSM8159068: injured tissue  myd88+/+  24 hpci 1; Danio rerio; RNA Seq,GSM8159068 r1,GSM8159068,1,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP497025,,loader:fastq load.py,Pinelopi_WT1_24h_pci_R1.fastq.gz,fastq,1060148110.0,14341826.0,GSM8159068 r1,0:73.92,A:290655996;C:222128471;G:247491826;T:299784598;N:87219,73,,,,290655996,222128471,247491826,299784598,87219,SRX24015866,SRS20810995,SRA1830778,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Germany,2024-03-21,Undetermined,Undetermined,Heart,Cardiovascular System
31506,SRR28411466,SRX24015865,SRS20810994,SRP497025,PRJNA1090509,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139,GSE262169,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing,parent bioproject:PRJNA1090894,pubmed:39271818,,injured tissue  myd88+/+  1 hpci 1,GSM8159067,,source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,injured tissue  myd88+/+  1 hpci 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts,cardiac ventricles,untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.,,tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury,GSM8159067,GSM8159067: injured tissue  myd88+/+  1 hpci 1; Danio rerio; RNA Seq,GSM8159067 r1,GSM8159067,1,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP497025,,loader:fastq load.py,Pinelopi_WT1_1h_pci_R1.fastq.gz,fastq,2594786024.0,34913792.0,GSM8159067 r1,0:74.32,A:689702458;C:551265040;G:603307580;T:750425733;N:85213,74,,,,689702458,551265040,603307580,750425733,85213,SRX24015865,SRS20810994,SRA1830778,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Germany,2024-03-21,Undetermined,Undetermined,Heart,Cardiovascular System
31507,SRR28411467,SRX24015864,SRS20810993,SRP497025,PRJNA1090509,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139,GSE262169,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing,parent bioproject:PRJNA1090894,pubmed:39271818,,ventricle  myd88+/+  untouched 1,GSM8159066,,source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment: |geo loc name:missing|collection date:missing,ventricle  myd88+/+  untouched 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts,cardiac ventricles,untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.,,tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment: ,GSM8159066,GSM8159066: ventricle  myd88+/+  untouched 1; Danio rerio; RNA Seq,GSM8159066 r1,GSM8159066,1,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP497025,,loader:fastq load.py,Pinelopi_WT1_0h_pci_R1.fastq.gz,fastq,2123516005.0,28595227.0,GSM8159066 r1,0:74.26,A:562046544;C:458761205;G:496224794;T:606313940;N:169522,74,,,,562046544,458761205,496224794,606313940,169522,SRX24015864,SRS20810993,SRA1830778,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Germany,2024-03-21,Undetermined,Undetermined,Heart,Cardiovascular System
31508,SRR28411468,SRX24015863,SRS20810992,SRP497025,PRJNA1090509,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139,GSE262169,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing,parent bioproject:PRJNA1090894,pubmed:39271818,,injured tissue  myd88 /   24 hpci 2,GSM8159065,,source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,injured tissue  myd88 /   24 hpci 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts,cardiac ventricles,untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.,,tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury,GSM8159065,GSM8159065: injured tissue  myd88 /   24 hpci 2; Danio rerio; RNA Seq,GSM8159065 r1,GSM8159065,1,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP497025,,loader:fastq load.py,Pinelopi_Homo2_24h_pci_R1.fastq.gz,fastq,2509143345.0,33915175.0,GSM8159065 r1,0:73.98,A:669128241;C:547606289;G:587771598;T:704439682;N:197535,73,,,,669128241,547606289,587771598,704439682,197535,SRX24015863,SRS20810992,SRA1830778,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Germany,2024-03-21,Undetermined,Undetermined,Heart,Cardiovascular System
31509,SRR28411469,SRX24015862,SRS20810991,SRP497025,PRJNA1090509,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139,GSE262169,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing,parent bioproject:PRJNA1090894,pubmed:39271818,,injured tissue  myd88 /   1 hpci 2,GSM8159064,,source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,injured tissue  myd88 /   1 hpci 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts,cardiac ventricles,untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.,,tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury,GSM8159064,GSM8159064: injured tissue  myd88 /   1 hpci 2; Danio rerio; RNA Seq,GSM8159064 r1,GSM8159064,1,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP497025,,loader:fastq load.py,Pinelopi_Homo2_1h_pci_R1.fastq.gz,fastq,2584847185.0,34784917.0,GSM8159064 r1,0:74.31,A:690941775;C:542509296;G:605002938;T:746301098;N:92078,74,,,,690941775,542509296,605002938,746301098,92078,SRX24015862,SRS20810991,SRA1830778,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Germany,2024-03-21,Undetermined,Undetermined,Heart,Cardiovascular System
31510,SRR28411470,SRX24015861,SRS20810990,SRP497025,PRJNA1090509,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139,GSE262169,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing,parent bioproject:PRJNA1090894,pubmed:39271818,,ventricle  myd88 /   untouched 2,GSM8159063,,source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment: |geo loc name:missing|collection date:missing,ventricle  myd88 /   untouched 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts,cardiac ventricles,untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.,,tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment: ,GSM8159063,GSM8159063: ventricle  myd88 /   untouched 2; Danio rerio; RNA Seq,GSM8159063 r1,GSM8159063,1,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP497025,,loader:fastq load.py,Pinelopi_Homo2_0h_pci_R1.fastq.gz,fastq,2178164776.0,29313471.0,GSM8159063 r1,0:74.31,A:588370831;C:457110464;G:507924919;T:624586577;N:171985,74,,,,588370831,457110464,507924919,624586577,171985,SRX24015861,SRS20810990,SRA1830778,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Germany,2024-03-21,Undetermined,Undetermined,Heart,Cardiovascular System
31511,SRR28411471,SRX24015860,SRS20810989,SRP497025,PRJNA1090509,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139,GSE262169,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing,parent bioproject:PRJNA1090894,pubmed:39271818,,injured tissue  myd88 /   24 hpci 1,GSM8159062,,source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,injured tissue  myd88 /   24 hpci 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts,cardiac ventricles,untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.,,tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury,GSM8159062,GSM8159062: injured tissue  myd88 /   24 hpci 1; Danio rerio; RNA Seq,GSM8159062 r1,GSM8159062,1,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP497025,,loader:fastq load.py,Pinelopi_Homo1_24h_pci_R1.fastq.gz,fastq,2323298254.0,31332951.0,GSM8159062 r1,0:74.15,A:621931320;C:501998000;G:541224122;T:657957821;N:186991,74,,,,621931320,501998000,541224122,657957821,186991,SRX24015860,SRS20810989,SRA1830778,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Germany,2024-03-21,Undetermined,Undetermined,Heart,Cardiovascular System
31512,SRR28411472,SRX24015859,SRS20810988,SRP497025,PRJNA1090509,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139,GSE262169,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing,parent bioproject:PRJNA1090894,pubmed:39271818,,injured tissue  myd88 /   1 hpci 1,GSM8159061,,source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,injured tissue  myd88 /   1 hpci 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts,cardiac ventricles,untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.,,tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury,GSM8159061,GSM8159061: injured tissue  myd88 /   1 hpci 1; Danio rerio; RNA Seq,GSM8159061 r1,GSM8159061,1,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP497025,,loader:fastq load.py,Pinelopi_Homo1_1h_pci_R1.fastq.gz,fastq,2585736865.0,34790236.0,GSM8159061 r1,0:74.32,A:679380332;C:554919862;G:604907160;T:746451941;N:77570,74,,,,679380332,554919862,604907160,746451941,77570,SRX24015859,SRS20810988,SRA1830778,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Germany,2024-03-21,Undetermined,Undetermined,Heart,Cardiovascular System
31513,SRR28411473,SRX24015858,SRS20810987,SRP497025,PRJNA1090509,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139,GSE262169,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing,parent bioproject:PRJNA1090894,pubmed:39271818,,ventricle  myd88 /   untouched 1,GSM8159060,,source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment: |geo loc name:missing|collection date:missing,ventricle  myd88 /   untouched 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts,cardiac ventricles,untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.,,tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment: ,GSM8159060,GSM8159060: ventricle  myd88 /   untouched 1; Danio rerio; RNA Seq,GSM8159060 r1,GSM8159060,1,RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP497025,,loader:fastq load.py,Pinelopi_Homo1_0h_pci_R1.fastq.gz,fastq,2321007700.0,31228476.0,GSM8159060 r1,0:74.32,A:623574024;C:490503071;G:538918126;T:667825381;N:187098,74,,,,623574024,490503071,538918126,667825381,187098,SRX24015858,SRS20810987,SRA1830778,MPI for heart and lung research,MPI for heart and lung research,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Germany,2024-03-21,Undetermined,Undetermined,Heart,Cardiovascular System
31545,SRR28435452,SRX24039370,SRS20832135,SRP497581,PRJNA1091566,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration,GSE262351,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 /  samples,,pubmed:39271818,,myd88 3,GSM8163706,,tissue:endocardial|cell type:endocardial|genotype:myd88 / |time:96 hpci|geo loc name:missing|collection date:missing,myd88 3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts.,endocardial,,RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.,,cell type:endocardial|genotype:myd88 / |time:96 hpci,GSM8163706,GSM8163706: myd88 3; Danio rerio; RNA Seq,GSM8163706 r1,GSM8163706,1,RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP497581,,loader:fastq load.py,myd88_3_1.fq.gz myd88_3_2.fq.gz,fastq fastq,6626254800.0,22087516.0,GSM8163706 r1,0:150 1:150,A:1858405504;C:1462442884;G:1470757827;T:1834548220;N:100365,150,150,,,1858405504,1462442884,1470757827,1834548220,100365,SRX24039370,SRS20832135,SRA1832826,"Bioinformatics, Max-Planck-Institute for Heart and Lung Research","Bioinformatics, Max-Planck-Institute for Heart and Lung Research",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2024-03-25,Undetermined,Undetermined,Heart,Cardiovascular System
31546,SRR28435455,SRX24039369,SRS20832134,SRP497581,PRJNA1091566,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration,GSE262351,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 /  samples,,pubmed:39271818,,myd88 2,GSM8163705,,tissue:endocardial|cell type:endocardial|genotype:myd88 / |time:96 hpci|geo loc name:missing|collection date:missing,myd88 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts.,endocardial,,RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.,,cell type:endocardial|genotype:myd88 / |time:96 hpci,GSM8163705,GSM8163705: myd88 2; Danio rerio; RNA Seq,GSM8163705 r1,GSM8163705,1,RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP497581,,loader:fastq load.py,myd88_2_1.fq.gz myd88_2_2.fq.gz,fastq fastq,6586163100.0,21953877.0,GSM8163705 r1,0:150 1:150,A:1856129657;C:1440403994;G:1451543521;T:1837982507;N:103421,150,150,,,1856129657,1440403994,1451543521,1837982507,103421,SRX24039369,SRS20832134,SRA1832826,"Bioinformatics, Max-Planck-Institute for Heart and Lung Research","Bioinformatics, Max-Planck-Institute for Heart and Lung Research",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2024-03-25,Undetermined,Undetermined,Heart,Cardiovascular System
31547,SRR28435453,SRX24039368,SRS20832133,SRP497581,PRJNA1091566,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration,GSE262351,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 /  samples,,pubmed:39271818,,myd88 1,GSM8163704,,tissue:endocardial|cell type:endocardial|genotype:myd88 / |time:96 hpci|geo loc name:missing|collection date:missing,myd88 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts.,endocardial,,RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.,,cell type:endocardial|genotype:myd88 / |time:96 hpci,GSM8163704,GSM8163704: myd88 1; Danio rerio; RNA Seq,GSM8163704 r1,GSM8163704,1,RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP497581,,loader:fastq load.py,myd88_1_1.fq.gz myd88_1_2.fq.gz,fastq fastq,6586212900.0,21954043.0,GSM8163704 r1,0:150 1:150,A:1835825607;C:1467677697;G:1474870953;T:1807740616;N:98027,150,150,,,1835825607,1467677697,1474870953,1807740616,98027,SRX24039368,SRS20832133,SRA1832826,"Bioinformatics, Max-Planck-Institute for Heart and Lung Research","Bioinformatics, Max-Planck-Institute for Heart and Lung Research",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2024-03-25,Undetermined,Undetermined,Heart,Cardiovascular System
31548,SRR28435454,SRX24039367,SRS20832132,SRP497581,PRJNA1091566,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration,GSE262351,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 /  samples,,pubmed:39271818,,WT 3,GSM8163703,,tissue:endocardial|cell type:endocardial|genotype:myd88+/+|time:96 hpci|geo loc name:missing|collection date:missing,WT 3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts.,endocardial,,RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.,,cell type:endocardial|genotype:myd88+/+|time:96 hpci,GSM8163703,GSM8163703: WT 3; Danio rerio; RNA Seq,GSM8163703 r1,GSM8163703,1,RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP497581,,loader:fastq load.py,WT_3_1.fq.gz WT_3_2.fq.gz,fastq fastq,6554345400.0,21847818.0,GSM8163703 r1,0:150 1:150,A:1829151207;C:1459298563;G:1466145928;T:1799650897;N:98805,150,150,,,1829151207,1459298563,1466145928,1799650897,98805,SRX24039367,SRS20832132,SRA1832826,"Bioinformatics, Max-Planck-Institute for Heart and Lung Research","Bioinformatics, Max-Planck-Institute for Heart and Lung Research",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2024-03-25,Undetermined,Undetermined,Heart,Cardiovascular System
31549,SRR28435456,SRX24039366,SRS20832131,SRP497581,PRJNA1091566,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration,GSE262351,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 /  samples,,pubmed:39271818,,WT 2,GSM8163702,,tissue:endocardial|cell type:endocardial|genotype:myd88+/+|time:96 hpci|geo loc name:missing|collection date:missing,WT 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts.,endocardial,,RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.,,cell type:endocardial|genotype:myd88+/+|time:96 hpci,GSM8163702,GSM8163702: WT 2; Danio rerio; RNA Seq,GSM8163702 r1,GSM8163702,1,RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP497581,,loader:fastq load.py,WT_2_1.fq.gz WT_2_2.fq.gz,fastq fastq,6440692500.0,21468975.0,GSM8163702 r1,0:150 1:150,A:1797022330;C:1433189990;G:1440263369;T:1770115464;N:101347,150,150,,,1797022330,1433189990,1440263369,1770115464,101347,SRX24039366,SRS20832131,SRA1832826,"Bioinformatics, Max-Planck-Institute for Heart and Lung Research","Bioinformatics, Max-Planck-Institute for Heart and Lung Research",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2024-03-25,Undetermined,Undetermined,Heart,Cardiovascular System
31550,SRR28435457,SRX24039365,SRS20832130,SRP497581,PRJNA1091566,The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration,GSE262351,Transcriptome Analysis,The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: Aim: Investigation of the MyD88 signaling in endocardial cells during zebrafish cardiac regeneration. Methods: Endocardial cells sorted from the ETkrt4:EGFPsqet33 1A line at 96 hours post cryoinjury hpci. Conditions: 3 myd88+/+ and 3 myd88 /  samples,,pubmed:39271818,,WT 1,GSM8163701,,tissue:endocardial|cell type:endocardial|genotype:myd88+/+|time:96 hpci|geo loc name:missing|collection date:missing,WT 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 109 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Assembly: danRer11 Supplementary files format and content: The tab delimited matrix shows DESeq normalized gene counts.,endocardial,,RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.,,cell type:endocardial|genotype:myd88+/+|time:96 hpci,GSM8163701,GSM8163701: WT 1; Danio rerio; RNA Seq,GSM8163701 r1,GSM8163701,1,RNA was isolated from FACS sorted endocardial cells from a pool of 4 ETkrt4:EGFP; myd88+/+ and 4 ETkrt4:EGFP; myd88 /  ventricles for each sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification. For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification.  The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms  according to effective library concentration and data amount.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP497581,,loader:fastq load.py,WT_1_1.fq.gz WT_1_2.fq.gz,fastq fastq,6343747500.0,21145825.0,GSM8163701 r1,0:150 1:150,A:1783890425;C:1396753566;G:1403241010;T:1759774134;N:88365,150,150,,,1783890425,1396753566,1403241010,1759774134,88365,SRX24039365,SRS20832130,SRA1832826,"Bioinformatics, Max-Planck-Institute for Heart and Lung Research","Bioinformatics, Max-Planck-Institute for Heart and Lung Research",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2024-03-25,Undetermined,Undetermined,Heart,Cardiovascular System
31896,SRR28745432,SRX24311225,SRS21073227,SRP502845,PRJNA1102356,flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response,GSE264406,Transcriptome Analysis,VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.,,pubmed:39612288,,wild type heart  96 hours post cryoinjury 3,GSM8217704,,source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,wild type heart  96 hours post cryoinjury 3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix,heart ventricle border zone and injured area,,A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4µg of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture’s protocol Vazyme.,,tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury,GSM8217704,GSM8217704: wild type heart  96 hours post cryoinjury 3; Danio rerio; RNA Seq,GSM8217704 r1,GSM8217704,1,A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4µg of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP502845,,loader:fastq load.py,E23_4173_Armaad_Lib_WT3_R1.fastq.gz,fastq,3257983192.0,47556048.0,GSM8217704 r1,0:68.51,A:848972796;C:741588101;G:760680137;T:905607069;N:1135089,68,,,,848972796,741588101,760680137,905607069,1135089,SRX24311225,SRS21073227,SRA1849558,MPI for heart and lung research,MPI for heart and lung research,1,0.94185,,0.087,,0.72478,,0.50388,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-04-19,Undetermined,Undetermined,Heart,Cardiovascular System
31897,SRR28745433,SRX24311224,SRS21073229,SRP502845,PRJNA1102356,flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response,GSE264406,Transcriptome Analysis,VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.,,pubmed:39612288,,wild type heart  96 hours post cryoinjury 2,GSM8217703,,source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,wild type heart  96 hours post cryoinjury 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix,heart ventricle border zone and injured area,,A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4µg of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture’s protocol Vazyme.,,tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury,GSM8217703,GSM8217703: wild type heart  96 hours post cryoinjury 2; Danio rerio; RNA Seq,GSM8217703 r1,GSM8217703,1,A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4µg of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP502845,,loader:fastq load.py,E23_4173_Armaad_Lib_WT2_R1.fastq.gz,fastq,3864619254.0,56519751.0,GSM8217703 r1,0:68.38,A:1003402543;C:880721584;G:903469106;T:1075304136;N:1721885,68,,,,1003402543,880721584,903469106,1075304136,1721885,SRX24311224,SRS21073229,SRA1849558,MPI for heart and lung research,MPI for heart and lung research,1,0.93928,,0.08915,,0.72348,,0.49993,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-04-19,Undetermined,Undetermined,Heart,Cardiovascular System
31898,SRR28745434,SRX24311223,SRS21073228,SRP502845,PRJNA1102356,flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response,GSE264406,Transcriptome Analysis,VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.,,pubmed:39612288,,wild type heart  96 hours post cryoinjury 1,GSM8217702,,source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,wild type heart  96 hours post cryoinjury 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix,heart ventricle border zone and injured area,,A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4µg of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture’s protocol Vazyme.,,tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury,GSM8217702,GSM8217702: wild type heart  96 hours post cryoinjury 1; Danio rerio; RNA Seq,GSM8217702 r1,GSM8217702,1,A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4µg of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP502845,,loader:fastq load.py,E23_4173_Armaad_Lib_WT1_R1.fastq.gz,fastq,3571478400.0,52133215.0,GSM8217702 r1,0:68.51,A:928171678;C:814216251;G:835024543;T:992630615;N:1435313,68,,,,928171678,814216251,835024543,992630615,1435313,SRX24311223,SRS21073228,SRA1849558,MPI for heart and lung research,MPI for heart and lung research,1,0.94111,,0.08647,,0.72922,,0.50812,,42,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-04-19,Undetermined,Undetermined,Heart,Cardiovascular System
31899,SRR28745435,SRX24311222,SRS21073226,SRP502845,PRJNA1102356,flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response,GSE264406,Transcriptome Analysis,VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.,,pubmed:39612288,,flt1 mutant heart  96 hours post cryoinjury 3,GSM8217701,,source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,flt1 mutant heart  96 hours post cryoinjury 3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix,heart ventricle border zone and injured area,,A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4µg of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture’s protocol Vazyme.,,tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury,GSM8217701,GSM8217701: flt1 mutant heart  96 hours post cryoinjury 3; Danio rerio; RNA Seq,GSM8217701 r1,GSM8217701,1,A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4µg of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP502845,,loader:fastq load.py,E23_4173_Armaad_Lib_FLT_MUT3_R1.fastq.gz,fastq,4085359270.0,59673604.0,GSM8217701 r1,0:68.46,A:1050667797;C:938174838;G:953989485;T:1140941596;N:1585554,68,,,,1050667797,938174838,953989485,1140941596,1585554,SRX24311222,SRS21073226,SRA1849558,MPI for heart and lung research,MPI for heart and lung research,1,0.94035,,0.08631,,0.72376,,0.49828,,69,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-04-19,Undetermined,Undetermined,Heart,Cardiovascular System
31900,SRR28745436,SRX24311221,SRS21073225,SRP502845,PRJNA1102356,flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response,GSE264406,Transcriptome Analysis,VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.,,pubmed:39612288,,flt1 mutant heart  96 hours post cryoinjury 2,GSM8217700,,source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,flt1 mutant heart  96 hours post cryoinjury 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix,heart ventricle border zone and injured area,,A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4µg of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture’s protocol Vazyme.,,tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury,GSM8217700,GSM8217700: flt1 mutant heart  96 hours post cryoinjury 2; Danio rerio; RNA Seq,GSM8217700 r1,GSM8217700,1,A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4µg of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP502845,,loader:fastq load.py,E23_4173_Armaad_Lib_FLT_MUT2_R1.fastq.gz,fastq,4696922408.0,68645737.0,GSM8217700 r1,0:68.42,A:1220019708;C:1072448104;G:1106194472;T:1296618556;N:1641568,68,,,,1220019708,1072448104,1106194472,1296618556,1641568,SRX24311221,SRS21073225,SRA1849558,MPI for heart and lung research,MPI for heart and lung research,1,0.94205,,0.08792,,0.72543,,0.50566,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-04-19,Undetermined,Undetermined,Heart,Cardiovascular System
31901,SRR28745437,SRX24311220,SRS21073224,SRP502845,PRJNA1102356,flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response,GSE264406,Transcriptome Analysis,VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.,,pubmed:39612288,,flt1 mutant heart  96 hours post cryoinjury 1,GSM8217699,,source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing,flt1 mutant heart  96 hours post cryoinjury 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix,heart ventricle border zone and injured area,,A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4µg of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture’s protocol Vazyme.,,tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury,GSM8217699,GSM8217699: flt1 mutant heart  96 hours post cryoinjury 1; Danio rerio; RNA Seq,GSM8217699 r1,GSM8217699,1,A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4µg of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP502845,,loader:fastq load.py,E23_4173_Armaad_Lib_FLT_MUT1_R1.fastq.gz,fastq,2897934017.0,42657803.0,GSM8217699 r1,0:67.93,A:749045495;C:662930035;G:683478060;T:800853726;N:1626701,67,,,,749045495,662930035,683478060,800853726,1626701,SRX24311220,SRS21073224,SRA1849558,MPI for heart and lung research,MPI for heart and lung research,1,0.94107,,0.08304,,0.72579,,0.50482,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-04-19,Undetermined,Undetermined,Heart,Cardiovascular System
33706,SRR30621736,SRX26043972,SRS22614948,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,wild type 21 dpi sample 2,GSM8506783,,source name:Heart ventricle|tissue:Heart ventricle|genotype:wild type|geo loc name:missing|collection date:missing,wild type 21 dpi sample 2,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:wild type,GSM8506783,GSM8506783: wild type 21 dpi sample 2; Danio rerio; RNA Seq,GSM8506783 r1,GSM8506783,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,wt_21dpi_2_1.fq.gz wt_21dpi_2_2.fq.gz,fastq fastq,7641378600.0,25471262.0,GSM8506783 r1,0:150 1:150,A:2079206538;C:1754420100;G:1752583773;T:2055108610;N:59579,150,150,,,2079206538,1754420100,1752583773,2055108610,59579,SRX26043972,SRS22614948,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33707,SRR30621737,SRX26043971,SRS22614947,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,wild type 21 dpi sample 1,GSM8506782,,source name:Heart ventricle|tissue:Heart ventricle|genotype:wild type|geo loc name:missing|collection date:missing,wild type 21 dpi sample 1,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:wild type,GSM8506782,GSM8506782: wild type 21 dpi sample 1; Danio rerio; RNA Seq,GSM8506782 r1,GSM8506782,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,wt_21dpi_1_1.fq.gz wt_21dpi_1_2.fq.gz,fastq fastq,8663480400.0,28878268.0,GSM8506782 r1,0:150 1:150,A:2358947065;C:1986782909;G:1985349061;T:2332333991;N:67374,150,150,,,2358947065,1986782909,1985349061,2332333991,67374,SRX26043971,SRS22614947,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33708,SRR30621738,SRX26043970,SRS22614946,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,wild type 7 dpi sample 2,GSM8506781,,source name:Heart ventricle|tissue:Heart ventricle|genotype:wild type|geo loc name:missing|collection date:missing,wild type 7 dpi sample 2,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:wild type,GSM8506781,GSM8506781: wild type 7 dpi sample 2; Danio rerio; RNA Seq,GSM8506781 r1,GSM8506781,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,wt_7dpi_2_1.fq.gz wt_7dpi_2_2.fq.gz,fastq fastq,8414243254.0,28200981.0,GSM8506781 r1,0:149.18 1:149.19,A:2273220495;C:1952762066;G:1928310101;T:2259829448;N:121144,149,149,,,2273220495,1952762066,1928310101,2259829448,121144,SRX26043970,SRS22614946,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33709,SRR30621739,SRX26043969,SRS22614945,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,wild type 7 dpi sample 1,GSM8506780,,source name:Heart ventricle|tissue:Heart ventricle|genotype:wild type|geo loc name:missing|collection date:missing,wild type 7 dpi sample 1,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:wild type,GSM8506780,GSM8506780: wild type 7 dpi sample 1; Danio rerio; RNA Seq,GSM8506780 r1,GSM8506780,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,wt_7dpi_1_1.fq.gz wt_7dpi_1_2.fq.gz,fastq fastq,6047075346.0,20278990.0,GSM8506780 r1,0:149.09 1:149.10,A:1633289750;C:1403959505;G:1385683308;T:1624058844;N:83939,149,149,,,1633289750,1403959505,1385683308,1624058844,83939,SRX26043969,SRS22614945,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33710,SRR30621740,SRX26043968,SRS22614944,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,wild type 2 dpi sample 2,GSM8506779,,source name:Heart ventricle|tissue:Heart ventricle|genotype:wild type|geo loc name:missing|collection date:missing,wild type 2 dpi sample 2,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:wild type,GSM8506779,GSM8506779: wild type 2 dpi sample 2; Danio rerio; RNA Seq,GSM8506779 r1,GSM8506779,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,wt_2dpi_2_1.fq.gz wt_2dpi_2_2.fq.gz,fastq fastq,6501507640.0,21847961.0,GSM8506779 r1,0:148.79 1:148.79,A:1751063874;C:1515880337;G:1494689364;T:1739782712;N:91353,148,148,,,1751063874,1515880337,1494689364,1739782712,91353,SRX26043968,SRS22614944,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33711,SRR30621741,SRX26043967,SRS22614943,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,wild type 2 dpi sample 1,GSM8506778,,source name:Heart ventricle|tissue:Heart ventricle|genotype:wild type|geo loc name:missing|collection date:missing,wild type 2 dpi sample 1,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:wild type,GSM8506778,GSM8506778: wild type 2 dpi sample 1; Danio rerio; RNA Seq,GSM8506778 r1,GSM8506778,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,wt_2dpi_1_1.fq.gz wt_2dpi_1_2.fq.gz,fastq fastq,6367687936.0,21382594.0,GSM8506778 r1,0:148.89 1:148.90,A:1717644272;C:1482451492;G:1461128189;T:1706373727;N:90256,148,148,,,1717644272,1482451492,1461128189,1706373727,90256,SRX26043967,SRS22614943,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33712,SRR30621742,SRX26043966,SRS22614942,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,wild type 0 dpi sample 2,GSM8506777,,source name:Heart ventricle|tissue:Heart ventricle|genotype:wild type|geo loc name:missing|collection date:missing,wild type 0 dpi sample 2,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:wild type,GSM8506777,GSM8506777: wild type 0 dpi sample 2; Danio rerio; RNA Seq,GSM8506777 r1,GSM8506777,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,wt_0dpi_2_1.fq.gz wt_0dpi_2_2.fq.gz,fastq fastq,10558249200.0,35194164.0,GSM8506777 r1,0:150 1:150,A:2893792627;C:2407838089;G:2396125046;T:2860411622;N:81816,150,150,,,2893792627,2407838089,2396125046,2860411622,81816,SRX26043966,SRS22614942,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33713,SRR30621743,SRX26043965,SRS22614941,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,wild type 0 dpi sample 1,GSM8506776,,source name:Heart ventricle|tissue:Heart ventricle|genotype:wild type|geo loc name:missing|collection date:missing,wild type 0 dpi sample 1,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:wild type,GSM8506776,GSM8506776: wild type 0 dpi sample 1; Danio rerio; RNA Seq,GSM8506776 r1,GSM8506776,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,wt_0dpi_1_1.fq.gz wt_0dpi_1_2.fq.gz,fastq fastq,10931466600.0,36438222.0,GSM8506776 r1,0:150 1:150,A:2980386716;C:2504687323;G:2500279931;T:2946028049;N:84581,150,150,,,2980386716,2504687323,2500279931,2946028049,84581,SRX26043965,SRS22614941,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33714,SRR30621744,SRX26043964,SRS22614940,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,nr4a1 mutant 21 dpi sample 2,GSM8506775,,source name:Heart ventricle|tissue:Heart ventricle|genotype:nr4a1 mutant|geo loc name:missing|collection date:missing,nr4a1 mutant 21 dpi sample 2,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:nr4a1 mutant,GSM8506775,GSM8506775: nr4a1 mutant 21 dpi sample 2; Danio rerio; RNA Seq,GSM8506775 r1,GSM8506775,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,nr4a1_21_2_1.fq.gz nr4a1_21_2_2.fq.gz,fastq fastq,8089743600.0,26965812.0,GSM8506775 r1,0:150 1:150,A:2204157080;C:1856260728;G:1849823127;T:2179439591;N:63074,150,150,,,2204157080,1856260728,1849823127,2179439591,63074,SRX26043964,SRS22614940,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33715,SRR30621745,SRX26043963,SRS22614939,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,nr4a1 mutant 21 dpi sample 1,GSM8506774,,source name:Heart ventricle|tissue:Heart ventricle|genotype:nr4a1 mutant|geo loc name:missing|collection date:missing,nr4a1 mutant 21 dpi sample 1,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:nr4a1 mutant,GSM8506774,GSM8506774: nr4a1 mutant 21 dpi sample 1; Danio rerio; RNA Seq,GSM8506774 r1,GSM8506774,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,nr4a1_21_1_1.fq.gz nr4a1_21_1_2.fq.gz,fastq fastq,8268177900.0,27560593.0,GSM8506774 r1,0:150 1:150,A:2258410899;C:1890202189;G:1886482508;T:2233018477;N:63827,150,150,,,2258410899,1890202189,1886482508,2233018477,63827,SRX26043963,SRS22614939,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33716,SRR30621746,SRX26043962,SRS22614938,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,nr4a1 mutant 7 dpi sample 2,GSM8506773,,source name:Heart ventricle|tissue:Heart ventricle|genotype:nr4a1 mutant|geo loc name:missing|collection date:missing,nr4a1 mutant 7 dpi sample 2,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:nr4a1 mutant,GSM8506773,GSM8506773: nr4a1 mutant 7 dpi sample 2; Danio rerio; RNA Seq,GSM8506773 r1,GSM8506773,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,nr4a1_7dpi_2_1.fq.gz nr4a1_7dpi_2_2.fq.gz,fastq fastq,5512600871.0,18517476.0,GSM8506773 r1,0:148.84 1:148.85,A:1483061100;C:1285068800;G:1269689220;T:1474711048;N:70703,148,148,,,1483061100,1285068800,1269689220,1474711048,70703,SRX26043962,SRS22614938,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33717,SRR30621747,SRX26043961,SRS22614937,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,nr4a1 mutant 7 dpi sample 1,GSM8506772,,source name:Heart ventricle|tissue:Heart ventricle|genotype:nr4a1 mutant|geo loc name:missing|collection date:missing,nr4a1 mutant 7 dpi sample 1,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:nr4a1 mutant,GSM8506772,GSM8506772: nr4a1 mutant 7 dpi sample 1; Danio rerio; RNA Seq,GSM8506772 r1,GSM8506772,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,nr4a1_7dpi_1_1.fq.gz nr4a1_7dpi_1_2.fq.gz,fastq fastq,6780831475.0,22750295.0,GSM8506772 r1,0:149.03 1:149.03,A:1831140932;C:1575183518;G:1554676178;T:1819734347;N:96500,149,149,,,1831140932,1575183518,1554676178,1819734347,96500,SRX26043961,SRS22614937,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33718,SRR30621748,SRX26043960,SRS22614936,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,nr4a1 mutant 2 dpi sample 2,GSM8506771,,source name:Heart ventricle|tissue:Heart ventricle|genotype:nr4a1 mutant|geo loc name:missing|collection date:missing,nr4a1 mutant 2 dpi sample 2,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:nr4a1 mutant,GSM8506771,GSM8506771: nr4a1 mutant 2 dpi sample 2; Danio rerio; RNA Seq,GSM8506771 r1,GSM8506771,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,nr4a1_2dpi_2_1.fq.gz nr4a1_2dpi_2_2.fq.gz,fastq fastq,6503531797.0,21834092.0,GSM8506771 r1,0:148.93 1:148.93,A:1739648368;C:1527224071;G:1508002505;T:1728567175;N:89678,148,148,,,1739648368,1527224071,1508002505,1728567175,89678,SRX26043960,SRS22614936,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33719,SRR30621749,SRX26043959,SRS22614935,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,nr4a1 mutant 2 dpi sample 1,GSM8506770,,source name:Heart ventricle|tissue:Heart ventricle|genotype:nr4a1 mutant|geo loc name:missing|collection date:missing,nr4a1 mutant 2 dpi sample 1,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:nr4a1 mutant,GSM8506770,GSM8506770: nr4a1 mutant 2 dpi sample 1; Danio rerio; RNA Seq,GSM8506770 r1,GSM8506770,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,nr4a1_2dpi_1_1.fq.gz nr4a1_2dpi_1_2.fq.gz,fastq fastq,5645476838.0,18937309.0,GSM8506770 r1,0:149.05 1:149.06,A:1522889953;C:1312356884;G:1296118643;T:1514035483;N:75875,149,149,,,1522889953,1312356884,1296118643,1514035483,75875,SRX26043959,SRS22614935,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33720,SRR30621750,SRX26043958,SRS22614934,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,nr4a1 mutant 0 dpi sample 2,GSM8506769,,source name:Heart ventricle|tissue:Heart ventricle|genotype:nr4a1 mutant|geo loc name:missing|collection date:missing,nr4a1 mutant 0 dpi sample 2,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:nr4a1 mutant,GSM8506769,GSM8506769: nr4a1 mutant 0 dpi sample 2; Danio rerio; RNA Seq,GSM8506769 r1,GSM8506769,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,nr4a1_0dpi_2_1.fq.gz nr4a1_0dpi_2_2.fq.gz,fastq fastq,9184630800.0,30615436.0,GSM8506769 r1,0:150 1:150,A:2514442400;C:2095585016;G:2092520078;T:2482011445;N:71861,150,150,,,2514442400,2095585016,2092520078,2482011445,71861,SRX26043958,SRS22614934,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
33721,SRR30621751,SRX26043957,SRS22614933,SRP531880,PRJNA1159283,Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish,GSE276850,Transcriptome Analysis,Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.,,,,nr4a1 mutant 0 dpi sample 1,GSM8506768,,source name:Heart ventricle|tissue:Heart ventricle|genotype:nr4a1 mutant|geo loc name:missing|collection date:missing,nr4a1 mutant 0 dpi sample 1,RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample,Heart ventricle,,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,tissue:Heart ventricle|genotype:nr4a1 mutant,GSM8506768,GSM8506768: nr4a1 mutant 0 dpi sample 1; Danio rerio; RNA Seq,GSM8506768 r1,GSM8506768,1,Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP531880,,,nr4a1_0dpi_1_1.fq.gz nr4a1_0dpi_1_2.fq.gz,fastq fastq,9290140800.0,30967136.0,GSM8506768 r1,0:150 1:150,A:2540516970;C:2120755706;G:2115163242;T:2513633143;N:71739,150,150,,,2540516970,2120755706,2115163242,2513633143,71739,SRX26043957,SRS22614933,SRA1968119,The University of North Carolina,The University of North Carolina,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-09-10,Undetermined,Undetermined,Heart,Cardiovascular System
34072,SRR31040127,SRX26425404,SRS22944868,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited UI L004,GSM8581895,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart|geo loc name:missing|collection date:missing,Cited UI L004,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart,GSM8581895,GSM8581895: Cited UI L004; Danio rerio; RNA Seq,GSM8581895 r1,GSM8581895,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L004 R1 001.fastq.gz   read2PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L004 R2 001.fastq.gz   read3PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L004 I1 001.fastq.gz   read4PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L004 I2 001.fastq.gz,pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L004_I1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L004_I2_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L004_R1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L004_R2_001.fastq.gz,fastq fastq fastq fastq,8751034986.0,63413297.0,GSM8581895 r1,0:28 1:90 2:10 3:10,A:1848966031;C:1012706988;G:1157260676;T:1688231038;N:31997,28,90,10,10,1848966031,1012706988,1157260676,1688231038,31997,SRX26425404,SRS22944868,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34073,SRR31040128,SRX26425403,SRS22944867,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited UI L003,GSM8581894,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart|geo loc name:missing|collection date:missing,Cited UI L003,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart,GSM8581894,GSM8581894: Cited UI L003; Danio rerio; RNA Seq,GSM8581894 r1,GSM8581894,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L003 R1 001.fastq.gz   read2PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L003 R2 001.fastq.gz   read3PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L003 I1 001.fastq.gz   read4PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L003 I2 001.fastq.gz,pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L003_I1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L003_I2_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L003_R1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L003_R2_001.fastq.gz,fastq fastq fastq fastq,8965044420.0,64964090.0,GSM8581894 r1,0:28 1:90 2:10 3:10,A:1889187704;C:1042838950;G:1192357586;T:1722353910;N:29950,28,90,10,10,1889187704,1042838950,1192357586,1722353910,29950,SRX26425403,SRS22944867,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34074,SRR31040129,SRX26425402,SRS22944866,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited UI L002,GSM8581893,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart|geo loc name:missing|collection date:missing,Cited UI L002,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart,GSM8581893,GSM8581893: Cited UI L002; Danio rerio; RNA Seq,GSM8581893 r1,GSM8581893,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L002 R1 001.fastq.gz   read2PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L002 R2 001.fastq.gz   read3PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L002 I1 001.fastq.gz   read4PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L002 I2 001.fastq.gz,pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L002_I1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L002_I2_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L002_R1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9234521850.0,66916825.0,GSM8581893 r1,0:28 1:90 2:10 3:10,A:1942032508;C:1074923961;G:1229240783;T:1776284178;N:32820,28,90,10,10,1942032508,1074923961,1229240783,1776284178,32820,SRX26425402,SRS22944866,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34075,SRR31040130,SRX26425401,SRS22944865,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited UI L001,GSM8581892,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart|geo loc name:missing|collection date:missing,Cited UI L001,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:Uninjured heart,GSM8581892,GSM8581892: Cited UI L001; Danio rerio; RNA Seq,GSM8581892 r1,GSM8581892,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L001 R1 001.fastq.gz   read2PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L001 R2 001.fastq.gz   read3PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L001 I1 001.fastq.gz   read4PairFiles=pt38a UI 022323 Tsang GEX LAF4954A26 S11 L001 I2 001.fastq.gz,pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L001_I1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L001_I2_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L001_R1_001.fastq.gz pt38a_UI_022323_Tsang_GEX_LAF4954A26_S11_L001_R2_001.fastq.gz,fastq fastq fastq fastq,9307917288.0,67448676.0,GSM8581892 r1,0:28 1:90 2:10 3:10,A:1956920944;C:1083084138;G:1238610324;T:1791739835;N:25599,28,90,10,10,1956920944,1083084138,1238610324,1791739835,25599,SRX26425401,SRS22944865,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34076,SRR31040131,SRX26425400,SRS22944864,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited 3dpa L004,GSM8581891,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,Cited 3dpa L004,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation,GSM8581891,GSM8581891: Cited 3dpa L004; Danio rerio; RNA Seq,GSM8581891 r1,GSM8581891,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L004 R1 001.fastq.gz   read2PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L004 R2 001.fastq.gz   read3PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L004 I1 001.fastq.gz   read4PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L004 I2 001.fastq.gz,pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L004_I1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L004_I2_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L004_R1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L004_R2_001.fastq.gz,fastq fastq fastq fastq,7170951684.0,51963418.0,GSM8581891 r1,0:28 1:90 2:10 3:10,A:1540735099;C:805699399;G:919379467;T:1410866922;N:26733,28,90,10,10,1540735099,805699399,919379467,1410866922,26733,SRX26425400,SRS22944864,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34077,SRR31040132,SRX26425399,SRS22944863,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited 3dpa L003,GSM8581890,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,Cited 3dpa L003,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation,GSM8581890,GSM8581890: Cited 3dpa L003; Danio rerio; RNA Seq,GSM8581890 r1,GSM8581890,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L003 R1 001.fastq.gz   read2PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L003 R2 001.fastq.gz   read3PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L003 I1 001.fastq.gz   read4PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L003 I2 001.fastq.gz,pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L003_I1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L003_I2_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L003_R1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L003_R2_001.fastq.gz,fastq fastq fastq fastq,7291420716.0,52836382.0,GSM8581890 r1,0:28 1:90 2:10 3:10,A:1561481957;C:822744414;G:938546253;T:1432477210;N:24546,28,90,10,10,1561481957,822744414,938546253,1432477210,24546,SRX26425399,SRS22944863,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34078,SRR31040133,SRX26425398,SRS22944862,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited 3dpa L002,GSM8581889,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,Cited 3dpa L002,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation,GSM8581889,GSM8581889: Cited 3dpa L002; Danio rerio; RNA Seq,GSM8581889 r1,GSM8581889,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L002 R1 001.fastq.gz   read2PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L002 R2 001.fastq.gz   read3PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L002 I1 001.fastq.gz   read4PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L002 I2 001.fastq.gz,pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L002_I1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L002_I2_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L002_R1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq,7477578162.0,54185349.0,GSM8581889 r1,0:28 1:90 2:10 3:10,A:1599788142;C:843874544;G:963283854;T:1469708656;N:26214,28,90,10,10,1599788142,843874544,963283854,1469708656,26214,SRX26425398,SRS22944862,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34079,SRR31040134,SRX26425397,SRS22944861,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,Cited 3dpa L001,GSM8581888,,source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,Cited 3dpa L001,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation,GSM8581888,GSM8581888: Cited 3dpa L001; Danio rerio; RNA Seq,GSM8581888 r1,GSM8581888,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 R1 001.fastq.gz   read2PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 R2 001.fastq.gz   read3PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 I1 001.fastq.gz   read4PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 I2 001.fastq.gz,pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_I1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_I2_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_R1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_R2_001.fastq.gz,fastq fastq fastq fastq,7511701146.0,54432617.0,GSM8581888 r1,0:28 1:90 2:10 3:10,A:1606850913;C:847555151;G:967521409;T:1476987489;N:20568,28,90,10,10,1606850913,847555151,967521409,1476987489,20568,SRX26425397,SRS22944861,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34080,SRR31040135,SRX26425396,SRS22944860,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT UI L004,GSM8581887,,source name:heart|tissue:heart|genotype:WT|treatment:Uninjured heart|geo loc name:missing|collection date:missing,WT UI L004,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:Uninjured heart,GSM8581887,GSM8581887: WT UI L004; Danio rerio; RNA Seq,GSM8581887 r1,GSM8581887,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L004 R1 001.fastq.gz   read2PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L004 R2 001.fastq.gz   read3PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L004 I1 001.fastq.gz   read4PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L004 I2 001.fastq.gz,WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L004_I1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L004_I2_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L004_R1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L004_R2_001.fastq.gz,fastq fastq fastq fastq,8744622816.0,63366832.0,GSM8581887 r1,0:28 1:90 2:10 3:10,A:1804235390;C:1112990195;G:1270205014;T:1515005620;N:578661,28,90,10,10,1804235390,1112990195,1270205014,1515005620,578661,SRX26425396,SRS22944860,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34081,SRR31040136,SRX26425395,SRS22944859,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT UI L003,GSM8581886,,source name:heart|tissue:heart|genotype:WT|treatment:Uninjured heart|geo loc name:missing|collection date:missing,WT UI L003,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:Uninjured heart,GSM8581886,GSM8581886: WT UI L003; Danio rerio; RNA Seq,GSM8581886 r1,GSM8581886,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L003 R1 001.fastq.gz   read2PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L003 R2 001.fastq.gz   read3PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L003 I1 001.fastq.gz   read4PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L003 I2 001.fastq.gz,WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L003_I1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L003_I2_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L003_R1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L003_R2_001.fastq.gz,fastq fastq fastq fastq,8629549722.0,62532969.0,GSM8581886 r1,0:28 1:90 2:10 3:10,A:1780671193;C:1097605584;G:1253098096;T:1495999781;N:592556,28,90,10,10,1780671193,1097605584,1253098096,1495999781,592556,SRX26425395,SRS22944859,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34082,SRR31040137,SRX26425394,SRS22944858,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT UI L002,GSM8581885,,source name:heart|tissue:heart|genotype:WT|treatment:Uninjured heart|geo loc name:missing|collection date:missing,WT UI L002,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:Uninjured heart,GSM8581885,GSM8581885: WT UI L002; Danio rerio; RNA Seq,GSM8581885 r1,GSM8581885,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L002 R1 001.fastq.gz   read2PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L002 R2 001.fastq.gz   read3PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L002 I1 001.fastq.gz   read4PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L002 I2 001.fastq.gz,WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L002_I1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L002_I2_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L002_R1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8810036748.0,63840846.0,GSM8581885 r1,0:28 1:90 2:10 3:10,A:1816298911;C:1122594552;G:1280394245;T:1525799551;N:588881,28,90,10,10,1816298911,1122594552,1280394245,1525799551,588881,SRX26425394,SRS22944858,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34083,SRR31040138,SRX26425393,SRS22944857,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT UI L001,GSM8581884,,source name:heart|tissue:heart|genotype:WT|treatment:Uninjured heart|geo loc name:missing|collection date:missing,WT UI L001,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:Uninjured heart,GSM8581884,GSM8581884: WT UI L001; Danio rerio; RNA Seq,GSM8581884 r1,GSM8581884,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L001 R1 001.fastq.gz   read2PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L001 R2 001.fastq.gz   read3PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L001 I1 001.fastq.gz   read4PairFiles=WTVI 101222 Tsang Multiome GEX LAF3807A40 S24 L001 I2 001.fastq.gz,WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L001_I1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L001_I2_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L001_R1_001.fastq.gz WTVI_101222_Tsang_Multiome_GEX_LAF3807A40_S24_L001_R2_001.fastq.gz,fastq fastq fastq fastq,8890601838.0,64424651.0,GSM8581884 r1,0:28 1:90 2:10 3:10,A:1831803855;C:1133337909;G:1293064278;T:1539489836;N:522712,28,90,10,10,1831803855,1133337909,1293064278,1539489836,522712,SRX26425393,SRS22944857,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34084,SRR31040139,SRX26425392,SRS22944856,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT 3dpa L004,GSM8581883,,source name:heart|tissue:heart|genotype:WT|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,WT 3dpa L004,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:3 dy post amputation,GSM8581883,GSM8581883: WT 3dpa L004; Danio rerio; RNA Seq,GSM8581883 r1,GSM8581883,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L004 R1 001.fastq.gz   read2PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L004 R2 001.fastq.gz   read3PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L004 I1 001.fastq.gz   read4PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L004 I2 001.fastq.gz,WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L004_I1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L004_I2_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L004_R1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L004_R2_001.fastq.gz,fastq fastq fastq fastq,10259680380.0,74345510.0,GSM8581883 r1,0:28 1:90 2:10 3:10,A:2030501498;C:1372342288;G:1610608028;T:1676971327;N:672759,28,90,10,10,2030501498,1372342288,1610608028,1676971327,672759,SRX26425392,SRS22944856,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34085,SRR31040140,SRX26425391,SRS22944855,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT 3dpa L003,GSM8581882,,source name:heart|tissue:heart|genotype:WT|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,WT 3dpa L003,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:3 dy post amputation,GSM8581882,GSM8581882: WT 3dpa L003; Danio rerio; RNA Seq,GSM8581882 r1,GSM8581882,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L003 R1 001.fastq.gz   read2PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L003 R2 001.fastq.gz   read3PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L003 I1 001.fastq.gz   read4PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L003 I2 001.fastq.gz,WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L003_I1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L003_I2_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L003_R1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L003_R2_001.fastq.gz,fastq fastq fastq fastq,10153022940.0,73572630.0,GSM8581882 r1,0:28 1:90 2:10 3:10,A:2010560616;C:1356907781;G:1592695197;T:1660694697;N:678409,28,90,10,10,2010560616,1356907781,1592695197,1660694697,678409,SRX26425391,SRS22944855,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34086,SRR31040141,SRX26425390,SRS22944854,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT 3dpa L002,GSM8581881,,source name:heart|tissue:heart|genotype:WT|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,WT 3dpa L002,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:3 dy post amputation,GSM8581881,GSM8581881: WT 3dpa L002; Danio rerio; RNA Seq,GSM8581881 r1,GSM8581881,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L002 R1 001.fastq.gz   read2PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L002 R2 001.fastq.gz   read3PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L002 I1 001.fastq.gz   read4PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L002 I2 001.fastq.gz,WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L002_I1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L002_I2_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L002_R1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10374062784.0,75174368.0,GSM8581881 r1,0:28 1:90 2:10 3:10,A:2050663376;C:1389631407;G:1629809936;T:1694915558;N:672843,28,90,10,10,2050663376,1389631407,1629809936,1694915558,672843,SRX26425390,SRS22944854,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
34087,SRR31040142,SRX26425389,SRS22944853,SRP539406,PRJNA1174776,cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq],GSE279845,Transcriptome Analysis,Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.,,pubmed:39713454,,WT 3dpa L001,GSM8581880,,source name:heart|tissue:heart|genotype:WT|treatment:3 dy post amputation|geo loc name:missing|collection date:missing,WT 3dpa L001,Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection  aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz   Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz   Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz   Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample.,heart,,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,tissue:heart|genotype:WT|treatment:3 dy post amputation,GSM8581880,GSM8581880: WT 3dpa L001; Danio rerio; RNA Seq,GSM8581880 r1,GSM8581880,1,Uninjured control hearts and 3 dy post amputation dpa were extracted  washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor  PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP539406,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L001 R1 001.fastq.gz   read2PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L001 R2 001.fastq.gz   read3PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L001 I1 001.fastq.gz   read4PairFiles=WT3dpa 101222 Tsang Multiome GEX LAF3807A41 S5 L001 I2 001.fastq.gz,WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L001_I1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L001_I2_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L001_R1_001.fastq.gz WT3dpa_101222_Tsang_Multiome_GEX_LAF3807A41_S5_L001_R2_001.fastq.gz,fastq fastq fastq fastq,10577377770.0,76647665.0,GSM8581880 r1,0:28 1:90 2:10 3:10,A:2089361892;C:1417156705;G:1662751139;T:1728402830;N:617284,28,90,10,10,2089361892,1417156705,1662751139,1728402830,617284,SRX26425389,SRS22944853,SRA1993641,"Cell Biology, University of Pittsburgh","Cell Biology, University of Pittsburgh",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-18,Undetermined,Undetermined,Heart,Cardiovascular System
37134,SRR997335,SRX355601,SRS483796,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Control  rep4,GSM1234963,,source name:Heart  Control|tissue:heart,Heart  Control  rep4,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Control,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234963,GSM1234963: Heart  Control  rep4; Danio rerio; RNA Seq,GSM1234963,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234963,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,C3PO_0053_s_7_sequence.txt.gz,fastq,1111882122.0,28509798.0,GSM1234963 r1,0:39,A:239964076;C:229590501;G:337557042;T:303257677;N:1512826,39,,,,239964076,229590501,337557042,303257677,1512826,SRX355601,SRS483796,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.11195,,0.03776,,0.98871,,0.16576,,39,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37135,SRR997334,SRX355600,SRS483795,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Control  rep3,GSM1234962,,source name:Heart  Control|tissue:heart,Heart  Control  rep3,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Control,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234962,GSM1234962: Heart  Control  rep3; Danio rerio; RNA Seq,GSM1234962,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234962,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,C3PO_0053_s_6_sequence.txt.gz,fastq,1221305046.0,31315514.0,GSM1234962 r1,0:39,A:263520584;C:251263128;G:372262308;T:332218529;N:2040497,39,,,,263520584,251263128,372262308,332218529,2040497,SRX355600,SRS483795,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.11552,,0.03865,,0.98679,,0.1927,,39,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37136,SRR997333,SRX355599,SRS483794,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Control  rep2,GSM1234961,,source name:Heart  Control|tissue:heart,Heart  Control  rep2,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Control,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234961,GSM1234961: Heart  Control  rep2; Danio rerio; RNA Seq,GSM1234961,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234961,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,R2D2_0122_s_7_sequence.txt.gz,fastq,1462542939.0,37501101.0,GSM1234961 r1,0:39,A:313173840;C:298865755;G:440814004;T:409066990;N:622350,39,,,,313173840,298865755,440814004,409066990,622350,SRX355599,SRS483794,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.01745,,0.00554,,0.99101,,0.42928,,39,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37137,SRR997332,SRX355598,SRS483793,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Control  rep1,GSM1234960,,source name:Heart  Control|tissue:heart,Heart  Control  rep1,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Control,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234960,GSM1234960: Heart  Control  rep1; Danio rerio; RNA Seq,GSM1234960,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234960,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,R2D2_0122_s_6_sequence.txt.gz,fastq,1447346355.0,37111445.0,GSM1234960 r1,0:39,A:311132663;C:297266985;G:441400778;T:396960907;N:585022,39,,,,311132663,297266985,441400778,396960907,585022,SRX355598,SRS483793,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.06118,,0.01997,,0.98752,,0.43741,,39,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37138,SRR997331,SRX355597,SRS483792,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Resected  rep4,GSM1234959,,source name:Heart  Resected|tissue:heart,Heart  Resected  rep4,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Resected,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234959,GSM1234959: Heart  Resected  rep4; Danio rerio; RNA Seq,GSM1234959,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234959,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,C3PO_0053_s_5_sequence.txt.gz,fastq,703519557.0,18038963.0,GSM1234959 r1,0:39,A:142685665;C:144259439;G:215526965;T:199924689;N:1122799,39,,,,142685665,144259439,215526965,199924689,1122799,SRX355597,SRS483792,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.00172,,0.00045,,0.99738,,0.34873,,39,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37139,SRR997330,SRX355596,SRS483791,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Resected  rep3,GSM1234958,,source name:Heart  Resected|tissue:heart,Heart  Resected  rep3,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Resected,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234958,GSM1234958: Heart  Resected  rep3; Danio rerio; RNA Seq,GSM1234958,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234958,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,C3PO_0053_s_4_sequence.txt.gz,fastq,918978177.0,23563543.0,GSM1234958 r1,0:39,A:188056254;C:191217660;G:283318445;T:255042736;N:1343082,39,,,,188056254,191217660,283318445,255042736,1343082,SRX355596,SRS483791,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.09453,,0.03085,,0.98559,,0.18337,,39,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37140,SRR997329,SRX355595,SRS483789,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Resected  rep2,GSM1234957,,source name:Heart  Resected|tissue:heart,Heart  Resected  rep2,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Resected,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234957,GSM1234957: Heart  Resected  rep2; Danio rerio; RNA Seq,GSM1234957,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234957,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,R2D2_0122_s_5_sequence.txt.gz,fastq,1420874247.0,36432673.0,GSM1234957 r1,0:39,A:290914118;C:295973738;G:440368910;T:393019696;N:597785,39,,,,290914118,295973738,440368910,393019696,597785,SRX355595,SRS483789,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.00472,,0.00131,,0.99431,,0.42832,,39,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
37141,SRR997328,SRX355594,SRS483790,SRP030036,PRJNA219641,Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways,GSE51018,Transcriptome Analysis,The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition,parent bioproject:PRJNA219631,pubmed:26857418,,Heart  Resected  rep1,GSM1234956,,source name:Heart  Resected|tissue:heart,Heart  Resected  rep1,Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format,Heart  Resected,,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,,tissue:heart,GSM1234956,GSM1234956: Heart  Resected  rep1; Danio rerio; RNA Seq,GSM1234956,,1,Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001,GEO Accession:GSM1234956,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP030036,,,C3PO_0054_s_8_sequence.txt.gz,fastq,1073339514.0,27521526.0,GSM1234956 r1,0:39,A:223670054;C:219603945;G:328718329;T:300891777;N:455409,39,,,,223670054,219603945,328718329,300891777,455409,SRX355594,SRS483790,SRA101779,GEO,"Vital-IT, SIB Swiss Institute of Bioinformatics",1,0.05133,,0.01643,,0.9893,,0.25792,,39,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,bulk,bulk,,Switzerland,2013-09-19,Undetermined,Undetermined,Heart,Cardiovascular System
39937,SRR2532445,SRX1293418,SRS1094785,SRP064261,PRJNA297221,Heart Chamber Evolution Reveals Roles of Gene/Genome Duplications on Continuous Character Evolution in Vertebrates,GSE73522,Other,We sequenced at mRNA level in adult hearts of zebrafish  pamprey and sea squirt. Combined with other 11 vertebrate heart RNA Seq data online  we conducted comprehensive evolutionary genomic analyses to address the contribution of gene/genome duplications on heart structure evolution. We observed that number of duplicate genes expressed in heart increased gradually with the increase of heart chamber number along the vertebrate phylogeny  despite that most of them were duplicated at the time near to the origin of vertebrates or more ancient. Our research provides a clear cut example to show the relationship among gene duplication  continuous character evolution like heart structure evolution and nature selection. Overall design: Examination of mRNA levels in thirteen vertebrate samples with different cardiac chamber number  and one invertebrate sea squirt.,,,,DRE mix 02,GSM1897224,,source name:Heart|tissue:Heart,DRE mix 02,The libraries were sequenced as paired end 100 bases using the HiSeq2000 Illumina Casava1.7 software used for basecalling. FastQC v0.10.1 was used to assess the quality of reads.then the raw reads were processed by using the FastX Toolkit v0.0.13. All processed reads were aligned to reference genome using TopHat v2.0.10 Kim et al. 2013 and bowtie2 v2.1.0 Langmead and Salzberg 2012 The unique mapped reads were assembled and the expression level of a gene were calculated as FPKM Fragments Per Kilobase of transcript per Million mapped reads using cufflinks v2.1.1 Trapnell et al. 2010 Genome build: KH Genome build: Pmarinus7.0 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,Heart,,All dissected heart tissues were stored in RNAlater Ambion before processing. Total RNA was extracted using the Trizol Invitrogen. following the manufacturer’s protocol. RNA quality was monitored using Narodrop 2000. The cDNA libraries were constructed according to the standard Illumina protocols.,,tissue:Heart,GSM1897224,GSM1897224: DRE mix 02; Danio rerio; RNA Seq,GSM1897224,,1,All dissected heart tissues were stored in RNAlater Ambion before processing. Total RNA was extracted using the Trizol Invitrogen. following the manufacturer’s protocol. RNA quality was monitored using Narodrop 2000. The cDNA libraries were constructed according to the standard Illumina protocols.,GEO Accession:GSM1897224,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP064261,,,XIN_R1_001.fastq.bz2 XIN_R2_001.fastq.bz2,fastq fastq,3846233924.0,19040762.0,GSM1897224 r1,0:101 1:101,A:1013374196;C:876654183;G:885048319;T:1029455120;N:41702106,101,101,,,1013374196,876654183,885048319,1029455120,41702106,SRX1293418,SRS1094785,SRA301217,GEO,"School of life science, Fudan univeristy",2,0.92587,0.93169,0.13736,0.13738,0.77697,0.77404,0.53305,0.5358,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2015-09-28,Undetermined,Undetermined,Heart,Cardiovascular System
40219,SRR3143916,SRX1474053,SRS1200114,SRP067229,PRJNA305621,Modulation of tissue repair by regeneration enhancer elements.,GSE75894,Other,We compared transcriptional and chromatin profiles of regenerating zebrafish hearts following genetic ablation with profiles from uninjured zebrafish hearts. Overall design: Examination of whole heart transcriptional profiles from ablated hearts 2 pools of 10 hearts and uninjured hearts 2 pools of 10 hearts. Examination of differential H3K27Ac marks following genetic ablation of cardiomyocytes regenerating hearts and uninjured hearts.,,pubmed:27049946,,ZF Uninjured Hearts 2 PG 2,GSM1969523,,tissue:Whole uninjured hearts|strain:EK/AB|line:gbactin2:loxP mCherry STOP loxP DTA176; cmlc2:CreER|treatment:Propylene glycol,ZF Uninjured Hearts 2 PG 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Reads cpms.txt"" is tab delimited text file.  CPMs were calculated using edgeR. Supplementary files format and content: ""Raw read counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Whole uninjured hearts,Animals were treated with Tamoxifen of propylene glycol,Hearts were collected 7 days post treatment.  10 ventricles were dissected  rinsed in heparin  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK/AB|line:gbactin2:loxP mCherry STOP loxP DTA176; cmlc2:CreER|treatment:Propylene glycol,GSM1969523,GSM1969523: ZF Uninjured Hearts 2 PG 2; Danio rerio; RNA Seq,GSM1969523,,1,Hearts were collected 7 days post treatment.  10 ventricles were dissected  rinsed in heparin  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM1969523,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP067229,,,PG2_TGACCA_L005_R1.gz,fastq,2681585050.0,53631701.0,GSM1969523 r11,0:50,A:725724149;C:626158732;G:607690303;T:721904776;N:107090,50,,,,725724149,626158732,607690303,721904776,107090,SRX1474053,SRS1200114,SRA316081,GEO,"Poss, Cell Biology, Duke",1,0.9015,,0.07041,,0.7625,,0.50968,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2015-12-10,Undetermined,Undetermined,Heart,Cardiovascular System
40220,SRR3143899,SRX1474052,SRS1200115,SRP067229,PRJNA305621,Modulation of tissue repair by regeneration enhancer elements.,GSE75894,Other,We compared transcriptional and chromatin profiles of regenerating zebrafish hearts following genetic ablation with profiles from uninjured zebrafish hearts. Overall design: Examination of whole heart transcriptional profiles from ablated hearts 2 pools of 10 hearts and uninjured hearts 2 pools of 10 hearts. Examination of differential H3K27Ac marks following genetic ablation of cardiomyocytes regenerating hearts and uninjured hearts.,,pubmed:27049946,,ZF Uninjured Hearts 1 PG 1,GSM1969522,,tissue:Whole uninjured hearts|strain:EK/AB|line:gbactin2:loxP mCherry STOP loxP DTA176; cmlc2:CreER|treatment:Propylene glycol,ZF Uninjured Hearts 1 PG 1,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Reads cpms.txt"" is tab delimited text file.  CPMs were calculated using edgeR. Supplementary files format and content: ""Raw read counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Whole uninjured hearts,Animals were treated with Tamoxifen of propylene glycol,Hearts were collected 7 days post treatment.  10 ventricles were dissected  rinsed in heparin  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK/AB|line:gbactin2:loxP mCherry STOP loxP DTA176; cmlc2:CreER|treatment:Propylene glycol,GSM1969522,GSM1969522: ZF Uninjured Hearts 1 PG 1; Danio rerio; RNA Seq,GSM1969522,,1,Hearts were collected 7 days post treatment.  10 ventricles were dissected  rinsed in heparin  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM1969522,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP067229,,,PG1_CGATGT_L005_R1.gz,fastq,2488196150.0,49763923.0,GSM1969522 r11,0:50,A:665282679;C:588643091;G:571791112;T:662380843;N:98425,50,,,,665282679,588643091,571791112,662380843,98425,SRX1474052,SRS1200115,SRA316081,GEO,"Poss, Cell Biology, Duke",1,0.91067,,0.07205,,0.74864,,0.496,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2015-12-10,Undetermined,Undetermined,Heart,Cardiovascular System
40221,SRR3143897,SRX1474051,SRS1200116,SRP067229,PRJNA305621,Modulation of tissue repair by regeneration enhancer elements.,GSE75894,Other,We compared transcriptional and chromatin profiles of regenerating zebrafish hearts following genetic ablation with profiles from uninjured zebrafish hearts. Overall design: Examination of whole heart transcriptional profiles from ablated hearts 2 pools of 10 hearts and uninjured hearts 2 pools of 10 hearts. Examination of differential H3K27Ac marks following genetic ablation of cardiomyocytes regenerating hearts and uninjured hearts.,,pubmed:27049946,,ZF Ablated Hearts 2 TAM 2,GSM1969521,,tissue:Whole hearts 7d post ablation|strain:EK/AB|line:gbactin2:loxP mCherry STOP loxP DTA176; cmlc2:CreER|treatment:Tamoxifen,ZF Ablated Hearts 2 TAM 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Reads cpms.txt"" is tab delimited text file.  CPMs were calculated using edgeR. Supplementary files format and content: ""Raw read counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Whole hearts 7d post ablation,Animals were treated with Tamoxifen of propylene glycol,Hearts were collected 7 days post treatment.  10 ventricles were dissected  rinsed in heparin  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK/AB|line:gbactin2:loxP mCherry STOP loxP DTA176; cmlc2:CreER|treatment:Tamoxifen,GSM1969521,GSM1969521: ZF Ablated Hearts 2 TAM 2; Danio rerio; RNA Seq,GSM1969521,,1,Hearts were collected 7 days post treatment.  10 ventricles were dissected  rinsed in heparin  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM1969521,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP067229,,,TAM2_CCGTCC_L005_R1.gz,fastq,2751574250.0,55031485.0,GSM1969521 r11,0:50,A:748951871;C:632985067;G:617593198;T:751936222;N:107892,50,,,,748951871,632985067,617593198,751936222,107892,SRX1474051,SRS1200116,SRA316081,GEO,"Poss, Cell Biology, Duke",1,0.90799,,0.09785,,0.72799,,0.49426,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2015-12-10,Undetermined,Undetermined,Heart,Cardiovascular System
40222,SRR3143894,SRX1474050,SRS1200117,SRP067229,PRJNA305621,Modulation of tissue repair by regeneration enhancer elements.,GSE75894,Other,We compared transcriptional and chromatin profiles of regenerating zebrafish hearts following genetic ablation with profiles from uninjured zebrafish hearts. Overall design: Examination of whole heart transcriptional profiles from ablated hearts 2 pools of 10 hearts and uninjured hearts 2 pools of 10 hearts. Examination of differential H3K27Ac marks following genetic ablation of cardiomyocytes regenerating hearts and uninjured hearts.,,pubmed:27049946,,ZF Ablated Hearts 1 TAM 1,GSM1969520,,tissue:Whole hearts 7d post ablation|strain:EK/AB|line:gbactin2:loxP mCherry STOP loxP DTA176; cmlc2:CreER|treatment:Tamoxifen,ZF Ablated Hearts 1 TAM 1,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Reads cpms.txt"" is tab delimited text file.  CPMs were calculated using edgeR. Supplementary files format and content: ""Raw read counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Whole hearts 7d post ablation,Animals were treated with Tamoxifen of propylene glycol,Hearts were collected 7 days post treatment.  10 ventricles were dissected  rinsed in heparin  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK/AB|line:gbactin2:loxP mCherry STOP loxP DTA176; cmlc2:CreER|treatment:Tamoxifen,GSM1969520,GSM1969520: ZF Ablated Hearts 1 TAM 1; Danio rerio; RNA Seq,GSM1969520,,1,Hearts were collected 7 days post treatment.  10 ventricles were dissected  rinsed in heparin  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM1969520,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP067229,,,TAM1_CAGATC_L005_R1.gz,fastq,3034608900.0,60692178.0,GSM1969520 r11,0:50,A:815498699;C:710279561;G:693267187;T:815442579;N:120874,50,,,,815498699,710279561,693267187,815442579,120874,SRX1474050,SRS1200117,SRA316081,GEO,"Poss, Cell Biology, Duke",1,0.90708,,0.09274,,0.72234,,0.49758,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2015-12-10,Undetermined,Undetermined,Heart,Cardiovascular System
41988,SRR5366723,SRX2661991,SRS2063957,SRP102311,PRJNA380129,H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [RNA seq],GSE96929,Transcriptome Analysis,We identify the global transcriptional changes that occur between homeostatic and proliferative cardiomyocytes in the zebrafish heart and uncover an essential role for H3K27me3 deposition in facilitating successful myocardial regeneration.  Specifically  we learned that cardiomyocyte proliferation is accompanied by downregulation of sarcomeric and cytoskeletal components and upregulation of the polycomb methylase Ezh2. Using ChIPseq  we demonstrate that this transcriptional repression is associated with deposition of new H3K27me3 modifications over the promoters. Using new genetic zebrafish lines that allow for inducible and cardiomyocyte specific expression of a mutant form of histone 3 that is unable to be tri methylated on lysine 27 H3.3K27M  we discovered that addition of H3K27me3 marks is essential for cardiac regeneration in vivo. Earlier in the regenerative window  we found that H3.3K27M–expressing wound edge cardiomyocytes aberrantly maintain homeostatic levels of sarcomeric and actomyosin gene expression and show significant retention of sarcomere structure. While DNA replication occurs normally in these H3.3K27M cardiomyocytes  we observed significant increases in cardiomyocyte nucleation  a phenotype indicative of cytokinesis failures. In addition  nuclear density at the wound edge increases as new cardiomyocytes fail to colonize the injured area. Together  our study reveals that production of new cardiomyocytes and their infiltration into the injured region relies on H3K27me3 mediated sarcomeric and actomyosin cytoskeletal gene repression. Overall design: Transcriptional profiling RNA seq of regenerting versus uninjured FACS purified cardiomyocytes from zebrafish ventricle apexes in triplicates,parent bioproject:PRJNA380125,pubmed:31427288,,Regenerating cardiomyocytes rep3,GSM2546213,,source name:Cardiac ventricle tissue|tissue:Cardiac ventricle apex|strain:Gata4:GFP|batch:5 days post ventricular apex resection,Regenerating cardiomyocytes rep3,Reads from three replicates of uninjured “uninjured” and 5 xxx post injury “5 dpa” heart samples were aligned against the GRCz10 genome assembly of the Zebrafish  ENSEMBL 89 annotation using STAR v. 2.5.3a in paired end mode with parameters   runThreadN 16   runMode alignReads   outFilterType BySJout    outFilterMultimapNmax 20   alignSJoverhangMin 8   alignSJDBoverhangMin 1    outFilterMismatchNmax 999   alignIntronMin 10   alignIntronMax 1000000    alignMatesGapMax 1000000   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM . The resulting Aligned.toTranscriptome.out.bam files were postprocessed using RSEM v. 1.3.0 using following flags   paired end   calc ci   alignments  p 8   forward prob 0. Posterior mean estimates of counts  RPKM and TPM were retrieved for each gene in each sample. Differential expression analysis between uninjured and 5 dpa samples was performed using DESeq2 in the R statistical environment v. 3.3.3 on protein coding genes according to ENSEMBL’s biotype assignments. Supplementary files format and content csv files are a DEseq2 estimations of changes in read density of protein coding genes according to ENSEMBL release 89’s biotype assignments between experimental groups. Supplementary files format and content: IGVtools utility 'count' was used on aligned bam files to compute the average alignment over 164 base windows across the genome and generate binary tiled data .tdf files Thorvaldsdottir et al. 2013.,Cardiac ventricle tissue,,Ventricle apexes were removed and cleared of injury tissue  then dissociated using the Miltenyi neonate heart dissociation kit  pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS sorted directly into RLT lysis buffer RNeasy micro prep RNA extraction kit  Qiagen. RNA integrity and concentration were checked on a Fragment Analyzer Advanced Analytical.  cDNA samples were generated using the Ovation low input v2 kit Nugen according to the manufacturer’s.  The resulting cDNA samples were then end repaired and adaptor ligated using the SPRI works Fragment Library System I Beckman Coulter Genomics and indexed during amplification. Libraries were quantified using the Fragment Analyzer Advanced Analytical and qPCR before being loaded for paired end sequencing 2X40 nt using the Illumina HiSeq 2000.,,tissue:Cardiac ventricle apex|strain:Gata4:GFP|batch:5 days post ventricular apex resection,GSM2546213,GSM2546213: Regenerating cardiomyocytes rep3; Danio rerio; RNA Seq,GSM2546213,,1,Ventricle apexes were removed and cleared of injury tissue  then dissociated using the Miltenyi neonate heart dissociation kit  pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS sorted directly into RLT lysis buffer RNeasy micro prep RNA extraction kit  Qiagen. RNA samples were prepared according to Qiagen protocol  cDNA libraries were generated and sequenced on an Illumina HiSeq 2000 RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2546213,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102311,,,Gata4amp3_end2.fq.gz Gata4amp3_end1.fq.gz,fastq fastq,2164398118.0,26395099.0,GSM2546213 r1,0:41 1:41,A:614270825;C:442298077;G:457720882;T:644864528;N:5243806,41,41,,,614270825,442298077,457720882,644864528,5243806,SRX2661991,SRS2063957,SRA548505,GEO,"Caroline Burns, CVRC, MGH",2,0.83674,0.87137,0.20355,0.21294,0.78344,0.77934,0.66919,0.67047,41,41,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-22,Undetermined,Undetermined,Heart,Cardiovascular System
41989,SRR5366722,SRX2661990,SRS2063956,SRP102311,PRJNA380129,H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [RNA seq],GSE96929,Transcriptome Analysis,We identify the global transcriptional changes that occur between homeostatic and proliferative cardiomyocytes in the zebrafish heart and uncover an essential role for H3K27me3 deposition in facilitating successful myocardial regeneration.  Specifically  we learned that cardiomyocyte proliferation is accompanied by downregulation of sarcomeric and cytoskeletal components and upregulation of the polycomb methylase Ezh2. Using ChIPseq  we demonstrate that this transcriptional repression is associated with deposition of new H3K27me3 modifications over the promoters. Using new genetic zebrafish lines that allow for inducible and cardiomyocyte specific expression of a mutant form of histone 3 that is unable to be tri methylated on lysine 27 H3.3K27M  we discovered that addition of H3K27me3 marks is essential for cardiac regeneration in vivo. Earlier in the regenerative window  we found that H3.3K27M–expressing wound edge cardiomyocytes aberrantly maintain homeostatic levels of sarcomeric and actomyosin gene expression and show significant retention of sarcomere structure. While DNA replication occurs normally in these H3.3K27M cardiomyocytes  we observed significant increases in cardiomyocyte nucleation  a phenotype indicative of cytokinesis failures. In addition  nuclear density at the wound edge increases as new cardiomyocytes fail to colonize the injured area. Together  our study reveals that production of new cardiomyocytes and their infiltration into the injured region relies on H3K27me3 mediated sarcomeric and actomyosin cytoskeletal gene repression. Overall design: Transcriptional profiling RNA seq of regenerting versus uninjured FACS purified cardiomyocytes from zebrafish ventricle apexes in triplicates,parent bioproject:PRJNA380125,pubmed:31427288,,Regenerating cardiomyocytes rep2,GSM2546212,,source name:Cardiac ventricle tissue|tissue:Cardiac ventricle apex|strain:Gata4:GFP|batch:5 days post ventricular apex resection,Regenerating cardiomyocytes rep2,Reads from three replicates of uninjured “uninjured” and 5 xxx post injury “5 dpa” heart samples were aligned against the GRCz10 genome assembly of the Zebrafish  ENSEMBL 89 annotation using STAR v. 2.5.3a in paired end mode with parameters   runThreadN 16   runMode alignReads   outFilterType BySJout    outFilterMultimapNmax 20   alignSJoverhangMin 8   alignSJDBoverhangMin 1    outFilterMismatchNmax 999   alignIntronMin 10   alignIntronMax 1000000    alignMatesGapMax 1000000   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM . The resulting Aligned.toTranscriptome.out.bam files were postprocessed using RSEM v. 1.3.0 using following flags   paired end   calc ci   alignments  p 8   forward prob 0. Posterior mean estimates of counts  RPKM and TPM were retrieved for each gene in each sample. Differential expression analysis between uninjured and 5 dpa samples was performed using DESeq2 in the R statistical environment v. 3.3.3 on protein coding genes according to ENSEMBL’s biotype assignments. Supplementary files format and content csv files are a DEseq2 estimations of changes in read density of protein coding genes according to ENSEMBL release 89’s biotype assignments between experimental groups. Supplementary files format and content: IGVtools utility 'count' was used on aligned bam files to compute the average alignment over 164 base windows across the genome and generate binary tiled data .tdf files Thorvaldsdottir et al. 2013.,Cardiac ventricle tissue,,Ventricle apexes were removed and cleared of injury tissue  then dissociated using the Miltenyi neonate heart dissociation kit  pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS sorted directly into RLT lysis buffer RNeasy micro prep RNA extraction kit  Qiagen. RNA integrity and concentration were checked on a Fragment Analyzer Advanced Analytical.  cDNA samples were generated using the Ovation low input v2 kit Nugen according to the manufacturer’s.  The resulting cDNA samples were then end repaired and adaptor ligated using the SPRI works Fragment Library System I Beckman Coulter Genomics and indexed during amplification. Libraries were quantified using the Fragment Analyzer Advanced Analytical and qPCR before being loaded for paired end sequencing 2X40 nt using the Illumina HiSeq 2000.,,tissue:Cardiac ventricle apex|strain:Gata4:GFP|batch:5 days post ventricular apex resection,GSM2546212,GSM2546212: Regenerating cardiomyocytes rep2; Danio rerio; RNA Seq,GSM2546212,,1,Ventricle apexes were removed and cleared of injury tissue  then dissociated using the Miltenyi neonate heart dissociation kit  pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS sorted directly into RLT lysis buffer RNeasy micro prep RNA extraction kit  Qiagen. RNA samples were prepared according to Qiagen protocol  cDNA libraries were generated and sequenced on an Illumina HiSeq 2000 RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2546212,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102311,,,Gata4amp2_end2.fq.gz Gata4amp2_end1.fq.gz,fastq fastq,2280765302.0,27814211.0,GSM2546212 r1,0:41 1:41,A:646461485;C:474632198;G:485498105;T:668669215;N:5504299,41,41,,,646461485,474632198,485498105,668669215,5504299,SRX2661990,SRS2063956,SRA548505,GEO,"Caroline Burns, CVRC, MGH",2,0.83265,0.87094,0.2154,0.2264,0.7791,0.77619,0.50816,0.64801,41,41,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-22,Undetermined,Undetermined,Heart,Cardiovascular System
41990,SRR5366721,SRX2661989,SRS2063955,SRP102311,PRJNA380129,H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [RNA seq],GSE96929,Transcriptome Analysis,We identify the global transcriptional changes that occur between homeostatic and proliferative cardiomyocytes in the zebrafish heart and uncover an essential role for H3K27me3 deposition in facilitating successful myocardial regeneration.  Specifically  we learned that cardiomyocyte proliferation is accompanied by downregulation of sarcomeric and cytoskeletal components and upregulation of the polycomb methylase Ezh2. Using ChIPseq  we demonstrate that this transcriptional repression is associated with deposition of new H3K27me3 modifications over the promoters. Using new genetic zebrafish lines that allow for inducible and cardiomyocyte specific expression of a mutant form of histone 3 that is unable to be tri methylated on lysine 27 H3.3K27M  we discovered that addition of H3K27me3 marks is essential for cardiac regeneration in vivo. Earlier in the regenerative window  we found that H3.3K27M–expressing wound edge cardiomyocytes aberrantly maintain homeostatic levels of sarcomeric and actomyosin gene expression and show significant retention of sarcomere structure. While DNA replication occurs normally in these H3.3K27M cardiomyocytes  we observed significant increases in cardiomyocyte nucleation  a phenotype indicative of cytokinesis failures. In addition  nuclear density at the wound edge increases as new cardiomyocytes fail to colonize the injured area. Together  our study reveals that production of new cardiomyocytes and their infiltration into the injured region relies on H3K27me3 mediated sarcomeric and actomyosin cytoskeletal gene repression. Overall design: Transcriptional profiling RNA seq of regenerting versus uninjured FACS purified cardiomyocytes from zebrafish ventricle apexes in triplicates,parent bioproject:PRJNA380125,pubmed:31427288,,Regenerating cardiomyocytes rep1,GSM2546211,,source name:Cardiac ventricle tissue|tissue:Cardiac ventricle apex|strain:Gata4:GFP|batch:5 days post ventricular apex resection,Regenerating cardiomyocytes rep1,Reads from three replicates of uninjured “uninjured” and 5 xxx post injury “5 dpa” heart samples were aligned against the GRCz10 genome assembly of the Zebrafish  ENSEMBL 89 annotation using STAR v. 2.5.3a in paired end mode with parameters   runThreadN 16   runMode alignReads   outFilterType BySJout    outFilterMultimapNmax 20   alignSJoverhangMin 8   alignSJDBoverhangMin 1    outFilterMismatchNmax 999   alignIntronMin 10   alignIntronMax 1000000    alignMatesGapMax 1000000   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM . The resulting Aligned.toTranscriptome.out.bam files were postprocessed using RSEM v. 1.3.0 using following flags   paired end   calc ci   alignments  p 8   forward prob 0. Posterior mean estimates of counts  RPKM and TPM were retrieved for each gene in each sample. Differential expression analysis between uninjured and 5 dpa samples was performed using DESeq2 in the R statistical environment v. 3.3.3 on protein coding genes according to ENSEMBL’s biotype assignments. Supplementary files format and content csv files are a DEseq2 estimations of changes in read density of protein coding genes according to ENSEMBL release 89’s biotype assignments between experimental groups. Supplementary files format and content: IGVtools utility 'count' was used on aligned bam files to compute the average alignment over 164 base windows across the genome and generate binary tiled data .tdf files Thorvaldsdottir et al. 2013.,Cardiac ventricle tissue,,Ventricle apexes were removed and cleared of injury tissue  then dissociated using the Miltenyi neonate heart dissociation kit  pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS sorted directly into RLT lysis buffer RNeasy micro prep RNA extraction kit  Qiagen. RNA integrity and concentration were checked on a Fragment Analyzer Advanced Analytical.  cDNA samples were generated using the Ovation low input v2 kit Nugen according to the manufacturer’s.  The resulting cDNA samples were then end repaired and adaptor ligated using the SPRI works Fragment Library System I Beckman Coulter Genomics and indexed during amplification. Libraries were quantified using the Fragment Analyzer Advanced Analytical and qPCR before being loaded for paired end sequencing 2X40 nt using the Illumina HiSeq 2000.,,tissue:Cardiac ventricle apex|strain:Gata4:GFP|batch:5 days post ventricular apex resection,GSM2546211,GSM2546211: Regenerating cardiomyocytes rep1; Danio rerio; RNA Seq,GSM2546211,,1,Ventricle apexes were removed and cleared of injury tissue  then dissociated using the Miltenyi neonate heart dissociation kit  pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS sorted directly into RLT lysis buffer RNeasy micro prep RNA extraction kit  Qiagen. RNA samples were prepared according to Qiagen protocol  cDNA libraries were generated and sequenced on an Illumina HiSeq 2000 RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2546211,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102311,,,Gata4amp1_end1.fq.gz Gata4amp1_end2.fq.gz,fastq fastq,1919737670.0,23411435.0,GSM2546211 r1,0:41 1:41,A:521670886;C:396329368;G:428464939;T:568620569;N:4651908,41,41,,,521670886,396329368,428464939,568620569,4651908,SRX2661989,SRS2063955,SRA548505,GEO,"Caroline Burns, CVRC, MGH",2,0.76997,0.78605,0.25141,0.25939,0.79801,0.79728,0.67952,0.67908,41,41,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-22,Undetermined,Undetermined,Heart,Cardiovascular System
41991,SRR5366720,SRX2661988,SRS2063954,SRP102311,PRJNA380129,H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [RNA seq],GSE96929,Transcriptome Analysis,We identify the global transcriptional changes that occur between homeostatic and proliferative cardiomyocytes in the zebrafish heart and uncover an essential role for H3K27me3 deposition in facilitating successful myocardial regeneration.  Specifically  we learned that cardiomyocyte proliferation is accompanied by downregulation of sarcomeric and cytoskeletal components and upregulation of the polycomb methylase Ezh2. Using ChIPseq  we demonstrate that this transcriptional repression is associated with deposition of new H3K27me3 modifications over the promoters. Using new genetic zebrafish lines that allow for inducible and cardiomyocyte specific expression of a mutant form of histone 3 that is unable to be tri methylated on lysine 27 H3.3K27M  we discovered that addition of H3K27me3 marks is essential for cardiac regeneration in vivo. Earlier in the regenerative window  we found that H3.3K27M–expressing wound edge cardiomyocytes aberrantly maintain homeostatic levels of sarcomeric and actomyosin gene expression and show significant retention of sarcomere structure. While DNA replication occurs normally in these H3.3K27M cardiomyocytes  we observed significant increases in cardiomyocyte nucleation  a phenotype indicative of cytokinesis failures. In addition  nuclear density at the wound edge increases as new cardiomyocytes fail to colonize the injured area. Together  our study reveals that production of new cardiomyocytes and their infiltration into the injured region relies on H3K27me3 mediated sarcomeric and actomyosin cytoskeletal gene repression. Overall design: Transcriptional profiling RNA seq of regenerting versus uninjured FACS purified cardiomyocytes from zebrafish ventricle apexes in triplicates,parent bioproject:PRJNA380125,pubmed:31427288,,Uninjured cardiomyocytes rep3,GSM2546210,,source name:Cardiac ventricle tissue|tissue:Cardiac ventricle apex|strain:Gata4:GFP|batch:uninjured,Uninjured cardiomyocytes rep3,Data Processing Reads from three replicates of uninjured “uninjured” and 5 xxx post injury “5 dpa” heart samples were aligned against the GRCz10 genome assembly of the Zebrafish  ENSEMBL 89 annotation using STAR v. 2.5.3a in paired end mode with parameters   runThreadN 16   runMode alignReads   outFilterType BySJout    outFilterMultimapNmax 20   alignSJoverhangMin 8   alignSJDBoverhangMin 1    outFilterMismatchNmax 999   alignIntronMin 10   alignIntronMax 1000000    alignMatesGapMax 1000000   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM . The resulting Aligned.toTranscriptome.out.bam files were postprocessed using RSEM v. 1.3.0 using following flags   paired end   calc ci   alignments  p 8   forward prob 0. Posterior mean estimates of counts  RPKM and TPM were retrieved for each gene in each sample. Differential expression analysis between uninjured and 5 dpa samples was performed using DESeq2 in the R statistical environment v. 3.3.3 on protein coding genes according to ENSEMBL’s biotype assignments. Supplementary files format and content csv files are a DEseq2 estimations of changes in read density of protein coding genes according to ENSEMBL release 89’s biotype assignments between experimental groups. Supplementary files format and content: IGVtools utility 'count' was used on aligned bam files to compute the average alignment over 164 base windows across the genome and generate binary tiled data .tdf files Thorvaldsdottir et al. 2013.,Cardiac ventricle tissue,,Ventricle apexes were removed and cleared of injury tissue  then dissociated using the Miltenyi neonate heart dissociation kit  pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS sorted directly into RLT lysis buffer RNeasy micro prep RNA extraction kit  Qiagen. RNA integrity and concentration were checked on a Fragment Analyzer Advanced Analytical.  cDNA samples were generated using the Ovation low input v2 kit Nugen according to the manufacturer’s.  The resulting cDNA samples were then end repaired and adaptor ligated using the SPRI works Fragment Library System I Beckman Coulter Genomics and indexed during amplification. Libraries were quantified using the Fragment Analyzer Advanced Analytical and qPCR before being loaded for paired end sequencing 2X40 nt using the Illumina HiSeq 2000.,,tissue:Cardiac ventricle apex|strain:Gata4:GFP|batch:uninjured,GSM2546210,GSM2546210: Uninjured cardiomyocytes rep3; Danio rerio; RNA Seq,GSM2546210,,1,Ventricle apexes were removed and cleared of injury tissue  then dissociated using the Miltenyi neonate heart dissociation kit  pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS sorted directly into RLT lysis buffer RNeasy micro prep RNA extraction kit  Qiagen. RNA samples were prepared according to Qiagen protocol  cDNA libraries were generated and sequenced on an Illumina HiSeq 2000 RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2546210,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102311,,,Gata4u3_end1.fq.gz Gata4u3_end2.fq.gz,fastq fastq,1737122276.0,21184418.0,GSM2546210 r1,0:41 1:41,A:493652860;C:355087018;G:366352026;T:517823158;N:4207214,41,41,,,493652860,355087018,366352026,517823158,4207214,SRX2661988,SRS2063954,SRA548505,GEO,"Caroline Burns, CVRC, MGH",2,0.81752,0.85408,0.22689,0.23817,0.81771,0.81566,0.70282,0.7105,41,41,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-22,Undetermined,Undetermined,Heart,Cardiovascular System
41992,SRR5366719,SRX2661987,SRS2063953,SRP102311,PRJNA380129,H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [RNA seq],GSE96929,Transcriptome Analysis,We identify the global transcriptional changes that occur between homeostatic and proliferative cardiomyocytes in the zebrafish heart and uncover an essential role for H3K27me3 deposition in facilitating successful myocardial regeneration.  Specifically  we learned that cardiomyocyte proliferation is accompanied by downregulation of sarcomeric and cytoskeletal components and upregulation of the polycomb methylase Ezh2. Using ChIPseq  we demonstrate that this transcriptional repression is associated with deposition of new H3K27me3 modifications over the promoters. Using new genetic zebrafish lines that allow for inducible and cardiomyocyte specific expression of a mutant form of histone 3 that is unable to be tri methylated on lysine 27 H3.3K27M  we discovered that addition of H3K27me3 marks is essential for cardiac regeneration in vivo. Earlier in the regenerative window  we found that H3.3K27M–expressing wound edge cardiomyocytes aberrantly maintain homeostatic levels of sarcomeric and actomyosin gene expression and show significant retention of sarcomere structure. While DNA replication occurs normally in these H3.3K27M cardiomyocytes  we observed significant increases in cardiomyocyte nucleation  a phenotype indicative of cytokinesis failures. In addition  nuclear density at the wound edge increases as new cardiomyocytes fail to colonize the injured area. Together  our study reveals that production of new cardiomyocytes and their infiltration into the injured region relies on H3K27me3 mediated sarcomeric and actomyosin cytoskeletal gene repression. Overall design: Transcriptional profiling RNA seq of regenerting versus uninjured FACS purified cardiomyocytes from zebrafish ventricle apexes in triplicates,parent bioproject:PRJNA380125,pubmed:31427288,,Uninjured cardiomyocytes rep2,GSM2546209,,source name:Cardiac ventricle tissue|tissue:Cardiac ventricle apex|strain:Gata4:GFP|batch:uninjured,Uninjured cardiomyocytes rep2,Data Processing Reads from three replicates of uninjured “uninjured” and 5 xxx post injury “5 dpa” heart samples were aligned against the GRCz10 genome assembly of the Zebrafish  ENSEMBL 89 annotation using STAR v. 2.5.3a in paired end mode with parameters   runThreadN 16   runMode alignReads   outFilterType BySJout    outFilterMultimapNmax 20   alignSJoverhangMin 8   alignSJDBoverhangMin 1    outFilterMismatchNmax 999   alignIntronMin 10   alignIntronMax 1000000    alignMatesGapMax 1000000   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM . The resulting Aligned.toTranscriptome.out.bam files were postprocessed using RSEM v. 1.3.0 using following flags   paired end   calc ci   alignments  p 8   forward prob 0. Posterior mean estimates of counts  RPKM and TPM were retrieved for each gene in each sample. Differential expression analysis between uninjured and 5 dpa samples was performed using DESeq2 in the R statistical environment v. 3.3.3 on protein coding genes according to ENSEMBL’s biotype assignments. Supplementary files format and content csv files are a DEseq2 estimations of changes in read density of protein coding genes according to ENSEMBL release 89’s biotype assignments between experimental groups. Supplementary files format and content: IGVtools utility 'count' was used on aligned bam files to compute the average alignment over 164 base windows across the genome and generate binary tiled data .tdf files Thorvaldsdottir et al. 2013.,Cardiac ventricle tissue,,Ventricle apexes were removed and cleared of injury tissue  then dissociated using the Miltenyi neonate heart dissociation kit  pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS sorted directly into RLT lysis buffer RNeasy micro prep RNA extraction kit  Qiagen. RNA integrity and concentration were checked on a Fragment Analyzer Advanced Analytical.  cDNA samples were generated using the Ovation low input v2 kit Nugen according to the manufacturer’s.  The resulting cDNA samples were then end repaired and adaptor ligated using the SPRI works Fragment Library System I Beckman Coulter Genomics and indexed during amplification. Libraries were quantified using the Fragment Analyzer Advanced Analytical and qPCR before being loaded for paired end sequencing 2X40 nt using the Illumina HiSeq 2000.,,tissue:Cardiac ventricle apex|strain:Gata4:GFP|batch:uninjured,GSM2546209,GSM2546209: Uninjured cardiomyocytes rep2; Danio rerio; RNA Seq,GSM2546209,,1,Ventricle apexes were removed and cleared of injury tissue  then dissociated using the Miltenyi neonate heart dissociation kit  pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS sorted directly into RLT lysis buffer RNeasy micro prep RNA extraction kit  Qiagen. RNA samples were prepared according to Qiagen protocol  cDNA libraries were generated and sequenced on an Illumina HiSeq 2000 RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2546209,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102311,,,Gata4u2_end1.fq.gz Gata4u2_end2.fq.gz,fastq fastq,2008272332.0,24491126.0,GSM2546209 r1,0:41 1:41,A:572896017;C:403127922;G:418854379;T:608518390;N:4875624,41,41,,,572896017,403127922,418854379,608518390,4875624,SRX2661987,SRS2063953,SRA548505,GEO,"Caroline Burns, CVRC, MGH",2,0.83539,0.86462,0.18665,0.19514,0.82791,0.82534,0.80998,0.80096,41,41,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-22,Undetermined,Undetermined,Heart,Cardiovascular System
41993,SRR5366718,SRX2661986,SRS2063952,SRP102311,PRJNA380129,H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [RNA seq],GSE96929,Transcriptome Analysis,We identify the global transcriptional changes that occur between homeostatic and proliferative cardiomyocytes in the zebrafish heart and uncover an essential role for H3K27me3 deposition in facilitating successful myocardial regeneration.  Specifically  we learned that cardiomyocyte proliferation is accompanied by downregulation of sarcomeric and cytoskeletal components and upregulation of the polycomb methylase Ezh2. Using ChIPseq  we demonstrate that this transcriptional repression is associated with deposition of new H3K27me3 modifications over the promoters. Using new genetic zebrafish lines that allow for inducible and cardiomyocyte specific expression of a mutant form of histone 3 that is unable to be tri methylated on lysine 27 H3.3K27M  we discovered that addition of H3K27me3 marks is essential for cardiac regeneration in vivo. Earlier in the regenerative window  we found that H3.3K27M–expressing wound edge cardiomyocytes aberrantly maintain homeostatic levels of sarcomeric and actomyosin gene expression and show significant retention of sarcomere structure. While DNA replication occurs normally in these H3.3K27M cardiomyocytes  we observed significant increases in cardiomyocyte nucleation  a phenotype indicative of cytokinesis failures. In addition  nuclear density at the wound edge increases as new cardiomyocytes fail to colonize the injured area. Together  our study reveals that production of new cardiomyocytes and their infiltration into the injured region relies on H3K27me3 mediated sarcomeric and actomyosin cytoskeletal gene repression. Overall design: Transcriptional profiling RNA seq of regenerting versus uninjured FACS purified cardiomyocytes from zebrafish ventricle apexes in triplicates,parent bioproject:PRJNA380125,pubmed:31427288,,Uninjured cardiomyocytes rep1,GSM2546208,,source name:Cardiac ventricle tissue|tissue:Cardiac ventricle apex|strain:Gata4:GFP|batch:uninjured,Uninjured cardiomyocytes rep1,Reads from three replicates of uninjured “uninjured” and 5 xxx post injury “5 dpa” heart samples were aligned against the GRCz10 genome assembly of the Zebrafish  ENSEMBL 89 annotation using STAR v. 2.5.3a in paired end mode with parameters   runThreadN 16   runMode alignReads   outFilterType BySJout    outFilterMultimapNmax 20   alignSJoverhangMin 8   alignSJDBoverhangMin 1    outFilterMismatchNmax 999   alignIntronMin 10   alignIntronMax 1000000    alignMatesGapMax 1000000   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM . The resulting Aligned.toTranscriptome.out.bam files were postprocessed using RSEM v. 1.3.0 using following flags   paired end   calc ci   alignments  p 8   forward prob 0. Posterior mean estimates of counts  RPKM and TPM were retrieved for each gene in each sample. Differential expression analysis between uninjured and 5 dpa samples was performed using DESeq2 in the R statistical environment v. 3.3.3 on protein coding genes according to ENSEMBL’s biotype assignments. Supplementary files format and content csv files are a DEseq2 estimations of changes in read density of protein coding genes according to ENSEMBL release 89’s biotype assignments between experimental groups. Supplementary files format and content: IGVtools utility 'count' was used on aligned bam files to compute the average alignment over 164 base windows across the genome and generate binary tiled data .tdf files Thorvaldsdottir et al. 2013.,Cardiac ventricle tissue,,Ventricle apexes were removed and cleared of injury tissue  then dissociated using the Miltenyi neonate heart dissociation kit  pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS sorted directly into RLT lysis buffer RNeasy micro prep RNA extraction kit  Qiagen. RNA integrity and concentration were checked on a Fragment Analyzer Advanced Analytical.  cDNA samples were generated using the Ovation low input v2 kit Nugen according to the manufacturer’s.  The resulting cDNA samples were then end repaired and adaptor ligated using the SPRI works Fragment Library System I Beckman Coulter Genomics and indexed during amplification. Libraries were quantified using the Fragment Analyzer Advanced Analytical and qPCR before being loaded for paired end sequencing 2X40 nt using the Illumina HiSeq 2000.,,tissue:Cardiac ventricle apex|strain:Gata4:GFP|batch:uninjured,GSM2546208,GSM2546208: Uninjured cardiomyocytes rep1; Danio rerio; RNA Seq,GSM2546208,,1,Ventricle apexes were removed and cleared of injury tissue  then dissociated using the Miltenyi neonate heart dissociation kit  pelleted and resuspended in PBS/serum. Cell suspensions were strained on a 50 micron nylon mesh and immediately FACS sorted directly into RLT lysis buffer RNeasy micro prep RNA extraction kit  Qiagen. RNA samples were prepared according to Qiagen protocol  cDNA libraries were generated and sequenced on an Illumina HiSeq 2000 RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM2546208,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102311,,,Gata4u1_end1.fq.gz Gata4u1_end2.fq.gz,fastq fastq,2243134682.0,27355301.0,GSM2546208 r1,0:41 1:41,A:637700051;C:456179088;G:471197897;T:672624830;N:5432816,41,41,,,637700051,456179088,471197897,672624830,5432816,SRX2661986,SRS2063952,SRA548505,GEO,"Caroline Burns, CVRC, MGH",2,0.83024,0.86786,0.17153,0.17971,0.82741,0.82345,0.80221,0.79802,41,41,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-22,Undetermined,Undetermined,Heart,Cardiovascular System
42495,SRR5666979,SRX2902577,SRS2269173,SRP108989,PRJNA390119,HLX & Hematopoiesis,PRJNA390119,Other,HLX &amp; Hematopoiesis,,,rnaseq and atacseq,hlx hematopoiesis,hlx,,isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal,,,,,,,,,kdrl GFP cells hlx1  MO rep2,3,kdrl GFP cells hlx1  MO rep2,SMART SEQ ultra low RNA seq kit Clonetech,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP108989,,assembly:danRer10,flk_gfp_hlx_8ng_48hrs_2_R1.fastq.gz flk_gfp_hlx_8ng_48hrs_2_R2.fastq.gz,fastq fastq,1887289200.0,12581928.0,flk gfp hlx 8ng 48hrs 2 R1.fastq.gz,0:75 1:75,A:493825524;C:448630716;G:436118597;T:508410442;N:303921,75,75,,,493825524,448630716,436118597,508410442,303921,SRX2902577,SRS2269173,SRA573518,BRFAA|Molecular Biology,BRFAA,2,0.9202,0.9216,0.09499,0.09558,0.73805,0.73878,0.48809,0.48787,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Greece,2017-06-13,Undetermined,Undetermined,Heart,Cardiovascular System
42496,SRR5666980,SRX2902576,SRS2269173,SRP108989,PRJNA390119,HLX & Hematopoiesis,PRJNA390119,Other,HLX &amp; Hematopoiesis,,,rnaseq and atacseq,hlx hematopoiesis,hlx,,isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal,,,,,,,,,kdrl GFP cells hlx1  MO rep1,2,kdrl GFP cells hlx1  MO rep1,SMART SEQ ultra low RNA seq kit Clonetech,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP108989,,assembly:danRer10,flk_gfp_hlx_8ng_48hrs_1_R1.fastq.gz flk_gfp_hlx_8ng_48hrs_1_R2.fastq.gz,fastq fastq,1561083900.0,10407226.0,flk gfp hlx 8ng 48hrs 1 R2.fastq.gz,0:75 1:75,A:412744284;C:366776465;G:356834742;T:424473871;N:254538,75,75,,,412744284,366776465,356834742,424473871,254538,SRX2902576,SRS2269173,SRA573518,BRFAA|Molecular Biology,BRFAA,2,0.9172,0.91824,0.09957,0.09961,0.73965,0.73975,0.48906,0.48977,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Greece,2017-06-13,Undetermined,Undetermined,Heart,Cardiovascular System
42497,SRR5666981,SRX2902575,SRS2269173,SRP108989,PRJNA390119,HLX & Hematopoiesis,PRJNA390119,Other,HLX &amp; Hematopoiesis,,,rnaseq and atacseq,hlx hematopoiesis,hlx,,isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal,,,,,,,,,kdrl GFP cells control 2,1,kdrl GFP cells control 2,SMART SEQ ultra low RNA seq kit Clonetech,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP108989,,assembly:danRer10,flk_gfp_48hrs_con2_R1.fastq.gz flk_gfp_48hrs_con2_R2.fastq.gz,fastq fastq,2042164500.0,13614430.0,flk gfp 48hrs con2 R1.fastq.gz,0:75 1:75,A:537008617;C:483956616;G:465380092;T:555490621;N:328554,75,75,,,537008617,483956616,465380092,555490621,328554,SRX2902575,SRS2269173,SRA573518,BRFAA|Molecular Biology,BRFAA,2,0.91492,0.91762,0.10575,0.10669,0.75519,0.75546,0.49482,0.49617,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Greece,2017-06-13,Undetermined,Undetermined,Heart,Cardiovascular System
42498,SRR5666982,SRX2902574,SRS2269173,SRP108989,PRJNA390119,HLX & Hematopoiesis,PRJNA390119,Other,HLX &amp; Hematopoiesis,,,rnaseq and atacseq,hlx hematopoiesis,hlx,,isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal,,,,,,,,,kdrl GFP cells control 1,0,kdrl GFP cells control 1,SMART SEQ ultra low RNA seq kit Clonetech,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP108989,,assembly:danRer10,flk_gfp_48hrs_con1_R2.fastq.gz flk_gfp_48hrs_con1_R1.fastq.gz,fastq fastq,1678987200.0,11193248.0,flk gfp 48hrs con1 R2.fastq.gz,0:75 1:75,A:437283407;C:401234553;G:387947515;T:452257282;N:264443,75,75,,,437283407,401234553,387947515,452257282,264443,SRX2902574,SRS2269173,SRA573518,BRFAA|Molecular Biology,BRFAA,2,0.91593,0.91737,0.08937,0.08988,0.75607,0.75696,0.50103,0.45539,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Greece,2017-06-13,Undetermined,Undetermined,Heart,Cardiovascular System
42499,SRR5666985,SRX2902571,SRS2269173,SRP108989,PRJNA390119,HLX & Hematopoiesis,PRJNA390119,Other,HLX &amp; Hematopoiesis,,,rnaseq and atacseq,hlx hematopoiesis,hlx,,isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal,,,,,,,,,fli GFP cells hHLXOE rep 2,5,fli GFP cells hHLXOE rep 2,SMART SEQ ultra low RNA seq kit Clonetech,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP108989,,assembly:danRer10,fli_gal4_uas_hlx_endo_48h_s2_R2.fastq.gz fli_gal4_uas_hlx_endo_48h_s2_R1.fastq.gz,fastq fastq,4490898450.0,29939323.0,fli gal4 uas hlx endo 48h s2 R2.fastq.gz,0:75 1:75,A:870349076;C:1346136891;G:1401796534;T:869066463;N:3549486,75,75,,,870349076,1346136891,1401796534,869066463,3549486,SRX2902571,SRS2269173,SRA573518,BRFAA|Molecular Biology,BRFAA,2,0.5714,0.57344,0.27957,0.28321,0.85102,0.85342,0.53304,0.53368,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Greece,2017-06-13,Undetermined,Undetermined,Heart,Cardiovascular System
42500,SRR5666986,SRX2902570,SRS2269173,SRP108989,PRJNA390119,HLX & Hematopoiesis,PRJNA390119,Other,HLX &amp; Hematopoiesis,,,rnaseq and atacseq,hlx hematopoiesis,hlx,,isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal,,,,,,,,,fli GFP cells hHLXOE rep 1,4,fli GFP cells hHLXOE rep 1,SMART SEQ ultra low RNA seq kit Clonetech,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP108989,,assembly:danRer10,fli_gal4_uas_hlx_endo_48h_s1_R1.fastq.gz fli_gal4_uas_hlx_endo_48h_s1_R2.fastq.gz,fastq fastq,3459602100.0,23064014.0,fli gal4 uas hlx endo 48h s1 R1.fastq.gz,0:75 1:75,A:658343595;C:1050309687;G:1097759573;T:650443491;N:2745754,75,75,,,658343595,1050309687,1097759573,650443491,2745754,SRX2902570,SRS2269173,SRA573518,BRFAA|Molecular Biology,BRFAA,2,0.57077,0.57481,0.2173,0.2185,0.79553,0.79762,0.50405,0.48708,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Greece,2017-06-13,Undetermined,Undetermined,Heart,Cardiovascular System
44926,SRR6298096,SRX3399039,SRS2693219,SRP125111,PRJNA418766,Age dependent increase of oxidative stress regulates microRNA 29 family preserving cardiac health,GSE107003,Transcriptome Analysis,The short lived turquoise killifish Nothobranchius furzeri Nfu is a valid model for aging studies. Here  we investigated its age associated cardiac function. We observed oxidative stress accumulation and an engagement of microRNAs miRNAs in the aging heart. MiRNA sequencing of 5 week young  12 21 week adult and 28 wpf 40 wpf Nfu hearts revealed 23 up regulated and 18 down regulated miRNAs with age. MiR 29 family turned out as one of the most up regulated miRNAs during aging. MiR 29 family increase induces a decrease of known targets like collagens and DNA methyl transferases DNMTs paralleled by 5´methyl cytosine 5mC level decrease. To further investigate miR 29 family role in the fish heart we generated a transgenic zebrafish model where miR 29 was knocked down. In this model we found significant morphological and functional cardiac alterations and an impairment of oxygen dependent pathways by transcriptome analysis leading to hypoxic marker up regulation. To get insights the possible hypoxic regulation of miR 29 family  we exposed human cardiac fibroblasts ttwo xxx% O2 levels. In hypoxic condition we found miR 29 down modulation responsible for the accumulation of collagens and 5mC. Overall  our data suggest that miR 29 family up regulation might represent an endogenous mechanism aimed at ameliorating the age dependent cardiac damage leading to hypertrophy and fibrosis. Overall design: RNA was isolated from zebrafish heart samples 3 wt and 3 miR 29 sponge and sequenced.,,pubmed:29203887,,ZF mir29 3,GSM2859325,,source name:Heart tissue|construct:mir29 sponge|tissue:heart,ZF mir29 3,Raw reads were assessed for quality  adapter content and duplication rates with FastQC version 0.11.2. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl zebrafish genome version GRCz10 using STAR 2.5.2b with the parameters “  outFilterMismatchNoverLmax 0.1   alignMatesGapMax 1000   alignIntronMax 200000”. The number of reads aligning to genes was counted with featureCounts 1.5.0 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Raw counts were normalized using DESeq2 and rounded to the next integer. Genome build: GRCz10 Supplementary files format and content: matrix.txt contains DESeq2 normalized count values for all genes overlapped by at least one read.,Heart tissue,,For next generation sequencing NGS RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA and libraries integrity were verified with a BioAnalyzer 2100 Agilent or LabChip Gx Touch 24 Perkin Elmer. 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   HI Mammalian Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry with 2x75bp paired end setup.,,construct:mir29 sponge|tissue:heart,GSM2859325,GSM2859325: ZF mir29 3; Danio rerio; RNA Seq,GSM2859325,,1,For next generation sequencing NGS RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA and libraries integrity were verified with a BioAnalyzer 2100 Agilent or LabChip Gx Touch 24 Perkin Elmer. 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   HI Mammalian Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry with 2x75bp paired end setup.,GEO Accession:GSM2859325,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP125111,,,ZF_mir29_3_R1.fastq.gz ZF_mir29_3_R2.fastq.gz,fastq fastq,4780181485.0,32142852.0,GSM2859325 r1,0:74.34 1:74.37,A:1327565597;C:1036147981;G:1072216923;T:1338967505;N:5283479,74,74,,,1327565597,1036147981,1072216923,1338967505,5283479,SRX3399039,SRS2693219,SRA631359,GEO,"Bioinformatics, Max Planck Institute for Heart and Lung Research",2,0.90823,0.91991,0.24769,0.24659,0.81115,0.82694,0.70195,0.70932,75,75,B,B,biological fallback assumption,illumina,nextseq,full_length,small_rna,smarter,bulk,unknown,unknown,,Germany,2017-11-16,Undetermined,Undetermined,Heart,Cardiovascular System
44927,SRR6298095,SRX3399038,SRS2693218,SRP125111,PRJNA418766,Age dependent increase of oxidative stress regulates microRNA 29 family preserving cardiac health,GSE107003,Transcriptome Analysis,The short lived turquoise killifish Nothobranchius furzeri Nfu is a valid model for aging studies. Here  we investigated its age associated cardiac function. We observed oxidative stress accumulation and an engagement of microRNAs miRNAs in the aging heart. MiRNA sequencing of 5 week young  12 21 week adult and 28 wpf 40 wpf Nfu hearts revealed 23 up regulated and 18 down regulated miRNAs with age. MiR 29 family turned out as one of the most up regulated miRNAs during aging. MiR 29 family increase induces a decrease of known targets like collagens and DNA methyl transferases DNMTs paralleled by 5´methyl cytosine 5mC level decrease. To further investigate miR 29 family role in the fish heart we generated a transgenic zebrafish model where miR 29 was knocked down. In this model we found significant morphological and functional cardiac alterations and an impairment of oxygen dependent pathways by transcriptome analysis leading to hypoxic marker up regulation. To get insights the possible hypoxic regulation of miR 29 family  we exposed human cardiac fibroblasts ttwo xxx% O2 levels. In hypoxic condition we found miR 29 down modulation responsible for the accumulation of collagens and 5mC. Overall  our data suggest that miR 29 family up regulation might represent an endogenous mechanism aimed at ameliorating the age dependent cardiac damage leading to hypertrophy and fibrosis. Overall design: RNA was isolated from zebrafish heart samples 3 wt and 3 miR 29 sponge and sequenced.,,pubmed:29203887,,ZF mir29 2,GSM2859324,,source name:Heart tissue|construct:mir29 sponge|tissue:heart,ZF mir29 2,Raw reads were assessed for quality  adapter content and duplication rates with FastQC version 0.11.2. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl zebrafish genome version GRCz10 using STAR 2.5.2b with the parameters “  outFilterMismatchNoverLmax 0.1   alignMatesGapMax 1000   alignIntronMax 200000”. The number of reads aligning to genes was counted with featureCounts 1.5.0 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Raw counts were normalized using DESeq2 and rounded to the next integer. Genome build: GRCz10 Supplementary files format and content: matrix.txt contains DESeq2 normalized count values for all genes overlapped by at least one read.,Heart tissue,,For next generation sequencing NGS RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA and libraries integrity were verified with a BioAnalyzer 2100 Agilent or LabChip Gx Touch 24 Perkin Elmer. 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   HI Mammalian Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry with 2x75bp paired end setup.,,construct:mir29 sponge|tissue:heart,GSM2859324,GSM2859324: ZF mir29 2; Danio rerio; RNA Seq,GSM2859324,,1,For next generation sequencing NGS RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA and libraries integrity were verified with a BioAnalyzer 2100 Agilent or LabChip Gx Touch 24 Perkin Elmer. 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   HI Mammalian Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry with 2x75bp paired end setup.,GEO Accession:GSM2859324,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP125111,,,ZF_mir29_2_R1.fastq.gz ZF_mir29_2_R2.fastq.gz,fastq fastq,5223966030.0,35120242.0,GSM2859324 r1,0:74.36 1:74.38,A:1451670293;C:1137962829;G:1175089584;T:1453388727;N:5854597,74,74,,,1451670293,1137962829,1175089584,1453388727,5854597,SRX3399038,SRS2693218,SRA631359,GEO,"Bioinformatics, Max Planck Institute for Heart and Lung Research",2,0.90954,0.92144,0.25373,0.25451,0.8421,0.85399,0.78535,0.75574,75,75,B,B,biological fallback assumption,illumina,nextseq,full_length,small_rna,smarter,bulk,unknown,unknown,,Germany,2017-11-16,Undetermined,Undetermined,Heart,Cardiovascular System
44928,SRR6298094,SRX3399037,SRS2693217,SRP125111,PRJNA418766,Age dependent increase of oxidative stress regulates microRNA 29 family preserving cardiac health,GSE107003,Transcriptome Analysis,The short lived turquoise killifish Nothobranchius furzeri Nfu is a valid model for aging studies. Here  we investigated its age associated cardiac function. We observed oxidative stress accumulation and an engagement of microRNAs miRNAs in the aging heart. MiRNA sequencing of 5 week young  12 21 week adult and 28 wpf 40 wpf Nfu hearts revealed 23 up regulated and 18 down regulated miRNAs with age. MiR 29 family turned out as one of the most up regulated miRNAs during aging. MiR 29 family increase induces a decrease of known targets like collagens and DNA methyl transferases DNMTs paralleled by 5´methyl cytosine 5mC level decrease. To further investigate miR 29 family role in the fish heart we generated a transgenic zebrafish model where miR 29 was knocked down. In this model we found significant morphological and functional cardiac alterations and an impairment of oxygen dependent pathways by transcriptome analysis leading to hypoxic marker up regulation. To get insights the possible hypoxic regulation of miR 29 family  we exposed human cardiac fibroblasts ttwo xxx% O2 levels. In hypoxic condition we found miR 29 down modulation responsible for the accumulation of collagens and 5mC. Overall  our data suggest that miR 29 family up regulation might represent an endogenous mechanism aimed at ameliorating the age dependent cardiac damage leading to hypertrophy and fibrosis. Overall design: RNA was isolated from zebrafish heart samples 3 wt and 3 miR 29 sponge and sequenced.,,pubmed:29203887,,ZF mir29 1,GSM2859323,,source name:Heart tissue|construct:mir29 sponge|tissue:heart,ZF mir29 1,Raw reads were assessed for quality  adapter content and duplication rates with FastQC version 0.11.2. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl zebrafish genome version GRCz10 using STAR 2.5.2b with the parameters “  outFilterMismatchNoverLmax 0.1   alignMatesGapMax 1000   alignIntronMax 200000”. The number of reads aligning to genes was counted with featureCounts 1.5.0 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Raw counts were normalized using DESeq2 and rounded to the next integer. Genome build: GRCz10 Supplementary files format and content: matrix.txt contains DESeq2 normalized count values for all genes overlapped by at least one read.,Heart tissue,,For next generation sequencing NGS RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA and libraries integrity were verified with a BioAnalyzer 2100 Agilent or LabChip Gx Touch 24 Perkin Elmer. 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   HI Mammalian Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry with 2x75bp paired end setup.,,construct:mir29 sponge|tissue:heart,GSM2859323,GSM2859323: ZF mir29 1; Danio rerio; RNA Seq,GSM2859323,,1,For next generation sequencing NGS RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA and libraries integrity were verified with a BioAnalyzer 2100 Agilent or LabChip Gx Touch 24 Perkin Elmer. 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   HI Mammalian Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry with 2x75bp paired end setup.,GEO Accession:GSM2859323,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP125111,,,ZF_mir29_1_R1.fastq.gz ZF_mir29_1_R2.fastq.gz,fastq fastq,5308216436.0,35690404.0,GSM2859323 r1,0:74.36 1:74.37,A:1509798660;C:1127748899;G:1159263867;T:1505497024;N:5907986,74,74,,,1509798660,1127748899,1159263867,1505497024,5907986,SRX3399037,SRS2693217,SRA631359,GEO,"Bioinformatics, Max Planck Institute for Heart and Lung Research",2,0.90409,0.91666,0.26447,0.2644,0.82615,0.83991,0.77524,0.76594,74,75,B,B,biological fallback assumption,illumina,nextseq,full_length,small_rna,smarter,bulk,unknown,unknown,,Germany,2017-11-16,Undetermined,Undetermined,Heart,Cardiovascular System
44929,SRR6298093,SRX3399036,SRS2693216,SRP125111,PRJNA418766,Age dependent increase of oxidative stress regulates microRNA 29 family preserving cardiac health,GSE107003,Transcriptome Analysis,The short lived turquoise killifish Nothobranchius furzeri Nfu is a valid model for aging studies. Here  we investigated its age associated cardiac function. We observed oxidative stress accumulation and an engagement of microRNAs miRNAs in the aging heart. MiRNA sequencing of 5 week young  12 21 week adult and 28 wpf 40 wpf Nfu hearts revealed 23 up regulated and 18 down regulated miRNAs with age. MiR 29 family turned out as one of the most up regulated miRNAs during aging. MiR 29 family increase induces a decrease of known targets like collagens and DNA methyl transferases DNMTs paralleled by 5´methyl cytosine 5mC level decrease. To further investigate miR 29 family role in the fish heart we generated a transgenic zebrafish model where miR 29 was knocked down. In this model we found significant morphological and functional cardiac alterations and an impairment of oxygen dependent pathways by transcriptome analysis leading to hypoxic marker up regulation. To get insights the possible hypoxic regulation of miR 29 family  we exposed human cardiac fibroblasts ttwo xxx% O2 levels. In hypoxic condition we found miR 29 down modulation responsible for the accumulation of collagens and 5mC. Overall  our data suggest that miR 29 family up regulation might represent an endogenous mechanism aimed at ameliorating the age dependent cardiac damage leading to hypertrophy and fibrosis. Overall design: RNA was isolated from zebrafish heart samples 3 wt and 3 miR 29 sponge and sequenced.,,pubmed:29203887,,ZF WT 3,GSM2859322,,source name:Heart tissue|construct:wild type|tissue:heart,ZF WT 3,Raw reads were assessed for quality  adapter content and duplication rates with FastQC version 0.11.2. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl zebrafish genome version GRCz10 using STAR 2.5.2b with the parameters “  outFilterMismatchNoverLmax 0.1   alignMatesGapMax 1000   alignIntronMax 200000”. The number of reads aligning to genes was counted with featureCounts 1.5.0 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Raw counts were normalized using DESeq2 and rounded to the next integer. Genome build: GRCz10 Supplementary files format and content: matrix.txt contains DESeq2 normalized count values for all genes overlapped by at least one read.,Heart tissue,,For next generation sequencing NGS RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA and libraries integrity were verified with a BioAnalyzer 2100 Agilent or LabChip Gx Touch 24 Perkin Elmer. 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   HI Mammalian Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry with 2x75bp paired end setup.,,construct:wild type|tissue:heart,GSM2859322,GSM2859322: ZF WT 3; Danio rerio; RNA Seq,GSM2859322,,1,For next generation sequencing NGS RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA and libraries integrity were verified with a BioAnalyzer 2100 Agilent or LabChip Gx Touch 24 Perkin Elmer. 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   HI Mammalian Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry with 2x75bp paired end setup.,GEO Accession:GSM2859322,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP125111,,,ZF_WT_3_R1.fastq.gz ZF_WT_3_R2.fastq.gz,fastq fastq,5071535430.0,34135276.0,GSM2859322 r1,0:74.28 1:74.29,A:1399783372;C:1119879368;G:1156853223;T:1388372256;N:6647211,74,74,,,1399783372,1119879368,1156853223,1388372256,6647211,SRX3399036,SRS2693216,SRA631359,GEO,"Bioinformatics, Max Planck Institute for Heart and Lung Research",2,0.91922,0.93012,0.19895,0.19987,0.86669,0.87827,0.82725,0.80963,75,74,B,B,biological fallback assumption,illumina,nextseq,full_length,small_rna,smarter,bulk,unknown,unknown,,Germany,2017-11-16,Undetermined,Undetermined,Heart,Cardiovascular System
44930,SRR6298092,SRX3399035,SRS2693215,SRP125111,PRJNA418766,Age dependent increase of oxidative stress regulates microRNA 29 family preserving cardiac health,GSE107003,Transcriptome Analysis,The short lived turquoise killifish Nothobranchius furzeri Nfu is a valid model for aging studies. Here  we investigated its age associated cardiac function. We observed oxidative stress accumulation and an engagement of microRNAs miRNAs in the aging heart. MiRNA sequencing of 5 week young  12 21 week adult and 28 wpf 40 wpf Nfu hearts revealed 23 up regulated and 18 down regulated miRNAs with age. MiR 29 family turned out as one of the most up regulated miRNAs during aging. MiR 29 family increase induces a decrease of known targets like collagens and DNA methyl transferases DNMTs paralleled by 5´methyl cytosine 5mC level decrease. To further investigate miR 29 family role in the fish heart we generated a transgenic zebrafish model where miR 29 was knocked down. In this model we found significant morphological and functional cardiac alterations and an impairment of oxygen dependent pathways by transcriptome analysis leading to hypoxic marker up regulation. To get insights the possible hypoxic regulation of miR 29 family  we exposed human cardiac fibroblasts ttwo xxx% O2 levels. In hypoxic condition we found miR 29 down modulation responsible for the accumulation of collagens and 5mC. Overall  our data suggest that miR 29 family up regulation might represent an endogenous mechanism aimed at ameliorating the age dependent cardiac damage leading to hypertrophy and fibrosis. Overall design: RNA was isolated from zebrafish heart samples 3 wt and 3 miR 29 sponge and sequenced.,,pubmed:29203887,,ZF WT 2,GSM2859321,,source name:Heart tissue|construct:wild type|tissue:heart,ZF WT 2,Raw reads were assessed for quality  adapter content and duplication rates with FastQC version 0.11.2. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl zebrafish genome version GRCz10 using STAR 2.5.2b with the parameters “  outFilterMismatchNoverLmax 0.1   alignMatesGapMax 1000   alignIntronMax 200000”. The number of reads aligning to genes was counted with featureCounts 1.5.0 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Raw counts were normalized using DESeq2 and rounded to the next integer. Genome build: GRCz10 Supplementary files format and content: matrix.txt contains DESeq2 normalized count values for all genes overlapped by at least one read.,Heart tissue,,For next generation sequencing NGS RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA and libraries integrity were verified with a BioAnalyzer 2100 Agilent or LabChip Gx Touch 24 Perkin Elmer. 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   HI Mammalian Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry with 2x75bp paired end setup.,,construct:wild type|tissue:heart,GSM2859321,GSM2859321: ZF WT 2; Danio rerio; RNA Seq,GSM2859321,,1,For next generation sequencing NGS RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA and libraries integrity were verified with a BioAnalyzer 2100 Agilent or LabChip Gx Touch 24 Perkin Elmer. 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   HI Mammalian Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry with 2x75bp paired end setup.,GEO Accession:GSM2859321,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP125111,,,ZF_WT_2_R2.fastq.gz ZF_WT_2_R1.fastq.gz,fastq fastq,5365284452.0,36076673.0,GSM2859321 r1,0:74.35 1:74.37,A:1471552741;C:1191759480;G:1228086754;T:1467760569;N:6124908,74,74,,,1471552741,1191759480,1228086754,1467760569,6124908,SRX3399035,SRS2693215,SRA631359,GEO,"Bioinformatics, Max Planck Institute for Heart and Lung Research",2,0.92197,0.93338,0.20522,0.20482,0.8506,0.86379,0.79468,0.72502,74,75,B,B,biological fallback assumption,illumina,nextseq,full_length,small_rna,smarter,bulk,unknown,unknown,,Germany,2017-11-16,Undetermined,Undetermined,Heart,Cardiovascular System
44931,SRR6298091,SRX3399034,SRS2693214,SRP125111,PRJNA418766,Age dependent increase of oxidative stress regulates microRNA 29 family preserving cardiac health,GSE107003,Transcriptome Analysis,The short lived turquoise killifish Nothobranchius furzeri Nfu is a valid model for aging studies. Here  we investigated its age associated cardiac function. We observed oxidative stress accumulation and an engagement of microRNAs miRNAs in the aging heart. MiRNA sequencing of 5 week young  12 21 week adult and 28 wpf 40 wpf Nfu hearts revealed 23 up regulated and 18 down regulated miRNAs with age. MiR 29 family turned out as one of the most up regulated miRNAs during aging. MiR 29 family increase induces a decrease of known targets like collagens and DNA methyl transferases DNMTs paralleled by 5´methyl cytosine 5mC level decrease. To further investigate miR 29 family role in the fish heart we generated a transgenic zebrafish model where miR 29 was knocked down. In this model we found significant morphological and functional cardiac alterations and an impairment of oxygen dependent pathways by transcriptome analysis leading to hypoxic marker up regulation. To get insights the possible hypoxic regulation of miR 29 family  we exposed human cardiac fibroblasts ttwo xxx% O2 levels. In hypoxic condition we found miR 29 down modulation responsible for the accumulation of collagens and 5mC. Overall  our data suggest that miR 29 family up regulation might represent an endogenous mechanism aimed at ameliorating the age dependent cardiac damage leading to hypertrophy and fibrosis. Overall design: RNA was isolated from zebrafish heart samples 3 wt and 3 miR 29 sponge and sequenced.,,pubmed:29203887,,ZF WT 1,GSM2859320,,source name:Heart tissue|construct:wild type|tissue:heart,ZF WT 1,Raw reads were assessed for quality  adapter content and duplication rates with FastQC version 0.11.2. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl zebrafish genome version GRCz10 using STAR 2.5.2b with the parameters “  outFilterMismatchNoverLmax 0.1   alignMatesGapMax 1000   alignIntronMax 200000”. The number of reads aligning to genes was counted with featureCounts 1.5.0 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Raw counts were normalized using DESeq2 and rounded to the next integer. Genome build: GRCz10 Supplementary files format and content: matrix.txt contains DESeq2 normalized count values for all genes overlapped by at least one read.,Heart tissue,,For next generation sequencing NGS RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA and libraries integrity were verified with a BioAnalyzer 2100 Agilent or LabChip Gx Touch 24 Perkin Elmer. 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   HI Mammalian Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry with 2x75bp paired end setup.,,construct:wild type|tissue:heart,GSM2859320,GSM2859320: ZF WT 1; Danio rerio; RNA Seq,GSM2859320,,1,For next generation sequencing NGS RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA and libraries integrity were verified with a BioAnalyzer 2100 Agilent or LabChip Gx Touch 24 Perkin Elmer. 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   HI Mammalian Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry with 2x75bp paired end setup.,GEO Accession:GSM2859320,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP125111,,,ZF_WT_1_R2.fastq.gz ZF_WT_1_R1.fastq.gz,fastq fastq,5853235105.0,39380123.0,GSM2859320 r1,0:74.31 1:74.33,A:1660925875;C:1233328558;G:1271454193;T:1680462040;N:7064439,74,74,,,1660925875,1233328558,1271454193,1680462040,7064439,SRX3399034,SRS2693214,SRA631359,GEO,"Bioinformatics, Max Planck Institute for Heart and Lung Research",2,0.89404,0.90726,0.26753,0.26916,0.82181,0.83808,0.71168,0.68778,73,75,B,B,biological fallback assumption,illumina,nextseq,full_length,small_rna,smarter,bulk,unknown,unknown,,Germany,2017-11-16,Undetermined,Undetermined,Heart,Cardiovascular System
47897,SRR6908713,SRX3856801,SRS3100393,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM6 lymphocytes,GSM3070139,,tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM6 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM6 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070139,GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq,GSM3070139,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM6_lymphocytes_L001_R1_001.fastq.gz WKM6_lymphocytes_L001_R2_001.fastq.gz,fastq fastq,1092718271.0,7238113.0,GSM3070139 r1,0:75.49 1:75.48,A:308417237;C:162459915;G:183666585;T:438104581;N:69953,75,75,,,308417237,162459915,183666585,438104581,69953,SRX3856801,SRS3100393,SRA675960,GEO,Hubrecht Institute,2,0.33032,0.81969,0.25647,0.49446,0.98587,0.93105,0.47765,0.53939,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47898,SRR6908714,SRX3856801,SRS3100393,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM6 lymphocytes,GSM3070139,,tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM6 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM6 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070139,GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq,GSM3070139,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM6_lymphocytes_L002_R1_001.fastq.gz WKM6_lymphocytes_L002_R2_001.fastq.gz,fastq fastq,988686695.0,6550079.0,GSM3070139 r2,0:75.49 1:75.46,A:281384679;C:146335731;G:165878017;T:395040397;N:47871,75,75,,,281384679,146335731,165878017,395040397,47871,SRX3856801,SRS3100393,SRA675960,GEO,Hubrecht Institute,2,0.31311,0.79325,0.23663,0.48843,0.99034,0.95471,0.47178,0.54622,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47899,SRR6908715,SRX3856801,SRS3100393,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM6 lymphocytes,GSM3070139,,tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM6 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM6 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070139,GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq,GSM3070139,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM6_lymphocytes_L003_R1_001.fastq.gz WKM6_lymphocytes_L003_R2_001.fastq.gz,fastq fastq,965970467.0,6397966.0,GSM3070139 r3,0:75.51 1:75.47,A:271037832;C:143188198;G:162584210;T:389145889;N:14338,75,75,,,271037832,143188198,162584210,389145889,14338,SRX3856801,SRS3100393,SRA675960,GEO,Hubrecht Institute,2,0.2983,0.81397,0.23255,0.49479,0.99377,0.94379,0.43187,0.54702,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47900,SRR6908716,SRX3856801,SRS3100393,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM6 lymphocytes,GSM3070139,,tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM6 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM6 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070139,GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq,GSM3070139,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM6_lymphocytes_L004_R1_001.fastq.gz WKM6_lymphocytes_L004_R2_001.fastq.gz,fastq fastq,845107841.0,5598430.0,GSM3070139 r4,0:75.50 1:75.46,A:239787549;C:124312776;G:144002735;T:336997076;N:7705,75,75,,,239787549,124312776,144002735,336997076,7705,SRX3856801,SRS3100393,SRA675960,GEO,Hubrecht Institute,2,0.27606,0.8077,0.21352,0.49895,0.99502,0.95511,0.37654,0.5537,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47905,SRR6908705,SRX3856799,SRS3100391,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 lymphocytes,GSM3070137,,tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM5 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070137,GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq,GSM3070137,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070137,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_lymphocytes_L001_R1_001.fastq.gz WKM5_lymphocytes_L001_R2_001.fastq.gz,fastq fastq,989705998.0,6559370.0,GSM3070137 r1,0:75.45 1:75.43,A:297302138;C:149495824;G:174348330;T:368343979;N:215727,75,75,,,297302138,149495824,174348330,368343979,215727,SRX3856799,SRS3100391,SRA675960,GEO,Hubrecht Institute,2,0.24742,0.6658,0.20828,0.41062,0.98214,0.85423,0.46204,0.47999,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47906,SRR6908706,SRX3856799,SRS3100391,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 lymphocytes,GSM3070137,,tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM5 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070137,GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq,GSM3070137,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070137,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_lymphocytes_L002_R1_001.fastq.gz WKM5_lymphocytes_L002_R2_001.fastq.gz,fastq fastq,966752947.0,6406981.0,GSM3070137 r2,0:75.44 1:75.45,A:289601664;C:144620642;G:173993992;T:358339663;N:196986,75,75,,,289601664,144620642,173993992,358339663,196986,SRX3856799,SRS3100391,SRA675960,GEO,Hubrecht Institute,2,0.23604,0.65405,0.20033,0.39718,0.98196,0.8636,0.50139,0.50729,74,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47907,SRR6908707,SRX3856799,SRS3100391,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 lymphocytes,GSM3070137,,tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM5 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070137,GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq,GSM3070137,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070137,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_lymphocytes_L003_R1_001.fastq.gz WKM5_lymphocytes_L003_R2_001.fastq.gz,fastq fastq,958861430.0,6354224.0,GSM3070137 r3,0:75.46 1:75.44,A:286188763;C:145686623;G:169054587;T:357878024;N:53433,75,75,,,286188763,145686623,169054587,357878024,53433,SRX3856799,SRS3100391,SRA675960,GEO,Hubrecht Institute,2,0.25215,0.67286,0.20951,0.41571,0.98707,0.84611,0.45707,0.51523,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System
47908,SRR6908708,SRX3856799,SRS3100391,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM5 lymphocytes,GSM3070137,,tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,WKM5 lymphocytes,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM5 lymphocytes,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes,GSM3070137,GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq,GSM3070137,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070137,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM5_lymphocytes_L004_R2_001.fastq.gz WKM5_lymphocytes_L004_R1_001.fastq.gz,fastq fastq,907053718.0,6010618.0,GSM3070137 r4,0:75.45 1:75.46,A:270238988;C:137187310;G:162483694;T:337104230;N:39496,75,75,,,270238988,137187310,162483694,337104230,39496,SRX3856799,SRS3100391,SRA675960,GEO,Hubrecht Institute,2,0.2382,0.66089,0.20055,0.40225,0.98537,0.86109,0.4862,0.51182,75,74,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Lymphatic System,Cardiovascular System