{"database": "metadata", "table": "run_metadata", "rows": [[52379, "SRR9189629", "SRX5961775", "SRS4871013", "SRP200281", "PRJNA546018", "TGF\u00df signaling in retinal tissue repair [Danio Rerio]", "GSE132141", "Transcriptome Analysis", "In mammals  retinal damage is followed by M\u00fcller 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 TGF\u00df signaling pathways. Overall design: Comparison of murine and fish M\u00fcller cell transcriptome post retinal injury", "parent bioproject:PRJNA546014", "pubmed:34593012", null, "MC  Zf day1 1", "GSM3847451", null, "source name:MC  Zf day1|strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|time point:1 day post retinal injury|tissue:retina|cell type:Muller cells", "MC  Zf day1 1", "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 day1", "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.\u00a0Each burn was produced with 70 mW of power for 100 ms and aimed to have a diameter of 50 \u00b5m 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 \u00b0C 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\u00ae Round Bottom Tubes with CellStrainer Cap 12x75 mm; Costar Corning  Cambridge  MA. Hoechst 33342 Ready Flow\u2122 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/\u03bcl above this threshold were collected from gfap:gfap GFP positive fish using FACS into separate 96 well plates containing 4 \u03bcl lysis buffer comprised of Buffer TCL 1031576; Qiagen plus 1% 2 mercaptoethanol 63689; Sigma Aldrich. post cell sorting  all samples were immediately frozen at \u221270\u00b0C. 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.", null, "strain background:AB|genotype/variation:gfap:gfap GFP|age:6 month 9 month|time point:1 day post retinal injury|tissue:retina|cell type:Muller cells", "GSM3847451", "GSM3847451: MC  Zf day1 1; Danio rerio; RNA Seq", "GSM3847451", null, "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 \u00b0C 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\u00ae Round Bottom Tubes with CellStrainer Cap 12x75 mm; Costar Corning  Cambridge  MA. Hoechst 33342 Ready Flow\u2122 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/\u03bcl above this threshold were collected from gfap:gfap GFP positive fish using FACS into separate 96 well plates containing 4 \u03bcl lysis buffer comprised of Buffer TCL 1031576; Qiagen plus 1% 2 mercaptoethanol 63689; Sigma Aldrich. post cell sorting  all samples were immediately frozen at \u221270\u00b0C. 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:GSM3847451", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200281", null, null, "20180726.A-MC__Zf_day1_1_R1.fastq.gz", "fastq", 2080602342.0, 16512717.0, "GSM3847451 r1", "0:126 1:0", "A:525963666;C:455898693;G:420126273;T:678474660;N:139050", 126, 0, null, null, 525963666, 455898693, 420126273, 678474660, 139050, "SRX5961775", "SRS4871013", "SRA893729", "GEO", "Inselspital-University of Bern", 1, 0.74651, null, 0.31086, null, 0.86529, null, 0.83706, null, 126, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2019-06-03", "Adult", "Adult", "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": ["52379"], "units": {}, "query_ms": 9.185521004837938}