{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_selection = \"cDNA\" and tissue_curation_coarse = \"Cardiovascular System\"", "rows": [[25170, "SRR25661605", "SRX21387413", "SRS18627977", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. 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Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 OE 20 hpf CMs rep2", "GSM7714397", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 OE 20 hpf CMs rep2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. 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. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS", "GSM7714397", "GSM7714397: hand2 OE 20 hpf CMs rep2; Danio rerio; RNA Seq", "GSM7714397 r1", "GSM7714397", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_OE_CMs_2_R1.fastq.gz", "fastq", 2197151812.0, 30722639.0, "GSM7714397 r1", "0:71.52", "A:617116635;C:461951919;G:481371246;T:636712012;N:0", 71, null, null, null, 617116635, 461951919, 481371246, 636712012, 0, "SRX21387406", "SRS18627970", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90877, null, 0.14744, null, 0.77191, null, 0.42845, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25178, "SRR25661613", "SRX21387405", "SRS18627969", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 OE 20 hpf CMs rep1", "GSM7714396", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 OE 20 hpf CMs rep1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. 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. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS", "GSM7714396", "GSM7714396: hand2 OE 20 hpf CMs rep1; Danio rerio; RNA Seq", "GSM7714396 r1", "GSM7714396", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_OE_CMs_1_R1.fastq.gz", "fastq", 1773398936.0, 24797998.0, "GSM7714396 r1", "0:71.51", "A:495618212;C:375438077;G:390377060;T:511965587;N:0", 71, null, null, null, 495618212, 375438077, 390377060, 511965587, 0, "SRX21387405", "SRS18627969", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90769, null, 0.1387, null, 0.7768, null, 0.42096, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25179, "SRR25661614", "SRX21387404", "SRS18627968", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD /  20 hpf CMs rep3", "GSM7714395", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD /  20 hpf CMs rep3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. 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. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS", "GSM7714395", "GSM7714395: hand2 FLD /  20 hpf CMs rep3; Danio rerio; RNA Seq", "GSM7714395 r1", "GSM7714395", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_Mut_3_R1.fastq.gz", "fastq", 2179400259.0, 30471965.0, "GSM7714395 r1", "0:71.52", "A:600555691;C:468535203;G:483122661;T:627186704;N:0", 71, null, null, null, 600555691, 468535203, 483122661, 627186704, 0, "SRX21387404", "SRS18627968", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91581, null, 0.12256, null, 0.75209, null, 0.43413, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25180, "SRR25661615", "SRX21387403", "SRS18627967", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD /  20 hpf CMs rep2", "GSM7714394", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD /  20 hpf CMs rep2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. 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. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS", "GSM7714394", "GSM7714394: hand2 FLD /  20 hpf CMs rep2; Danio rerio; RNA Seq", "GSM7714394 r1", "GSM7714394", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_Mut_2_R1.fastq.gz", "fastq", 2340991168.0, 32733068.0, "GSM7714394 r1", "0:71.52", "A:647423337;C:500120073;G:514803152;T:678644606;N:0", 71, null, null, null, 647423337, 500120073, 514803152, 678644606, 0, "SRX21387403", "SRS18627967", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91231, null, 0.12561, null, 0.75118, null, 0.44445, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25181, "SRR25661616", "SRX21387402", "SRS18627966", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD /  20 hpf CMs rep1", "GSM7714393", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD /  20 hpf CMs rep1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. 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. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS", "GSM7714393", "GSM7714393: hand2 FLD /  20 hpf CMs rep1; Danio rerio; RNA Seq", "GSM7714393 r1", "GSM7714393", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_Mut_1_R1.fastq.gz", "fastq", 2727863036.0, 38140997.0, "GSM7714393 r1", "0:71.52", "A:760867462;C:577539041;G:596986102;T:792470431;N:0", 71, null, null, null, 760867462, 577539041, 596986102, 792470431, 0, "SRX21387402", "SRS18627966", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91175, null, 0.1342, null, 0.75282, null, 0.44063, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25196, "SRR25685540", "SRX21410747", "SRS18649229", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 4", "GSM7717538", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 4", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717538", "GSM7717538: Hmga1a overexpression sample 4; Danio rerio; RNA Seq", "GSM7717538 r1", "GSM7717538", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L001_OE4_cbc.fastq.gz", "fastq", 373009260.0, 6216821.0, "GSM7717538 r1", "0:60", "A:154344754;C:67291339;G:55785796;T:95519920;N:67451", 60, null, null, null, 154344754, 67291339, 55785796, 95519920, 67451, "SRX21410747", "SRS18649229", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.89552, null, 0.06993, null, 0.9276, null, 0.58138, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25197, "SRR25685541", "SRX21410747", "SRS18649229", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 4", "GSM7717538", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 4", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717538", "GSM7717538: Hmga1a overexpression sample 4; Danio rerio; RNA Seq", "GSM7717538 r1", "GSM7717538", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L002_OE4_cbc.fastq.gz", "fastq", 362301060.0, 6038351.0, "GSM7717538 r2", "0:60", "A:106180158;C:75387781;G:73886850;T:106761396;N:84875", 60, null, null, null, 106180158, 75387781, 73886850, 106761396, 84875, "SRX21410747", "SRS18649229", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.89159, null, 0.06701, null, 0.87081, null, 0.62237, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25198, "SRR25685542", "SRX21410747", "SRS18649229", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 4", "GSM7717538", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 4", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717538", "GSM7717538: Hmga1a overexpression sample 4; Danio rerio; RNA Seq", "GSM7717538 r1", "GSM7717538", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L003_OE4_cbc.fastq.gz", "fastq", 384538200.0, 6408970.0, "GSM7717538 r3", "0:60", "A:113163070;C:80510291;G:76775008;T:114062728;N:27103", 60, null, null, null, 113163070, 80510291, 76775008, 114062728, 27103, "SRX21410747", "SRS18649229", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.90032, null, 0.06985, null, 0.87008, null, 0.61631, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25199, "SRR25685543", "SRX21410747", "SRS18649229", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 4", "GSM7717538", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 4", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717538", "GSM7717538: Hmga1a overexpression sample 4; Danio rerio; RNA Seq", "GSM7717538 r1", "GSM7717538", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L004_OE4_cbc.fastq.gz", "fastq", 369674700.0, 6161245.0, "GSM7717538 r4", "0:60", "A:108130666;C:76988468;G:75491768;T:109027980;N:35818", 60, null, null, null, 108130666, 76988468, 75491768, 109027980, 35818, "SRX21410747", "SRS18649229", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.89622, null, 0.06895, null, 0.86854, null, 0.61464, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25200, "SRR25685544", "SRX21410746", "SRS18649228", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 3", "GSM7717537", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 3", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717537", "GSM7717537: Hmga1a overexpression sample 3; Danio rerio; RNA Seq", "GSM7717537 r1", "GSM7717537", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L001_OE3_cbc.fastq.gz", "fastq", 172977180.0, 2882953.0, "GSM7717537 r1", "0:60", "A:75387211;C:31808233;G:24071421;T:41679068;N:31247", 60, null, null, null, 75387211, 31808233, 24071421, 41679068, 31247, "SRX21410746", "SRS18649228", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.88458, null, 0.06987, null, 0.92788, null, 0.58263, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25201, "SRR25685545", "SRX21410746", "SRS18649228", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 3", "GSM7717537", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 3", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717537", "GSM7717537: Hmga1a overexpression sample 3; Danio rerio; RNA Seq", "GSM7717537 r1", "GSM7717537", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L002_OE3_cbc.fastq.gz", "fastq", 168370020.0, 2806167.0, "GSM7717537 r2", "0:60", "A:49447288;C:35622124;G:34182575;T:49078813;N:39220", 60, null, null, null, 49447288, 35622124, 34182575, 49078813, 39220, "SRX21410746", "SRS18649228", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.88366, null, 0.06639, null, 0.87519, null, 0.43134, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25202, "SRR25685546", "SRX21410746", "SRS18649228", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 3", "GSM7717537", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 3", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717537", "GSM7717537: Hmga1a overexpression sample 3; Danio rerio; RNA Seq", "GSM7717537 r1", "GSM7717537", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L003_OE3_cbc.fastq.gz", "fastq", 177341340.0, 2955689.0, "GSM7717537 r3", "0:60", "A:52304623;C:37759158;G:35264433;T:52000964;N:12162", 60, null, null, null, 52304623, 37759158, 35264433, 52000964, 12162, "SRX21410746", "SRS18649228", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.8907, null, 0.06795, null, 0.87405, null, 0.57596, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25203, "SRR25685547", "SRX21410746", "SRS18649228", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 3", "GSM7717537", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 3", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717537", "GSM7717537: Hmga1a overexpression sample 3; Danio rerio; RNA Seq", "GSM7717537 r1", "GSM7717537", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L004_OE3_cbc.fastq.gz", "fastq", 172482600.0, 2874710.0, "GSM7717537 r4", "0:60", "A:50610545;C:36521080;G:35043934;T:50291237;N:15804", 60, null, null, null, 50610545, 36521080, 35043934, 50291237, 15804, "SRX21410746", "SRS18649228", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.88558, null, 0.06686, null, 0.87373, null, 0.57425, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25204, "SRR25685548", "SRX21410745", "SRS18649227", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 2", "GSM7717536", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 2", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717536", "GSM7717536: Hmga1a overexpression sample 2; Danio rerio; RNA Seq", "GSM7717536 r1", "GSM7717536", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L001_OE2_cbc.fastq.gz", "fastq", 420273960.0, 7004566.0, "GSM7717536 r1", "0:60", "A:172608345;C:77102289;G:65053968;T:105434207;N:75151", 60, null, null, null, 172608345, 77102289, 65053968, 105434207, 75151, "SRX21410745", "SRS18649227", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.90654, null, 0.06306, null, 0.92904, null, 0.38886, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25205, "SRR25685549", "SRX21410745", "SRS18649227", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 2", "GSM7717536", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 2", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717536", "GSM7717536: Hmga1a overexpression sample 2; Danio rerio; RNA Seq", "GSM7717536 r1", "GSM7717536", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L002_OE2_cbc.fastq.gz", "fastq", 408658800.0, 6810980.0, "GSM7717536 r2", "0:60", "A:118741152;C:85204554;G:86928543;T:117687807;N:96744", 60, null, null, null, 118741152, 85204554, 86928543, 117687807, 96744, "SRX21410745", "SRS18649227", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.90277, null, 0.06298, null, 0.87302, null, 0.66727, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25206, "SRR25685550", "SRX21410745", "SRS18649227", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 2", "GSM7717536", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 2", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717536", "GSM7717536: Hmga1a overexpression sample 2; Danio rerio; RNA Seq", "GSM7717536 r1", "GSM7717536", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L003_OE2_cbc.fastq.gz", "fastq", 433893360.0, 7231556.0, "GSM7717536 r3", "0:60", "A:126666020;C:91068379;G:90449908;T:125677088;N:31965", 60, null, null, null, 126666020, 91068379, 90449908, 125677088, 31965, "SRX21410745", "SRS18649227", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.90833, null, 0.06364, null, 0.87351, null, 0.66644, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25207, "SRR25685551", "SRX21410745", "SRS18649227", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 2", "GSM7717536", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 2", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717536", "GSM7717536: Hmga1a overexpression sample 2; Danio rerio; RNA Seq", "GSM7717536 r1", "GSM7717536", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L004_OE2_cbc.fastq.gz", "fastq", 418311900.0, 6971865.0, "GSM7717536 r4", "0:60", "A:121375806;C:87324728;G:89011817;T:120559021;N:40528", 60, null, null, null, 121375806, 87324728, 89011817, 120559021, 40528, "SRX21410745", "SRS18649227", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.90583, null, 0.06349, null, 0.87156, null, 0.36876, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25208, "SRR25685552", "SRX21410744", "SRS18649226", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 1", "GSM7717535", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 1", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717535", "GSM7717535: Hmga1a overexpression sample 1; Danio rerio; RNA Seq", "GSM7717535 r1", "GSM7717535", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L001_OE1_cbc.fastq.gz", "fastq", 219019680.0, 3650328.0, "GSM7717535 r1", "0:60", "A:89205341;C:39777204;G:33514473;T:56486057;N:36605", 60, null, null, null, 89205341, 39777204, 33514473, 56486057, 36605, "SRX21410744", "SRS18649226", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.89316, null, 0.08503, null, 0.92125, null, 0.51486, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25209, "SRR25685553", "SRX21410744", "SRS18649226", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 1", "GSM7717535", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 1", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717535", "GSM7717535: Hmga1a overexpression sample 1; Danio rerio; RNA Seq", "GSM7717535 r1", "GSM7717535", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L002_OE1_cbc.fastq.gz", "fastq", 213035040.0, 3550584.0, "GSM7717535 r2", "0:60", "A:60747442;C:44096249;G:44275929;T:63866231;N:49189", 60, null, null, null, 60747442, 44096249, 44275929, 63866231, 49189, "SRX21410744", "SRS18649226", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.89017, null, 0.08631, null, 0.86543, null, 0.52632, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25210, "SRR25685554", "SRX21410744", "SRS18649226", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 1", "GSM7717535", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 1", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717535", "GSM7717535: Hmga1a overexpression sample 1; Danio rerio; RNA Seq", "GSM7717535 r1", "GSM7717535", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L003_OE1_cbc.fastq.gz", "fastq", 226019460.0, 3766991.0, "GSM7717535 r3", "0:60", "A:64732665;C:47081812;G:46018051;T:68171208;N:15724", 60, null, null, null, 64732665, 47081812, 46018051, 68171208, 15724, "SRX21410744", "SRS18649226", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.89632, null, 0.08716, null, 0.86661, null, 0.54361, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25211, "SRR25685555", "SRX21410744", "SRS18649226", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "Hmga1a overexpression sample 1", "GSM7717535", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "Hmga1a overexpression sample 1", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717535", "GSM7717535: Hmga1a overexpression sample 1; Danio rerio; RNA Seq", "GSM7717535 r1", "GSM7717535", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L004_OE1_cbc.fastq.gz", "fastq", 217742460.0, 3629041.0, "GSM7717535 r4", "0:60", "A:61973072;C:45113665;G:45294805;T:65339336;N:21582", 60, null, null, null, 61973072, 45113665, 45294805, 65339336, 21582, "SRX21410744", "SRS18649226", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.89237, null, 0.08517, null, 0.86454, null, 0.54639, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25212, "SRR25685556", "SRX21410743", "SRS18649225", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 4", "GSM7717534", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 4", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717534", "GSM7717534: control sample 4; Danio rerio; RNA Seq", "GSM7717534 r1", "GSM7717534", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L001_Ctrl4_cbc.fastq.gz", "fastq", 242809260.0, 4046821.0, "GSM7717534 r1", "0:60", "A:101286554;C:44368173;G:36112695;T:60997635;N:44203", 60, null, null, null, 101286554, 44368173, 36112695, 60997635, 44203, "SRX21410743", "SRS18649225", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.87519, null, 0.14838, null, 0.9362, null, 0.79824, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25213, "SRR25685557", "SRX21410743", "SRS18649225", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 4", "GSM7717534", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 4", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717534", "GSM7717534: control sample 4; Danio rerio; RNA Seq", "GSM7717534 r1", "GSM7717534", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L002_Ctrl4_cbc.fastq.gz", "fastq", 235587720.0, 3926462.0, "GSM7717534 r2", "0:60", "A:71954218;C:50127333;G:45371371;T:68077780;N:57018", 60, null, null, null, 71954218, 50127333, 45371371, 68077780, 57018, "SRX21410743", "SRS18649225", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.8759, null, 0.14468, null, 0.88075, null, 0.74532, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25214, "SRR25685558", "SRX21410743", "SRS18649225", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 4", "GSM7717534", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 4", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717534", "GSM7717534: control sample 4; Danio rerio; RNA Seq", "GSM7717534 r1", "GSM7717534", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L003_Ctrl4_cbc.fastq.gz", "fastq", 248320680.0, 4138678.0, "GSM7717534 r3", "0:60", "A:76188968;C:53138643;G:46699955;T:72274599;N:18515", 60, null, null, null, 76188968, 53138643, 46699955, 72274599, 18515, "SRX21410743", "SRS18649225", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.88396, null, 0.1471, null, 0.87864, null, 0.74275, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25215, "SRR25685559", "SRX21410743", "SRS18649225", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 4", "GSM7717534", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 4", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717534", "GSM7717534: control sample 4; Danio rerio; RNA Seq", "GSM7717534 r1", "GSM7717534", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L004_Ctrl4_cbc.fastq.gz", "fastq", 239678820.0, 3994647.0, "GSM7717534 r4", "0:60", "A:73122694;C:51017089;G:46184519;T:69330703;N:23815", 60, null, null, null, 73122694, 51017089, 46184519, 69330703, 23815, "SRX21410743", "SRS18649225", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.88113, null, 0.14666, null, 0.88045, null, 0.79921, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25216, "SRR25685560", "SRX21410742", "SRS18649224", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 3", "GSM7717533", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 3", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717533", "GSM7717533: control sample 3; Danio rerio; RNA Seq", "GSM7717533 r1", "GSM7717533", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L001_Ctrl3_cbc.fastq.gz", "fastq", 164862000.0, 2747700.0, "GSM7717533 r1", "0:60", "A:67317722;C:30175032;G:25320195;T:42019155;N:29896", 60, null, null, null, 67317722, 30175032, 25320195, 42019155, 29896, "SRX21410742", "SRS18649224", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.8874, null, 0.16231, null, 0.93513, null, 0.45903, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25217, "SRR25685561", "SRX21410742", "SRS18649224", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 3", "GSM7717533", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 3", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717533", "GSM7717533: control sample 3; Danio rerio; RNA Seq", "GSM7717533 r1", "GSM7717533", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L002_Ctrl3_cbc.fastq.gz", "fastq", 159878880.0, 2664648.0, "GSM7717533 r2", "0:60", "A:48277840;C:33800190;G:31556276;T:46206979;N:37595", 60, null, null, null, 48277840, 33800190, 31556276, 46206979, 37595, "SRX21410742", "SRS18649224", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.8874, null, 0.15941, null, 0.88038, null, 0.79589, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25218, "SRR25685562", "SRX21410742", "SRS18649224", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 3", "GSM7717533", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 3", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717533", "GSM7717533: control sample 3; Danio rerio; RNA Seq", "GSM7717533 r1", "GSM7717533", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L003_Ctrl3_cbc.fastq.gz", "fastq", 169506240.0, 2825104.0, "GSM7717533 r3", "0:60", "A:51435401;C:36027782;G:32684721;T:49346338;N:11998", 60, null, null, null, 51435401, 36027782, 32684721, 49346338, 11998, "SRX21410742", "SRS18649224", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.89554, null, 0.16117, null, 0.87947, null, 0.795, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25219, "SRR25685563", "SRX21410742", "SRS18649224", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 3", "GSM7717533", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 3", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717533", "GSM7717533: control sample 3; Danio rerio; RNA Seq", "GSM7717533 r1", "GSM7717533", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L004_Ctrl3_cbc.fastq.gz", "fastq", 163347840.0, 2722464.0, "GSM7717533 r4", "0:60", "A:49253957;C:34538564;G:32268358;T:47272095;N:14866", 60, null, null, null, 49253957, 34538564, 32268358, 47272095, 14866, "SRX21410742", "SRS18649224", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.89252, null, 0.15956, null, 0.8784, null, 0.79732, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25220, "SRR25685564", "SRX21410741", "SRS18649223", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 2", "GSM7717532", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 2", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717532", "GSM7717532: control sample 2; Danio rerio; RNA Seq", "GSM7717532 r1", "GSM7717532", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L001_Ctrl2_cbc.fastq.gz", "fastq", 19885560.0, 331426.0, "GSM7717532 r1", "0:60", "A:8615440;C:3592607;G:2886695;T:4787767;N:3051", 60, null, null, null, 8615440, 3592607, 2886695, 4787767, 3051, "SRX21410741", "SRS18649223", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.84848, null, 0.13671, null, 0.96136, null, 0.84253, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25221, "SRR25685565", "SRX21410741", "SRS18649223", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 2", "GSM7717532", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 2", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717532", "GSM7717532: control sample 2; Danio rerio; RNA Seq", "GSM7717532 r1", "GSM7717532", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L002_Ctrl2_cbc.fastq.gz", "fastq", 19226760.0, 320446.0, "GSM7717532 r2", "0:60", "A:5898378;C:4022375;G:3854218;T:5447181;N:4608", 60, null, null, null, 5898378, 4022375, 3854218, 5447181, 4608, "SRX21410741", "SRS18649223", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.84542, null, 0.13731, null, 0.94004, null, 0.38758, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25222, "SRR25685566", "SRX21410741", "SRS18649223", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 2", "GSM7717532", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 2", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717532", "GSM7717532: control sample 2; Danio rerio; RNA Seq", "GSM7717532 r1", "GSM7717532", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L003_Ctrl2_cbc.fastq.gz", "fastq", 20360520.0, 339342.0, "GSM7717532 r3", "0:60", "A:6273552;C:4289098;G:3982791;T:5813710;N:1369", 60, null, null, null, 6273552, 4289098, 3982791, 5813710, 1369, "SRX21410741", "SRS18649223", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.85213, null, 0.13819, null, 0.93929, null, 0.83913, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25223, "SRR25685567", "SRX21410741", "SRS18649223", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 2", "GSM7717532", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 2", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717532", "GSM7717532: control sample 2; Danio rerio; RNA Seq", "GSM7717532 r1", "GSM7717532", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L004_Ctrl2_cbc.fastq.gz", "fastq", 19742340.0, 329039.0, "GSM7717532 r4", "0:60", "A:6042722;C:4140425;G:3955209;T:5601961;N:2023", 60, null, null, null, 6042722, 4140425, 3955209, 5601961, 2023, "SRX21410741", "SRS18649223", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.84722, null, 0.13682, null, 0.93933, null, 0.83301, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25224, "SRR25685568", "SRX21410740", "SRS18649222", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 1", "GSM7717531", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 1", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717531", "GSM7717531: control sample 1; Danio rerio; RNA Seq", "GSM7717531 r1", "GSM7717531", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L001_Ctrl1_cbc.fastq.gz", "fastq", 296163420.0, 4936057.0, "GSM7717531 r1", "0:60", "A:121966307;C:53233433;G:44972413;T:75936522;N:54745", 60, null, null, null, 121966307, 53233433, 44972413, 75936522, 54745, "SRX21410740", "SRS18649222", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.88546, null, 0.17055, null, 0.92681, null, 0.76028, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25225, "SRR25685569", "SRX21410740", "SRS18649222", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 1", "GSM7717531", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 1", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717531", "GSM7717531: control sample 1; Danio rerio; RNA Seq", "GSM7717531 r1", "GSM7717531", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L002_Ctrl1_cbc.fastq.gz", "fastq", 287707980.0, 4795133.0, "GSM7717531 r2", "0:60", "A:87738683;C:59468794;G:56448494;T:83984130;N:67879", 60, null, null, null, 87738683, 59468794, 56448494, 83984130, 67879, "SRX21410740", "SRS18649222", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.88284, null, 0.16626, null, 0.86561, null, 0.74308, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25226, "SRR25685570", "SRX21410740", "SRS18649222", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 1", "GSM7717531", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 1", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717531", "GSM7717531: control sample 1; Danio rerio; RNA Seq", "GSM7717531 r1", "GSM7717531", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L003_Ctrl1_cbc.fastq.gz", "fastq", 303833460.0, 5063891.0, "GSM7717531 r3", "0:60", "A:93092013;C:63221167;G:58235370;T:89262119;N:22791", 60, null, null, null, 93092013, 63221167, 58235370, 89262119, 22791, "SRX21410740", "SRS18649222", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.89102, null, 0.16657, null, 0.86336, null, 0.75396, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25227, "SRR25685571", "SRX21410740", "SRS18649222", "SRP455779", "PRJNA1006658", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]", "GSE241157", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "control sample 1", "GSM7717531", null, "source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing", "control sample 1", "FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts", "adult heart", "zebrafish were treated with tamoxifen to induce Hmga1a overexpression", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:control|cell type:cardiomyocytes|treatment:14 days post tamoxifen", "GSM7717531", "GSM7717531: control sample 1; Danio rerio; RNA Seq", "GSM7717531 r1", "GSM7717531", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP455779", null, null, "HUB-PN-b004_HHHK2BGXN_S1_L004_Ctrl1_cbc.fastq.gz", "fastq", 293865840.0, 4897764.0, "GSM7717531 r4", "0:60", "A:89531768;C:60796725;G:57688758;T:85819485;N:29104", 60, null, null, null, 89531768, 60796725, 57688758, 85819485, 29104, "SRX21410740", "SRS18649222", "SRA1695358", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 1, 0.88911, null, 0.16498, null, 0.86145, null, 0.75653, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [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 12\u00b5l 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", null, "pubmed:38748804", null, "egr3 wild type siblings 2", "GSM7745909", null, "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", null, "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 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "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 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP457576", null, "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, null, null, null, 943794847, 792135324, 792042625, 945083925, 262663, "SRX21533024", "SRS18745490", "SRA1702458", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.68549, null, 0.04588, null, 0.76865, null, 0.44964, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "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 12\u00b5l 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", null, "pubmed:38748804", null, "egr3 wild type siblings 1", "GSM7745908", null, "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", null, "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 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "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 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP457576", null, "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, null, null, null, 1048107387, 905014546, 907455489, 1048528690, 142504, "SRX21533023", "SRS18745489", "SRA1702458", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94958, null, 0.06298, null, 0.74819, null, 0.45762, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "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 12\u00b5l 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", null, "pubmed:38748804", null, "egr3 mutants 2", "GSM7745907", null, "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", null, "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 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "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 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP457576", null, "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, null, null, null, 925832958, 788551205, 790129536, 927993012, 168547, "SRX21533022", "SRS18745488", "SRA1702458", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.75652, null, 0.04046, null, 0.76455, null, 0.46333, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "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 12\u00b5l 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", null, "pubmed:38748804", null, "egr3 mutants 1", "GSM7745906", null, "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", null, "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 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "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 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP457576", null, "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, null, null, null, 1016913415, 902500250, 903033204, 1016194618, 327860, "SRX21533021", "SRS18745487", "SRA1702458", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.9511, null, 0.05017, null, 0.75341, null, 0.47152, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-08-30", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [29086, "SRR27015250", "SRX22707800", "SRS19700101", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 3", "GSM7927521", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 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 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. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf", "GSM7927521", "GSM7927521: Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 3; Danio rerio; RNA Seq", "GSM7927521 r1", "GSM7927521", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___72h_b03_t01_m01_R1.fastq.gz", "fastq", 1709509823.0, 28403358.0, "GSM7927521 r1", "0:60.19", "A:400293032;C:330429588;G:326652799;T:383291002;N:268843402", 60, null, null, null, 400293032, 330429588, 326652799, 383291002, 268843402, "SRX22707800", "SRS19700101", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90079, null, 0.0827, null, 0.81406, null, 0.64557, null, 35, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [29087, "SRR27015251", "SRX22707799", "SRS19700100", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 2", "GSM7927520", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 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 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. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf", "GSM7927520", "GSM7927520: Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 2; Danio rerio; RNA Seq", "GSM7927520 r1", "GSM7927520", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___72h_b02_t01_m01_R1.fastq.gz", "fastq", 1740891025.0, 28211981.0, "GSM7927520 r1", "0:61.71", "A:419094150;C:347792831;G:345450108;T:407537501;N:221016435", 61, null, null, null, 419094150, 347792831, 345450108, 407537501, 221016435, "SRX22707799", "SRS19700100", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90091, null, 0.13293, null, 0.78464, null, 0.54281, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [29088, "SRR27015252", "SRX22707798", "SRS19700099", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 1", "GSM7927519", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 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 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. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf", "GSM7927519", "GSM7927519: Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 1; Danio rerio; RNA Seq", "GSM7927519 r1", "GSM7927519", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___72h_b01_t01_m01_R1.fastq.gz", "fastq", 1930552948.0, 30996774.0, "GSM7927519 r1", "0:62.28", "A:468769814;C:389869994;G:387622687;T:454801262;N:229489191", 62, null, null, null, 468769814, 389869994, 387622687, 454801262, 229489191, "SRX22707798", "SRS19700099", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90465, null, 0.10656, null, 0.79586, null, 0.55674, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [29089, "SRR27015253", "SRX22707797", "SRS19700098", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 3", "GSM7927518", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 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 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. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf", "GSM7927518", "GSM7927518: Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 3; Danio rerio; RNA Seq", "GSM7927518 r1", "GSM7927518", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___48h_b03_t01_m01_R1.fastq.gz", "fastq", 2161847345.0, 35921817.0, "GSM7927518 r1", "0:60.18", "A:505467877;C:418329045;G:416403136;T:483063599;N:338583688", 60, null, null, null, 505467877, 418329045, 416403136, 483063599, 338583688, "SRX22707797", "SRS19700098", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.89532, null, 0.08355, null, 0.82012, null, 0.68413, null, 35, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [29090, "SRR27015254", "SRX22707796", "SRS19700097", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 2", "GSM7927517", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 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 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. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf", "GSM7927517", "GSM7927517: Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 2; Danio rerio; RNA Seq", "GSM7927517 r1", "GSM7927517", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___48h_b02_t01_m01_R1.fastq.gz", "fastq", 2065547064.0, 31863833.0, "GSM7927517 r1", "0:64.82", "A:530497695;C:434164388;G:434118538;T:518043928;N:148722515", 64, null, null, null, 530497695, 434164388, 434118538, 518043928, 148722515, "SRX22707796", "SRS19700097", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91772, null, 0.17863, null, 0.76828, null, 0.49567, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [29091, "SRR27015255", "SRX22707795", "SRS19700096", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 1", "GSM7927516", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 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 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. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf", "GSM7927516", "GSM7927516: Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 1; Danio rerio; RNA Seq", "GSM7927516 r1", "GSM7927516", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___48h_b01_t01_m01_R1.fastq.gz", "fastq", 1619268089.0, 24941754.0, "GSM7927516 r1", "0:64.92", "A:410578311;C:344485123;G:343852178;T:401558739;N:118793738", 64, null, null, null, 410578311, 344485123, 343852178, 401558739, 118793738, "SRX22707795", "SRS19700096", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91693, null, 0.13175, null, 0.77082, null, 0.47511, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [29145, "SRR32025076", "SRX27375413", "SRS23810876", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 5  biol rep 1  adult aorta  3 aortas pooled", "GSM8741276", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 5  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741276", "GSM8741276: qKO 5  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741276 r1", "GSM8741276", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "10_qKO_B9_R1.fastq.gz", "fastq", 1749103950.0, 23321386.0, "GSM8741276 r1", "0:75", "A:608737363;C:302455983;G:338119173;T:499492171;N:299260", 75, null, null, null, 608737363, 302455983, 338119173, 499492171, 299260, "SRX27375413", "SRS23810876", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29146, "SRR32025077", "SRX27375412", "SRS23810877", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 4  biol rep 1  adult aorta  3 aortas pooled", "GSM8741275", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 4  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741275", "GSM8741275: qKO 4  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741275 r1", "GSM8741275", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "9_qKO_A9_R1.fastq.gz", "fastq", 1391151150.0, 18548682.0, "GSM8741275 r1", "0:75", "A:493715157;C:235480005;G:265878909;T:395857913;N:219166", 75, null, null, null, 493715157, 235480005, 265878909, 395857913, 219166, "SRX27375412", "SRS23810877", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29147, "SRR32025078", "SRX27375411", "SRS23810875", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 3  biol rep 1  adult aorta  3 aortas pooled", "GSM8741274", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 3  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741274", "GSM8741274: qKO 3  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741274 r1", "GSM8741274", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "8_qKO_H8_R1.fastq.gz", "fastq", 1548693000.0, 20649240.0, "GSM8741274 r1", "0:75", "A:546086416;C:265907989;G:302995102;T:433434795;N:268698", 75, null, null, null, 546086416, 265907989, 302995102, 433434795, 268698, "SRX27375411", "SRS23810875", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29148, "SRR32025079", "SRX27375410", "SRS23810873", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 2  biol rep 1  adult aorta  3 aortas pooled", "GSM8741273", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 2  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741273", "GSM8741273: qKO 2  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741273 r1", "GSM8741273", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "7_qKO_G8_R1.fastq.gz", "fastq", 1420837575.0, 18944501.0, "GSM8741273 r1", "0:75", "A:505066296;C:237130175;G:277345211;T:401058536;N:237357", 75, null, null, null, 505066296, 237130175, 277345211, 401058536, 237357, "SRX27375410", "SRS23810873", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29149, "SRR32025080", "SRX27375409", "SRS23810874", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 1  biol rep 1  adult aorta  3 aortas pooled", "GSM8741272", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 1  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741272", "GSM8741272: qKO 1  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741272 r1", "GSM8741272", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "6_qKO_F8_R1.fastq.gz", "fastq", 1486031025.0, 19813747.0, "GSM8741272 r1", "0:75", "A:520876345;C:250796628;G:293184034;T:420907913;N:266105", 75, null, null, null, 520876345, 250796628, 293184034, 420907913, 266105, "SRX27375409", "SRS23810874", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29150, "SRR32025081", "SRX27375408", "SRS23810872", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 5  biol rep 1  adult aorta  3 aortas pooled", "GSM8741271", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 5  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741271", "GSM8741271: control 5  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741271 r1", "GSM8741271", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "5_wt_control_E8_R1.fastq.gz", "fastq", 1415975175.0, 18879669.0, "GSM8741271 r1", "0:75", "A:499498659;C:237283969;G:278581269;T:400389063;N:222215", 75, null, null, null, 499498659, 237283969, 278581269, 400389063, 222215, "SRX27375408", "SRS23810872", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29151, "SRR32025082", "SRX27375407", "SRS23810871", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 4  biol rep 1  adult aorta  3 aortas pooled", "GSM8741270", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 4  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741270", "GSM8741270: control 4  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741270 r1", "GSM8741270", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "4_wt_control_D8_R1.fastq.gz", "fastq", 1448565375.0, 19314205.0, "GSM8741270 r1", "0:75", "A:515361139;C:240035739;G:286658162;T:406262131;N:248204", 75, null, null, null, 515361139, 240035739, 286658162, 406262131, 248204, "SRX27375407", "SRS23810871", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29152, "SRR32025083", "SRX27375406", "SRS23810870", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 3  biol rep 1  adult aorta  3 aortas pooled", "GSM8741269", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 3  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741269", "GSM8741269: control 3  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741269 r1", "GSM8741269", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "3_wt_control_C8_R1.fastq.gz", "fastq", 1171513275.0, 15620177.0, "GSM8741269 r1", "0:75", "A:417371801;C:198042286;G:227929434;T:328006138;N:163616", 75, null, null, null, 417371801, 198042286, 227929434, 328006138, 163616, "SRX27375406", "SRS23810870", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29153, "SRR32025084", "SRX27375405", "SRS23810869", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 2  biol rep 1  adult aorta  3 aortas pooled", "GSM8741268", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 2  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741268", "GSM8741268: control 2  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741268 r1", "GSM8741268", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "2_wt_control_B8_R1.fastq.gz", "fastq", 1379973000.0, 18399640.0, "GSM8741268 r1", "0:75", "A:487735196;C:232122567;G:270442978;T:389464154;N:208105", 75, null, null, null, 487735196, 232122567, 270442978, 389464154, 208105, "SRX27375405", "SRS23810869", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29154, "SRR32025085", "SRX27375404", "SRS23810868", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 1  biol rep 1  adult aorta  3 aortas pooled", "GSM8741267", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 1  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741267", "GSM8741267: control 1  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741267 r1", "GSM8741267", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "1_wt_control_A8_R1.fastq.gz", "fastq", 1068193125.0, 14242575.0, "GSM8741267 r1", "0:75", "A:379776425;C:179521683;G:209337737;T:299415096;N:142184", 75, null, null, null, 379776425, 179521683, 209337737, 299415096, 142184, "SRX27375404", "SRS23810868", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29569, "SRR27368685", "SRX23045203", "SRS20006222", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "500kGFPneg6 Non cardiomyocytes", "GSM7995233", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control|geo loc name:missing|collection date:missing", "500kGFPneg6 Non cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control", "GSM7995233", "GSM7995233: 500kGFPneg6 Non cardiomyocytes; Danio rerio; RNA Seq", "GSM7995233 r1", "GSM7995233", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "500kGFPneg6_S42_L008_R1_001.fastq.gz", "fastq", 527477356.0, 10449387.0, "GSM7995233 r1", "0:50.48", "A:141759410;C:113279303;G:116384028;T:155860577;N:194038", 50, null, null, null, 141759410, 113279303, 116384028, 155860577, 194038, "SRX23045203", "SRS20006222", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.79175, null, 0.2711, null, 0.7587, null, 0.61924, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29570, "SRR27368686", "SRX23045202", "SRS20006221", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "500kGFPneg5 Non cardiomyocytes", "GSM7995232", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control|geo loc name:missing|collection date:missing", "500kGFPneg5 Non cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control", "GSM7995232", "GSM7995232: 500kGFPneg5 Non cardiomyocytes; Danio rerio; RNA Seq", "GSM7995232 r1", "GSM7995232", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "500kGFPneg5_S41_L008_R1_001.fastq.gz", "fastq", 3356204764.0, 66511806.0, "GSM7995232 r1", "0:50.46", "A:860342578;C:766593257;G:774473426;T:953992775;N:802728", 50, null, null, null, 860342578, 766593257, 774473426, 953992775, 802728, "SRX23045202", "SRS20006221", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.70469, null, 0.23332, null, 0.76992, null, 0.62712, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29571, "SRR27368687", "SRX23045201", "SRS20006220", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "500kGFPneg4 Non cardiomyocytes", "GSM7995231", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control|geo loc name:missing|collection date:missing", "500kGFPneg4 Non cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control", "GSM7995231", "GSM7995231: 500kGFPneg4 Non cardiomyocytes; Danio rerio; RNA Seq", "GSM7995231 r1", "GSM7995231", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "500kGFPneg4_S40_L008_R1_001.fastq.gz", "fastq", 3075367681.0, 60986692.0, "GSM7995231 r1", "0:50.43", "A:807059039;C:682279458;G:696326840;T:888937765;N:764579", 50, null, null, null, 807059039, 682279458, 696326840, 888937765, 764579, "SRX23045201", "SRS20006220", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.74255, null, 0.26699, null, 0.76786, null, 0.63053, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29572, "SRR27368688", "SRX23045200", "SRS20006219", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "30kGFPpos3 Cardiomyocytes", "GSM7995230", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control|geo loc name:missing|collection date:missing", "30kGFPpos3 Cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control", "GSM7995230", "GSM7995230: 30kGFPpos3 Cardiomyocytes; Danio rerio; RNA Seq", "GSM7995230 r1", "GSM7995230", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "30kGFPpos3_S39_L008_R1_001.fastq.gz", "fastq", 2938808771.0, 58361915.0, "GSM7995230 r1", "0:50.35", "A:533261626;C:883704329;G:825929620;T:694986734;N:926462", 50, null, null, null, 533261626, 883704329, 825929620, 694986734, 926462, "SRX23045200", "SRS20006219", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.12924, null, 0.05415, null, 0.92034, null, 0.70896, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29573, "SRR27368689", "SRX23045199", "SRS20006218", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "30kGFPpos2 Cardiomyocytes", "GSM7995229", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control|geo loc name:missing|collection date:missing", "30kGFPpos2 Cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control", "GSM7995229", "GSM7995229: 30kGFPpos2 Cardiomyocytes; Danio rerio; RNA Seq", "GSM7995229 r1", "GSM7995229", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "30kGFPpos2_S38_L008_R1_001.fastq.gz", "fastq", 3006409096.0, 59645543.0, "GSM7995229 r1", "0:50.40", "A:560839480;C:885691877;G:830121593;T:728932219;N:823927", 50, null, null, null, 560839480, 885691877, 830121593, 728932219, 823927, "SRX23045199", "SRS20006218", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.17805, null, 0.06115, null, 0.89769, null, 0.68731, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29574, "SRR27368690", "SRX23045198", "SRS20006217", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "30kGFPpos1 Cardiomyocytes", "GSM7995228", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control|geo loc name:missing|collection date:missing", "30kGFPpos1 Cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control", "GSM7995228", "GSM7995228: 30kGFPpos1 Cardiomyocytes; Danio rerio; RNA Seq", "GSM7995228 r1", "GSM7995228", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "30kGFPpos1_S37_L008_R1_001.fastq.gz", "fastq", 3254639839.0, 64665631.0, "GSM7995228 r1", "0:50.33", "A:545193535;C:1023804678;G:938318027;T:746302007;N:1021592", 50, null, null, null, 545193535, 1023804678, 938318027, 746302007, 1021592, "SRX23045198", "SRS20006217", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.05453, null, 0.01921, null, 0.9643, null, 0.78064, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [30006, "SRR27663958", "SRX23331822", "SRS20194274", "SRP484810", "PRJNA1066877", "p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation", "GSE253758", "Transcriptome Analysis", "While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.", null, "pubmed:39242546", null, "NFKB   biol rep 3", "GSM8027552", null, "tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted|geo loc name:missing|collection date:missing", "NFKB   biol rep 3", "Data was analyzed by ROSALIND\u00ae https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene", "endothelial cells", "22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 \u00b5g/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco\u2032s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 \u00b5m nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX\u2122 Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 \u00b5l of RLT buffer.", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer\u2019s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", "Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 \u00b0C on a 14 hr light/10 hr dark cycle.", "cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted", "GSM8027552", "GSM8027552: NFKB   biol rep 3; Danio rerio; RNA Seq", "GSM8027552 r1", "GSM8027552", "1", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484810", null, "loader:fastq load.py", "6-RNA-1001_S6_L001_R1_001.fastq.gz", "fastq", 7566894200.0, 75668942.0, "GSM8027552 r1", "0:100", "A:2055514007;C:1776454819;G:1779667416;T:1955100553;N:157405", 100, null, null, null, 2055514007, 1776454819, 1779667416, 1955100553, 157405, "SRX23331822", "SRS20194274", "SRA1788753", "Iowa State University", "Iowa State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-01-19", "Multi-stage", "Multi-stage", "Endothelium", "Cardiovascular System"], [30007, "SRR27663959", "SRX23331821", "SRS20194275", "SRP484810", "PRJNA1066877", "p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation", "GSE253758", "Transcriptome Analysis", "While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.", null, "pubmed:39242546", null, "NFKB   biol rep 2", "GSM8027551", null, "tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted|geo loc name:missing|collection date:missing", "NFKB   biol rep 2", "Data was analyzed by ROSALIND\u00ae https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene", "endothelial cells", "22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 \u00b5g/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco\u2032s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 \u00b5m nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX\u2122 Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 \u00b5l of RLT buffer.", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer\u2019s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", "Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 \u00b0C on a 14 hr light/10 hr dark cycle.", "cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted", "GSM8027551", "GSM8027551: NFKB   biol rep 2; Danio rerio; RNA Seq", "GSM8027551 r1", "GSM8027551", "1", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484810", null, "loader:fastq load.py", "5-RNA-0901_S5_L001_R1_001.fastq.gz", "fastq", 8077393600.0, 80773936.0, "GSM8027551 r1", "0:100", "A:2195547260;C:1863472493;G:1887149224;T:2131055526;N:169097", 100, null, null, null, 2195547260, 1863472493, 1887149224, 2131055526, 169097, "SRX23331821", "SRS20194275", "SRA1788753", "Iowa State University", "Iowa State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-01-19", "Multi-stage", "Multi-stage", "Endothelium", "Cardiovascular System"], [30008, "SRR27663960", "SRX23331820", "SRS20194273", "SRP484810", "PRJNA1066877", "p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation", "GSE253758", "Transcriptome Analysis", "While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.", null, "pubmed:39242546", null, "NFKB   biol rep 1", "GSM8027550", null, "tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted|geo loc name:missing|collection date:missing", "NFKB   biol rep 1", "Data was analyzed by ROSALIND\u00ae https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene", "endothelial cells", "22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 \u00b5g/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco\u2032s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 \u00b5m nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX\u2122 Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 \u00b5l of RLT buffer.", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer\u2019s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", "Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 \u00b0C on a 14 hr light/10 hr dark cycle.", "cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted", "GSM8027550", "GSM8027550: NFKB   biol rep 1; Danio rerio; RNA Seq", "GSM8027550 r1", "GSM8027550", "1", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484810", null, "loader:fastq load.py", "4-RNA-1001_S4_L001_R1_001.fastq.gz", "fastq", 6536957300.0, 65369573.0, "GSM8027550 r1", "0:100", "A:1764502914;C:1531091007;G:1533764634;T:1707464708;N:134037", 100, null, null, null, 1764502914, 1531091007, 1533764634, 1707464708, 134037, "SRX23331820", "SRS20194273", "SRA1788753", "Iowa State University", "Iowa State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-01-19", "Multi-stage", "Multi-stage", "Endothelium", "Cardiovascular System"], [30009, "SRR27663961", "SRX23331819", "SRS20194272", "SRP484810", "PRJNA1066877", "p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation", "GSE253758", "Transcriptome Analysis", "While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.", null, "pubmed:39242546", null, "NFKB+  biol rep 3", "GSM8027549", null, "tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing", "NFKB+  biol rep 3", "Data was analyzed by ROSALIND\u00ae https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene", "endothelial cells", "22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 \u00b5g/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco\u2032s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 \u00b5m nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX\u2122 Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 \u00b5l of RLT buffer.", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer\u2019s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", "Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 \u00b0C on a 14 hr light/10 hr dark cycle.", "cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted", "GSM8027549", "GSM8027549: NFKB+  biol rep 3; Danio rerio; RNA Seq", "GSM8027549 r1", "GSM8027549", "1", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484810", null, "loader:fastq load.py", "3-RNA-1001_S3_L001_R1_001.fastq.gz", "fastq", 10375249700.0, 103752497.0, "GSM8027549 r1", "0:100", "A:2873369145;C:2335823279;G:2356855554;T:2808985435;N:216287", 100, null, null, null, 2873369145, 2335823279, 2356855554, 2808985435, 216287, "SRX23331819", "SRS20194272", "SRA1788753", "Iowa State University", "Iowa State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-01-19", "Multi-stage", "Multi-stage", "Endothelium", "Cardiovascular System"], [30010, "SRR27663962", "SRX23331818", "SRS20194271", "SRP484810", "PRJNA1066877", "p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation", "GSE253758", "Transcriptome Analysis", "While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.", null, "pubmed:39242546", null, "NFKB+  biol rep 2", "GSM8027548", null, "tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing", "NFKB+  biol rep 2", "Data was analyzed by ROSALIND\u00ae https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene", "endothelial cells", "22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 \u00b5g/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco\u2032s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 \u00b5m nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX\u2122 Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 \u00b5l of RLT buffer.", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer\u2019s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", "Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 \u00b0C on a 14 hr light/10 hr dark cycle.", "cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted", "GSM8027548", "GSM8027548: NFKB+  biol rep 2; Danio rerio; RNA Seq", "GSM8027548 r1", "GSM8027548", "1", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484810", null, "loader:fastq load.py", "2-RNA-1001_S2_L001_R1_001.fastq.gz", "fastq", 5743794100.0, 57437941.0, "GSM8027548 r1", "0:100", "A:1588561398;C:1297479370;G:1310669617;T:1546965673;N:118042", 100, null, null, null, 1588561398, 1297479370, 1310669617, 1546965673, 118042, "SRX23331818", "SRS20194271", "SRA1788753", "Iowa State University", "Iowa State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-01-19", "Multi-stage", "Multi-stage", "Endothelium", "Cardiovascular System"], [30011, "SRR27663963", "SRX23331817", "SRS20194270", "SRP484810", "PRJNA1066877", "p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation", "GSE253758", "Transcriptome Analysis", "While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.", null, "pubmed:39242546", null, "NFKB+  biol rep 1", "GSM8027547", null, "tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing", "NFKB+  biol rep 1", "Data was analyzed by ROSALIND\u00ae https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene", "endothelial cells", "22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 \u00b5g/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco\u2032s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 \u00b5m nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX\u2122 Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 \u00b5l of RLT buffer.", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer\u2019s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", "Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 \u00b0C on a 14 hr light/10 hr dark cycle.", "cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted", "GSM8027547", "GSM8027547: NFKB+  biol rep 1; Danio rerio; RNA Seq", "GSM8027547 r1", "GSM8027547", "1", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484810", null, "loader:fastq load.py", "1-RNA-0917_S1_L001_R1_001.fastq.gz", "fastq", 6201542500.0, 62015425.0, "GSM8027547 r1", "0:100", "A:1696049302;C:1431941155;G:1441395671;T:1632027072;N:129300", 100, null, null, null, 1696049302, 1431941155, 1441395671, 1632027072, 129300, "SRX23331817", "SRS20194270", "SRA1788753", "Iowa State University", "Iowa State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-01-19", "Multi-stage", "Multi-stage", "Endothelium", "Cardiovascular System"], [30512, "SRR27764782", "SRX23429747", "SRS20284188", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 4", "GSM8042779", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 4", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042779", "GSM8042779: Cardiac ventricle  cox7a1 /   replicate 4; Danio rerio; RNA Seq", "GSM8042779 r1", "GSM8042779", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_10_Directional_S8_R1_001.fastq.gz", "fastq", 8619450300.0, 86194503.0, "GSM8042779 r1", "0:100", "A:2183264320;C:2042597849;G:2002385828;T:2389908983;N:1293320", 100, null, null, null, 2183264320, 2042597849, 2002385828, 2389908983, 1293320, "SRX23429747", "SRS20284188", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30513, "SRR27764783", "SRX23429746", "SRS20284187", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 3", "GSM8042778", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 3", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042778", "GSM8042778: Cardiac ventricle  cox7a1 /   replicate 3; Danio rerio; RNA Seq", "GSM8042778 r1", "GSM8042778", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_9_Directional_S7_R1_001.fastq.gz", "fastq", 6466746100.0, 64667461.0, "GSM8042778 r1", "0:100", "A:1708351950;C:1464168743;G:1452219209;T:1841033764;N:972434", 100, null, null, null, 1708351950, 1464168743, 1452219209, 1841033764, 972434, "SRX23429746", "SRS20284187", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30514, "SRR27764784", "SRX23429745", "SRS20284186", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 2", "GSM8042777", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 2", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042777", "GSM8042777: Cardiac ventricle  cox7a1 /   replicate 2; Danio rerio; RNA Seq", "GSM8042777 r1", "GSM8042777", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_8_Directional_S6_R1_001.fastq.gz", "fastq", 6766795300.0, 67667953.0, "GSM8042777 r1", "0:100", "A:1803038642;C:1540664299;G:1518741633;T:1903355305;N:995421", 100, null, null, null, 1803038642, 1540664299, 1518741633, 1903355305, 995421, "SRX23429745", "SRS20284186", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30515, "SRR27764785", "SRX23429744", "SRS20284185", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 1", "GSM8042776", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 1", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042776", "GSM8042776: Cardiac ventricle  cox7a1 /   replicate 1; Danio rerio; RNA Seq", "GSM8042776 r1", "GSM8042776", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_7_Directional_S5_R1_001.fastq.gz", "fastq", 5583049300.0, 55830493.0, "GSM8042776 r1", "0:100", "A:1479820662;C:1265599242;G:1251078421;T:1585727832;N:823143", 100, null, null, null, 1479820662, 1265599242, 1251078421, 1585727832, 823143, "SRX23429744", "SRS20284185", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30516, "SRR27764786", "SRX23429743", "SRS20284184", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 4", "GSM8042775", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 4", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042775", "GSM8042775: Cardiac ventricle  wt sibling  replicate 4; Danio rerio; RNA Seq", "GSM8042775 r1", "GSM8042775", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_5_Directional_S4_R1_001.fastq.gz", "fastq", 6851217800.0, 68512178.0, "GSM8042775 r1", "0:100", "A:1837112549;C:1539284911;G:1515596368;T:1958221274;N:1002698", 100, null, null, null, 1837112549, 1539284911, 1515596368, 1958221274, 1002698, "SRX23429743", "SRS20284184", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30517, "SRR27764787", "SRX23429742", "SRS20284183", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 3", "GSM8042774", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 3", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042774", "GSM8042774: Cardiac ventricle  wt sibling  replicate 3; Danio rerio; RNA Seq", "GSM8042774 r1", "GSM8042774", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_3_Directional_S3_R1_001.fastq.gz", "fastq", 7036251700.0, 70362517.0, "GSM8042774 r1", "0:100", "A:1881612688;C:1574593657;G:1570342252;T:2008668471;N:1034632", 100, null, null, null, 1881612688, 1574593657, 1570342252, 2008668471, 1034632, "SRX23429742", "SRS20284183", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30518, "SRR27764788", "SRX23429741", "SRS20284182", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 2", "GSM8042773", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 2", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042773", "GSM8042773: Cardiac ventricle  wt sibling  replicate 2; Danio rerio; RNA Seq", "GSM8042773 r1", "GSM8042773", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_2_Directional_S2_R1_001.fastq.gz", "fastq", 6856428200.0, 68564282.0, "GSM8042773 r1", "0:100", "A:1790369167;C:1572129686;G:1566120109;T:1926782247;N:1026991", 100, null, null, null, 1790369167, 1572129686, 1566120109, 1926782247, 1026991, "SRX23429741", "SRS20284182", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30519, "SRR27764789", "SRX23429740", "SRS20284181", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 1", "GSM8042772", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 1", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042772", "GSM8042772: Cardiac ventricle  wt sibling  replicate 1; Danio rerio; RNA Seq", "GSM8042772 r1", "GSM8042772", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_1_Directional_S1_R1_001.fastq.gz", "fastq", 7089416800.0, 70894168.0, "GSM8042772 r1", "0:100", "A:1855346146;C:1626812736;G:1599932420;T:2006283874;N:1041624", 100, null, null, null, 1855346146, 1626812736, 1599932420, 2006283874, 1041624, "SRX23429740", "SRS20284181", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "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", null, "injured tissue  myd88+/+  24 hpci 2", "GSM8159071", null, "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\u2019s protocol Vazyme.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "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, null, null, null, 660213492, 527347733, 572126573, 694765347, 192831, "SRX24015869", "SRS20810998", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "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", null, "injured tissue  myd88+/+  1 hpci 2", "GSM8159070", null, "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\u2019s protocol Vazyme.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "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, null, null, null, 713621237, 556223861, 630990745, 773686189, 132510, "SRX24015868", "SRS20810997", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "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", null, "ventricle  myd88+/+  untouched 2", "GSM8159069", null, "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\u2019s protocol Vazyme.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "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, null, null, null, 560190602, 446185315, 485011548, 601082958, 161983, "SRX24015867", "SRS20810996", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "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", null, "injured tissue  myd88+/+  24 hpci 1", "GSM8159068", null, "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\u2019s protocol Vazyme.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "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, null, null, null, 290655996, 222128471, 247491826, 299784598, 87219, "SRX24015866", "SRS20810995", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "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", null, "injured tissue  myd88+/+  1 hpci 1", "GSM8159067", null, "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\u2019s protocol Vazyme.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "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, null, null, null, 689702458, 551265040, 603307580, 750425733, 85213, "SRX24015865", "SRS20810994", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "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", null, "ventricle  myd88+/+  untouched 1", "GSM8159066", null, "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\u2019s protocol Vazyme.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "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, null, null, null, 562046544, 458761205, 496224794, 606313940, 169522, "SRX24015864", "SRS20810993", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "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", null, "injured tissue  myd88 /   24 hpci 2", "GSM8159065", null, "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\u2019s protocol Vazyme.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "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, null, null, null, 669128241, 547606289, 587771598, 704439682, 197535, "SRX24015863", "SRS20810992", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "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", null, "injured tissue  myd88 /   1 hpci 2", "GSM8159064", null, "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\u2019s protocol Vazyme.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "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, null, null, null, 690941775, 542509296, 605002938, 746301098, 92078, "SRX24015862", "SRS20810991", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "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", null, "ventricle  myd88 /   untouched 2", "GSM8159063", null, "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\u2019s protocol Vazyme.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "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, null, null, null, 588370831, 457110464, 507924919, 624586577, 171985, "SRX24015861", "SRS20810990", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "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", null, "injured tissue  myd88 /   24 hpci 1", "GSM8159062", null, "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\u2019s protocol Vazyme.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "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, null, null, null, 621931320, 501998000, 541224122, 657957821, 186991, "SRX24015860", "SRS20810989", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "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", null, "injured tissue  myd88 /   1 hpci 1", "GSM8159061", null, "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\u2019s protocol Vazyme.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "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, null, null, null, 679380332, 554919862, 604907160, 746451941, 77570, "SRX24015859", "SRS20810988", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "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", null, "ventricle  myd88 /   untouched 1", "GSM8159060", null, "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\u2019s protocol Vazyme.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "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, null, null, null, 623574024, 490503071, 538918126, 667825381, 187098, "SRX24015858", "SRS20810987", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2024-03-21", "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.", null, "pubmed:39612288", null, "wild type heart  96 hours post cryoinjury 3", "GSM8217704", null, "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", null, "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 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "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 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "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, null, null, null, 848972796, 741588101, 760680137, 905607069, 1135089, "SRX24311225", "SRS21073227", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94185, null, 0.087, null, 0.72478, null, 0.50388, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:39612288", null, "wild type heart  96 hours post cryoinjury 2", "GSM8217703", null, "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", null, "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 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "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 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "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, null, null, null, 1003402543, 880721584, 903469106, 1075304136, 1721885, "SRX24311224", "SRS21073229", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.93928, null, 0.08915, null, 0.72348, null, 0.49993, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:39612288", null, "wild type heart  96 hours post cryoinjury 1", "GSM8217702", null, "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", null, "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 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "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 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "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, null, null, null, 928171678, 814216251, 835024543, 992630615, 1435313, "SRX24311223", "SRS21073228", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94111, null, 0.08647, null, 0.72922, null, 0.50812, null, 42, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:39612288", null, "flt1 mutant heart  96 hours post cryoinjury 3", "GSM8217701", null, "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", null, "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 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "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 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "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, null, null, null, 1050667797, 938174838, 953989485, 1140941596, 1585554, "SRX24311222", "SRS21073226", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94035, null, 0.08631, null, 0.72376, null, 0.49828, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", 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