{"database": "metadata", "table": "run_metadata", "rows": [[76699, "SRR25258795", "SRX21004794", "SRS18278659", "SRP449335", "PRJNA994500", "Infection induced inflammation impairs wound healing through IL 1b signaling", "GSE237265", "Transcriptome Analysis", "Wound healing is impaired by infection; however  how microbe induced inflammation modulates tissue repair remains unclear. We took advantage of the optical transparency of zebrafish and a genetically tractable microbe  Listeria monocytogenes  to probe the role of infection and inflammation in wound healing. We found a critical window of microbial clearance necessary to limit persistent inflammation and enable efficient wound repair. Infection with bacteria engineered to activate the inflammasome  Lm Pyro  induced persistent inflammation and impaired healing despite low bacterial burden. In contrast  infection with an anti inflammatory  apoptosis inducing strain  Lm Apo  had similar infectious burden but was associated with rapid wound repair. Inflammatory infections induced il 1b expression and blocking IL 1R signaling partially rescued wound healing in the presence of persistent infection. Taken together  our findings suggest that the dynamics of microbe induced tissue inflammation impacts repair in complex tissue damage independent of bacterial load  with a critical early window for efficient tissue repair. Overall design: RNA seq gene expression analysis of caudal fins of 4 dpf zebrafish post wounding and infection n = 9: 3 replicates from each of 3 treatments", null, "pubmed:38577110", null, "D9 uninfected", "GSM7598093", null, "source name:caudal fin|tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:control|treatment id:EFO:0001461|geo loc name:missing|collection date:missing", "D9 uninfected", "Reads were aligned to the genome using STAR v2.7.8a with default parameters except for except for outFilterMismatchNoverLmax 0.1  outFilterScoreMinOverLread 0.33  and outFilterMatchNminOverLread 0.33  Gene abundances were estimated using RSEM v1.3.3 with additonal parameters   paired end    estimate rspd  and   strandedness none Assembly: GRCz11 Ensembl 95 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file", "caudal fin", "3 dpf zebrafish were placed in 5 mL E3 medium containing Tricaine with 5x108 CFU L. monocytogenes and caudal fins of larvae were transected using surgical blade Feather no. 10 at the tip of the notochord without xxx to the notochord. For uninfected wounds  sterile PBS was added in the medium instead of bacterial resuspension.", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", "Upon fertilization  zebrafish embryos were transferred into E3 medium and maintained at 28.5\u00b0C.", "tissue:caudal fin|tissue id:ZFA:0001058|line:AB|age:Larval:Day 4|age id:ZFS:0000036|treatment:control|treatment id:EFO:0001461", "GSM7598093", "GSM7598093: D9 uninfected; Danio rerio; RNA Seq", "GSM7598093 r1", "GSM7598093", "1", "Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit Invitrogen. PolyA  NEBNext\u00ae Ultra\u2122 II RNA Library Prep Kit for Illumina\u00ae was used for library construction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP449335", null, "loader:fastq load.py", "D9_R1_001.fastq.gz D9_R2_001.fastq.gz", "fastq fastq", 8686889570.0, 28764535.0, "GSM7598093 r1", "0:151 1:151", "A:2296370538;C:2049767640;G:2085089469;T:2255082220;N:579703", 151, 151, null, null, 2296370538, 2049767640, 2085089469, 2255082220, 579703, "SRX21004794", "SRS18278659", "SRA1672430", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.936, 0.93538, 0.07614, 0.07655, 0.70153, 0.70826, 0.48553, 0.48537, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-07-13", "Larval", "Larval", "Fin", "Surface Structure"]], "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": ["76699"], "units": {}, "query_ms": 11.544621998837101}