run_metadata: 52372

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
52372	SRR9189636	SRX5961782	SRS4871020	SRP200281	PRJNA546018	TGFß signaling in retinal tissue repair [Danio Rerio]	GSE132141	Transcriptome Analysis	In mammals retinal damage is followed by Müller glia cell activation and proliferation. While retinal gliosis persists in adult mammals post an insult or disease some vertebrates including zebrafish have the capacity to regenerate. We believe we are the first group to show that gliosis is a fibrotic like process in mammals' eyes caused by differential activation of canonical and non canonical TGFß signaling pathways. Overall design: Comparison of murine and fish Müller cell transcriptome post retinal injury	parent bioproject:PRJNA546014	pubmed:34593012		MC Zf day7 2	GSM3847458		source name:MC Zf day7\|strain background:AB\|genotype/variation:gfap:gfap GFP\|age:6 month 9 month\|time point:7 day post retinal injury\|tissue:retina\|cell type:Muller cells	MC Zf day7 2	The raw reads were first cleaned by removing adapter sequences trimming low quality ends and filtering reads with low quality phred quality <20 using Trimmomatic Version 0.36 18. The read alignment was done with STAR v2.6.0c 19. As reference we used the Ensembl zebrafish genome build GRCz10 from 2017 06 07 release 89 and respectively the Ensembl mouse genome build GRCm38.p5 with the gene annotations downloaded on 2018 02 26 from Ensembl release 91. The STAR alignment options were " outFilterType BySJout outFilterMatchNmin 30 outFilterMismatchNmax 10 outFilterMismatchNoverLmax 0.05 alignSJDBoverhangMin 1 alignSJoverhangMin 8 alignIntronMax 1000000 alignMatesGapMax 1000000 outFilterMultimapNmax 50". Gene expression values were computed with the function featureCounts from the R package Rsubread v1.26.0 20. The options for featureCounts were: min mapping quality 10 min feature overlap 10bp count multi mapping reads count only primary alignments count reads also if they overlap multiple genes. To detect differentially expressed genes we applied a count based negative binomial model implemented in the software package DESeq2 R version: 3.5.0 DESeq2 version: 1.20.0. The differential expression was assessed using an exact test adapted for over dispersed data. Genes showing altered expression with an adjusted p value < 0.05 Benjamini and Hochberg method were considered differentially expressed. Genome build: zebrafish genome build GRCz10 Supplementary files format and content: text files holding gread counts per gene	MC Zf day7	For the zebrafish post anesthesia with 0.16 mg/mL ethyl 3 aminobenzoate methanesulfonate salt Tricaine; Sigma Aldrich Buchs Switzerland dissolved in the tank water 1 2 drops of 2% hydroxypropyl methylcellulose Methocel OmniVision AG Neuhausen Switzerland were topically applied to the cornea. A diode laser with a wavelength of 532 nm Visulas 532s Carl Zeiss Meditec AG Oberkochen Germany was used to create retinal lesions at the region of the posterior pole around the optic nerve 6. These were confined to the ONL and surrounded by apparently healthy retinal tissue. Four laser burns were applied to the left eye: two superior and two inferior to the optic nerve separated from the nerve by at least two lesion diameters. For the RNAseq analysis 20 laser burns were created in both eyes. Each burn was produced with 70 mW of power for 100 ms and aimed to have a diameter of 50 µm 6. The right eye was used as internal negative control. To focus the laser aiming beam on the retina a 2.0 mm laser lens was employed Ocular Instruments Bellevue WA USA. post laser treatment fish were revived by placing them in a container with fresh tank water and creating a water flow over the gills.	At different time xxx post injury induction Day 1 3 and 7 both retinas of three gfap:gfap GFP zebrafish per time point were dissected and kept in cold diethyl pyrocarbonate phosphate buffered saline DEPC PBS 12. Enzymatically dissociation was initiated by 0.05% trypsin ThermoFisher Scientific diluted in DEPC PBS at 37 °C for 10 min. Cell suspension was then mechanically triturated trypsin inhibitor 10 mg/ml; Sigma Aldrich added and the solution centrifuged at 1200 rpm for 5 min. Dissociated retinas were resuspended in DEPC PBS with 10% FBS and DNase I 200 U/ml; Roche filtered and collected in Falcon® Round Bottom Tubes with CellStrainer Cap 12x75 mm; Costar Corning Cambridge MA. Hoechst 33342 Ready Flow™ Reagent ThermoFisher Scientific was added as a DNA dye for cell cycle analysis. Cells from gfap:gfap GFP negative siblings were used to determine background fluorescence levels. 100 cells/μl above this threshold were collected from gfap:gfap GFP positive fish using FACS into separate 96 well plates containing 4 μl lysis buffer comprised of Buffer TCL 1031576; Qiagen plus 1% 2 mercaptoethanol 63689; Sigma Aldrich. post cell sorting all samples were immediately frozen at −70°C. Sorted cells were processed using the published Smart seq2 protocol 17 to generate the cDNA libraries. The quality of the RNA cDNA and final libraries was determined using an Agilent 4200 TapeStation System Agilent Santa Clara CA USA. The libraries were pooled and sequenced in an Illumina HiSeq2500 Illumina San Diego CA USA with a depth of around 20 Mio reads per sample.		strain background:AB\|genotype/variation:gfap:gfap GFP\|age:6 month 9 month\|time point:7 day post retinal injury\|tissue:retina\|cell type:Muller cells	GSM3847458	GSM3847458: MC Zf day7 2; Danio rerio; RNA Seq	GSM3847458		1	At different time xxx post injury induction Day 1 3 and 7 both retinas of three gfap:gfap GFP zebrafish per time point were dissected and kept in cold diethyl pyrocarbonate phosphate buffered saline DEPC PBS 12. Enzymatically dissociation was initiated by 0.05% trypsin ThermoFisher Scientific diluted in DEPC PBS at 37 °C for 10 min. Cell suspension was then mechanically triturated trypsin inhibitor 10 mg/ml; Sigma Aldrich added and the solution centrifuged at 1200 rpm for 5 min. Dissociated retinas were resuspended in DEPC PBS with 10% FBS and DNase I 200 U/ml; Roche filtered and collected in Falcon® Round Bottom Tubes with CellStrainer Cap 12x75 mm; Costar Corning Cambridge MA. Hoechst 33342 Ready Flow™ Reagent ThermoFisher Scientific was added as a DNA dye for cell cycle analysis. Cells from gfap:gfap GFP negative siblings were used to determine background fluorescence levels. 100 cells/μl above this threshold were collected from gfap:gfap GFP positive fish using FACS into separate 96 well plates containing 4 μl lysis buffer comprised of Buffer TCL 1031576; Qiagen plus 1% 2 mercaptoethanol 63689; Sigma Aldrich. post cell sorting all samples were immediately frozen at −70°C. Sorted cells were processed using the published Smart seq2 protocol 17 to generate the cDNA libraries. The quality of the RNA cDNA and final libraries was determined using an Agilent 4200 TapeStation System Agilent Santa Clara CA USA. The libraries were pooled and sequenced in an Illumina HiSeq2500 Illumina San Diego CA USA with a depth of around 20 Mio reads per sample.	GEO Accession:GSM3847458	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP200281			20180726.A-MC__Zf_day7_2_R1.fastq.gz	fastq	3124904832.0	24800832.0	GSM3847458 r1	0:126 1:0	A:822659597;C:714047534;G:680615719;T:907389743;N:192239	126	0			822659597	714047534	680615719	907389743	192239	SRX5961782	SRS4871020	SRA893729	GEO	Inselspital-University of Bern	1	0.80643		0.36409		0.79403		0.75604		126		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq		Switzerland	2019-06-03	Adult	Adult	Eye	Sensory System