{"database": "metadata", "table": "run_metadata", "rows": [[33851, "SRR30769776", "SRX26172021", "SRS22716035", "SRP534198", "PRJNA1164198", "Analysis of The Senescence Secretome During Zebrafish Retina Regeneration", "GSE277792", "Transcriptome Analysis", "Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with M\u00fcller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor \u201cRegeneration associated Senescence Signature\u201d RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.", null, "pubmed:40308558", null, "NMDA Only 20dpi Rep 1", "GSM8530624", null, "source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing", "NMDA Only 20dpi Rep 1", "Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode", "Retina", null, "RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit", null, "tissue:Retina|genotype:NMDA Damage|treatment:Control", "GSM8530624", "GSM8530624: NMDA Only 20dpi Rep 1; Danio rerio; RNA Seq", "GSM8530624 r1", "GSM8530624", "1", "RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP534198", null, null, "11384-GK-0013_S1_L005_R1_001.fastq.gz 11384-GK-0013_S1_L005_R2_001.fastq.gz", "fastq fastq", 17211645306.0, 56992203.0, "GSM8530624 r1", "0:151 1:151", "A:4570848139;C:3941519932;G:4229510898;T:4466558031;N:3208306", 151, 151, null, null, 4570848139, 3941519932, 4229510898, 4466558031, 3208306, "SRX26172021", "SRS22716035", "SRA1977341", "Patton Lab, Biological Sciences, Vanderbilt University", "Patton Lab, Biological Sciences, Vanderbilt University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-09-23", "Undetermined", "Undetermined", "Eye", "Sensory 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": ["33851"], "units": {}, "query_ms": 9.890814995742403}