{"database": "metadata", "table": "run_metadata", "rows": [[68171, "SRR17642805", "SRX13811072", "SRS11691791", "SRP355390", "PRJNA797959", "Analysis of gene expression in zebrafish cornea during wound healing", "GSE193784", "Transcriptome Analysis", "The cornea  transparent and outermost structure of camera type eyes  is prone to environmental challenges  but has remarkable wound healing capabilities which enables to preserve vision. The manner in which cell plasticity impacts wound healing remains to be determined. In this study  we report rapid wound closure post zebrafish corneal epithelium abrasion. Furthermore  by investigating the cellular and molecular events taking place during corneal epithelial closure  we show the induction of a bilateral response to a unilateral wound. Our transcriptomic results  together with our TGF beta receptor inhibition experiments  demonstrate conclusively the crucial role of TGF beta signaling in corneal wound healing. Finally  our results on Pax6 expression and bilateral wound healing  demonstrate the decisive impact of epithelial cell plasticity on the pace of healing. Altogether  our study describes terminally differentiated cell competencies in the healing of an injured cornea. These findings will enhance the translation of research on cell plasticity to organ regeneration. Overall design: For RNA sequencing  same age fish were grouped one day prior to the experiment into four tanks 14 fish per 3 litres. Aged matched 145  148  180 or 183 dpf control and wound specimens were collected from the same tank. With respect to wounding  abrasion in both corneas of the animals was performed as described above. Control animals were anesthetized and placed onto a sponge for an equal duration as for the wounded animals. post 1.5hrs' recovery  the fish were anesthetized again in 0.02% Tricaine and decapitated. Eyes were enucleated and cornea dissected in PBS. For one sample  6 corneas from 3 individuals were pooled in 100\u00b5l of Tri reagent T9424  Sigma. RNA was isolated from TRI reagent T9424  Sigma using Precellys beads and standard protocols P000912 LYSK0 A.0  Bertin Technologies  Montigny Le Bretonneux  France. RNA was further purified using the Qiagen Rneasy MiniElute Cleanup kit #74204  Qiagen  Hilden  Germany. Polyadenylated mRNA was purified from 50ng of Total RNA using NEBNext PolyA mRNA Magnetic Isolation Module #E7490  New England Biolabs  Ipswich  Massachusetts  USA.  The following steps were performed by the Biomedicum Functional Genomics Unit FuGu at the Helsinki Institute of Life Science and Biocenter Finland at the University of Helsinki. Library preparation was completed on purified mRNA using the NEBNext Ultra Directional RNA Library prep kit  #E7420L  New England Biolabs using 14 cycles of PCR amplification and indexed using single i7 indexing. Indexed library preps from each sample were then pooled and sequenced at a pool concentration of 1.3pM on the NextSeq 500 using a NextSeq High Output 75 cycle flow cell Illumina  San Diego  California  USA with 75SE reads. Basecalling and demultiplexing was performed using Illumina bcl2fastq v2.20.0.422 software. Reads were mapped to zebrafish GRCz11 genome using STAR aligner 2.6.0c. Gene counts were calculated using the featureCounts tool from the Subread package v1.22.2 using Ensembl release 97 zebrafish gtf files. Differential expression analysis was performed using R package DESeq2 v1.22.2 [63]. One sample was excluded based on visual PCA inspection Fig S2A. For downstream analyses  only genes with an entrezgene id were consider  therefore excluding predicted genes Table S1. Gene Ontology GO term analysis was performed using g:Profiler version e98 eg45 p14 ce5b097  [64] online tool with default parameters. Volcano plots and heatmaps were generated using GraphPad Prism 8 version 8.3.0  Graphpad Software  San Diego  California  USA.", null, "pubmed:34997071", null, "T4 S6", "GSM5821078", null, "source name:Cornea|strain:Wild type AB background|tissue:Cornea|age:183 dpf|treatment:Abrasion", "T4 S6", "bcl2fastq2 Conversion Software was used to convert BCL files to FASTQ file format and demultiplex samples. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using Trimmomatic. Parameters used: :2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 Trimmed reads were mapped to zebrafish GRCz11 genome using STAR aligner 2.6.0c with parameters\u00a0   runThreadN 20   chimSegmentMin 12   chimJunctionOverhangMin 12   chimSegmentReadGapMax 3   alignSJoverhangMin 8   alignSJDBoverhangMin 1   alignIntronMin 20   alignIntronMax 1000000   alignMatesGapMax 1000000   alignSJstitchMismatchNmax 5  1 5 5   outFilterType BySJout   outFilterMismatchNmax 999   outSAMattributes NH HI NM MD AS nM jM jI XS   outSAMtype BAM SortedByCoordinate   outSAMmapqUnique 60   quantMode GeneCounts   twopassMode Basic Counts per gene were calculated using featureCounts software using Ensembl release 97 zebrafish gtf files. Parameters used:  s 2  T 20  t exon  g gene id Differential expression analysis used the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric mean  estimation of sample wise factors to correct for library size variability for example  estimation of dispersion i.e. variance  scatter of gene wise values between conditions  negative binomial linear model and Wald test to produce p values  removal of low expression outliers using Cook's distance results to optimize for p value adjustment and finally  multiple testing adjustment of p values with Benjamini Hochberg procedure. Genome build: zebrafish GRCz11 GCA 000002035.4 Supplementary files format and content: Raw count matrix of sequencing reads featureCounts meta feature level as .xlsx", "Cornea", null, "Illumina protocols", null, "strain:Wild type AB background|tissue:Cornea|age:183 dpf|treatment:Abrasion", "GSM5821078", "GSM5821078: T4 S6; Danio rerio; RNA Seq", "GSM5821078 r1", "GSM5821078", "1", "Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP355390", null, "loader:fastq load.py", "T4_S6_R1_001.fastq.gz", "fastq", 4104657468.0, 54852093.0, "GSM5821078 r1", "0:74.83", "A:1018061637;C:979511059;G:929536029;T:1153056348;N:24492395", 74, null, null, null, 1018061637, 979511059, 929536029, 1153056348, 24492395, "SRX13811072", "SRS11691791", "SRA1357820", "Institute of Biotechnology, University of Helsinki", "Institute of Biotechnology, University of Helsinki", 1, 0.9279, null, 0.0881, null, 0.75643, null, 0.46503, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Finland", "2022-01-17", "Adult", "Adult", "Cell Line", "Cell Line"]], "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": ["68171"], "units": {}, "query_ms": 9.22984700082452}