run_metadata: 68174

This data as json

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
68174	SRR17642808	SRX13811069	SRS11691788	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 100µl 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.		pubmed:34997071		T1 S1	GSM5821075		source name:Cornea\|strain:Wild type AB background\|tissue:Cornea\|age:180 dpf\|treatment:Abrasion	T1 S1	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 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		Illumina protocols		strain:Wild type AB background\|tissue:Cornea\|age:180 dpf\|treatment:Abrasion	GSM5821075	GSM5821075: T1 S1; Danio rerio; RNA Seq	GSM5821075 r1	GSM5821075	1	Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP355390		loader:fastq load.py	T1_S1_R1_001.fastq.gz	fastq	4002069308.0	53311729.0	GSM5821075 r1	0:75.07	A:1061994611;C:897032924;G:878383397;T:1151727049;N:12931327	75				1061994611	897032924	878383397	1151727049	12931327	SRX13811069	SRS11691788	SRA1357820	Institute of Biotechnology, University of Helsinki	Institute of Biotechnology, University of Helsinki	1	0.90669		0.10256		0.75065		0.47438		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown		Finland	2022-01-17	Adult	Adult	Cell Line	Cell Line