metadata: run_metadata: 8 rows where devstage_curation_coarse = "Adult" and tissue

8 rows where devstage_curation_coarse = "Adult" and tissue_curation = "Cell Line"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
68171	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 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 m…	pubmed:34997071	T4 S6	GSM5821078	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 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:183 dpf\|treatment:Abrasion	GSM5821078	GSM5821078: T4 S6; Danio rerio; RNA Seq	GSM5821078 r1	GSM5821078	1	Illumina protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP355390	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	1018061637	979511059	929536029	1153056348	24492395	SRX13811072	SRS11691791	SRA1357820	Institute of Biotechnology, University of Helsinki	Institute of Biotechnology, University of Helsinki	1	0.9279	0.0881	0.75643	0.46503	74	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Finland	2022-01-17	Adult	Adult	Cell Line	Cell Line
68172	68172	SRR17642806	SRX13811071	SRS11691790	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 m…	pubmed:34997071	T3 S5	GSM5821077	source name:Cornea\|strain:Wild type AB background\|tissue:Cornea\|age:148 dpf\|treatment:Abrasion	T3 S5	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:148 dpf\|treatment:Abrasion	GSM5821077	GSM5821077: T3 S5; Danio rerio; RNA Seq	GSM5821077 r1	GSM5821077	1	Illumina protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP355390	loader:fastq load.py	T3_S5_R1_001.fastq.gz	fastq	3947279678.0	52654285.0	GSM5821077 r1	0:74.97	A:979614659;C:945412811;G:897085141;T:1107588181;N:17578886	74	979614659	945412811	897085141	1107588181	17578886	SRX13811071	SRS11691790	SRA1357820	Institute of Biotechnology, University of Helsinki	Institute of Biotechnology, University of Helsinki	1	0.93295	0.08343	0.76169	0.45979	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Finland	2022-01-17	Adult	Adult	Cell Line	Cell Line
68173	68173	SRR17642807	SRX13811070	SRS11691789	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 m…	pubmed:34997071	T2 S2	GSM5821076	source name:Cornea\|strain:Wild type AB background\|tissue:Cornea\|age:145 dpf\|treatment:Abrasion	T2 S2	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:145 dpf\|treatment:Abrasion	GSM5821076	GSM5821076: T2 S2; Danio rerio; RNA Seq	GSM5821076 r1	GSM5821076	1	Illumina protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP355390	loader:fastq load.py	T2_S2_R1_001.fastq.gz	fastq	4051078305.0	54063824.0	GSM5821076 r1	0:74.93	A:1007991527;C:970758628;G:916961781;T:1134913467;N:20452902	74	1007991527	970758628	916961781	1134913467	20452902	SRX13811070	SRS11691789	SRA1357820	Institute of Biotechnology, University of Helsinki	Institute of Biotechnology, University of Helsinki	1	0.91558	0.08053	0.75808	0.45488	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Finland	2022-01-17	Adult	Adult	Cell Line	Cell Line
68174	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 m…	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
68175	68175	SRR17642809	SRX13811068	SRS11691787	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 m…	pubmed:34997071	C4 S8	GSM5821074	source name:Cornea\|strain:Wild type AB background\|tissue:Cornea\|age:183 dpf\|treatment:No treatment	C4 S8	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:183 dpf\|treatment:No treatment	GSM5821074	GSM5821074: C4 S8; Danio rerio; RNA Seq	GSM5821074 r1	GSM5821074	1	Illumina protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP355390	loader:fastq load.py	C4_S8_R1_001.fastq.gz	fastq	4256283935.0	56666229.0	GSM5821074 r1	0:75.11	A:1059997683;C:1014167830;G:963129633;T:1204744857;N:14243932	75	1059997683	1014167830	963129633	1204744857	14243932	SRX13811068	SRS11691787	SRA1357820	Institute of Biotechnology, University of Helsinki	Institute of Biotechnology, University of Helsinki	1	0.93325	0.08717	0.75986	0.46711	74	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Finland	2022-01-17	Adult	Adult	Cell Line	Cell Line
68176	68176	SRR17642810	SRX13811067	SRS11691786	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 m…	pubmed:34997071	C3 S7	GSM5821073	source name:Cornea\|strain:Wild type AB background\|tissue:Cornea\|age:148 dpf\|treatment:No treatment	C3 S7	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:148 dpf\|treatment:No treatment	GSM5821073	GSM5821073: C3 S7; Danio rerio; RNA Seq	GSM5821073 r1	GSM5821073	1	Illumina protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP355390	loader:fastq load.py	C3_S7_R1_001.fastq.gz	fastq	3947230596.0	52760312.0	GSM5821073 r1	0:74.81	A:974659855;C:943382604;G:895729254;T:1109923901;N:23534982	74	974659855	943382604	895729254	1109923901	23534982	SRX13811067	SRS11691786	SRA1357820	Institute of Biotechnology, University of Helsinki	Institute of Biotechnology, University of Helsinki	1	0.92667	0.08408	0.76228	0.45537	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Finland	2022-01-17	Adult	Adult	Cell Line	Cell Line
68177	68177	SRR17642811	SRX13811066	SRS11691785	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 m…	pubmed:34997071	C2 S4	GSM5821072	source name:Cornea\|strain:Wild type AB background\|tissue:Cornea\|age:145 dpf\|treatment:No treatment	C2 S4	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:145 dpf\|treatment:No treatment	GSM5821072	GSM5821072: C2 S4; Danio rerio; RNA Seq	GSM5821072 r1	GSM5821072	1	Illumina protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP355390	loader:fastq load.py	C2_S4_R1_001.fastq.gz	fastq	3999460717.0	53108441.0	GSM5821072 r1	0:75.31	A:991482732;C:962175098;G:912208461;T:1127643677;N:5950749	75	991482732	962175098	912208461	1127643677	5950749	SRX13811066	SRS11691785	SRA1357820	Institute of Biotechnology, University of Helsinki	Institute of Biotechnology, University of Helsinki	1	0.92663	0.08134	0.75	0.46829	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Finland	2022-01-17	Adult	Adult	Cell Line	Cell Line
68178	68178	SRR17642812	SRX13811065	SRS11691784	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 m…	pubmed:34997071	C1 S3	GSM5821071	source name:Cornea\|strain:Wild type AB background\|tissue:Cornea\|age:180 dpf\|treatment:No treatment	C1 S3	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:No treatment	GSM5821071	GSM5821071: C1 S3; Danio rerio; RNA Seq	GSM5821071 r1	GSM5821071	1	Illumina protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP355390	loader:fastq load.py	C1_S3_R1_001.fastq.gz	fastq	3917238464.0	52204535.0	GSM5821071 r1	0:75.04	A:978004776;C:941144815;G:882587856;T:1099985167;N:15515850	75	978004776	941144815	882587856	1099985167	15515850	SRX13811065	SRS11691784	SRA1357820	Institute of Biotechnology, University of Helsinki	Institute of Biotechnology, University of Helsinki	1	0.92016	0.08051	0.76053	0.46469	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Finland	2022-01-17	Adult	Adult	Cell Line	Cell Line

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;