{"database": "metadata", "table": "run_metadata", "rows": [[52895, "SRR9336429", "SRX6102335", "SRS5002791", "SRP202197", "PRJNA550047", "Transcriptomic profiling of non regenerative vegfchy / ;vegfd /  mutant hearts reveals a marked inflammatory response [fixed tissue]", "GSE133129", "Transcriptome Analysis", "To determine whether lymphangiogenesis is required for cardiac regeneration  vegfchy / ;vegfd /  double mutants and control hearts were collected and analyzed at 180 days post cryoinjury  this corresponds to a time point when the regenerative response is normally completed in wild type zebrafish. Surprisingly  the vast majority 70% of vegfchy / ;vegfd /  mutants  which completely lack cardiac lymphatics  were able to mount a complete regenerative response without xxx signs of fibrosis. We found that the cardiac regenerative response was impaired only in a subset 3/8 of vegfchy / ;vegfd /  mutants  which were characterized by large deposits of fibrotic scar tissue present at the injury site. To profile vegfc/d dependent genetic pathways contributing to lymphangiogenesis in cardiac regeneration  we performed RNA seq on cryosections from control and mutant ventricles at 180 days following cryoinjury. Overall  vegfchy / ;vegfd /  mutant ventricles were characterized by an up regulation of pathways related to metabolism  inflammation  hemostasis  negative regulation of FGFR signaling  translation  protein maturation and nonsense mediated decay compared to control hearts. These findings are consistent with the cardiac hypertrophy phenotype in vegfchy / ;vegfd /  mutants. To determine the molecular basis of the regenerative capacity within the mutant fish population  we next compared the transcriptional profiles of vegfchy / ;vegfd /  mutant hearts that did not regenerate n=3 with the profiles of mutant hearts which recovered completely n=5 at 180 days post cryoinjury. The subset of vegfchy / ;vegfd /  mutant hearts that failed to regenerate were characterized by an enrichment of inflammatory pathways  in particular TRAF6 mediated IRF7 activation  interferon alpha beta signaling and regulation of IFNA signaling. These findings suggest that loss of the vegfc/d signaling axis causes a sustained and pronounced inflammatory response following injury. This change in the cardiac micro environment seems to favor adverse conditions which impair the regenerative process. Overall design: Transcriptional analysis of hearts from 2 different zebrafish lines following cryoinjury.", "parent bioproject:PRJNA550046", "pubmed:31452940", null, "WC7", "GSM3900720", null, "source name:zebrafish ventricle with cryoinjury|tissue:heart|chamber:ventricle|genotype:vegfc+/+:vegfd+/+", "WC7", "Trimming using the Skewer version 0.2.2. Aligned to the zebrafish genome GRCz11.95 using Burrows Wheeler Aligner BWA  version 0.7.17. Mapped reads were counted with featureCounts v1.5.0. Genes were filtered if the sums of reads across all samples was less than 10. Genome build: GRCz11.95 Supplementary files format and content: Filtered raw counts of sequencing reads.", "zebrafish ventricle with cryoinjury", null, "RNA extraction was performed from PFA fixed 4% PFA and Tissue Tek\u00ae O.C.T. compound ProSciTech embedded heart cryosections 8\u03bcm. A scalpel was used to collect 12 sections of the ventricle per sample. Sections were transferred to a tube on ice containing 100\u03bcl of TRIzol\u00ae Reagent 15596018  Invitrogen and then processed with Direct zol\u2122 RNA Microprep kit Zymo/ Integrated Science  R2061. Ribosomal RNA was depleted from total RNA using NEBNext rRNA Depletion Kit Human/Mouse/Rat E6310  New England Biolabs followed by library generation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina E7760  New England Biolabs to select library fragment sizes of 200 400bp.", null, "tissue:heart|chamber:ventricle|genotype:vegfc+/+:vegfd+/+", "GSM3900720", "GSM3900720: WC7; Danio rerio; RNA Seq", "GSM3900720", null, "1", "RNA extraction was performed from PFA fixed 4% PFA and Tissue Tek\u00ae O.C.T. compound ProSciTech embedded heart cryosections 8\u03bcm. A scalpel was used to collect 12 sections of the ventricle per sample. Sections were transferred to a tube on ice containing 100\u03bcl of TRIzol\u00ae Reagent 15596018  Invitrogen and then processed with Direct zol\u2122 RNA Microprep kit Zymo/ Integrated Science  R2061. Ribosomal RNA was depleted from total RNA using NEBNext rRNA Depletion Kit Human/Mouse/Rat E6310  New England Biolabs followed by library generation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina E7760  New England Biolabs to select library fragment sizes of 200 400bp.", "GEO Accession:GSM3900720", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP202197", null, null, "WC7_R1.fastq.gz WC7_R2.fastq.gz", "fastq fastq", 6290292944.0, 20908933.0, "GSM3900720 r1", "0:150.47 1:150.37", "A:1329641164;C:1807654552;G:1814704317;T:1337768126;N:524785", 150, 150, null, null, 1329641164, 1807654552, 1814704317, 1337768126, 524785, "SRX6102335", "SRS5002791", "SRA902344", "GEO", "Cardiac Regeneration, Cell Biology, Murdoch Children's Research Institute", 2, 0.17546, 0.18657, 0.159, 0.16765, 0.99679, 0.99691, 0.66677, 0.67512, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "Australia", "2019-06-21", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["52895"], "units": {}, "query_ms": 11.660681000648765}