{"database": "metadata", "table": "run_metadata", "rows": [[29101, "SRR27010849", "SRX22703635", "SRS19696110", "SRP475451", "PRJNA1047750", "Differential expression in Muller glia of injured zebrafish in a mych /  context", "GSE249115", "Transcriptome Analysis", "This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.", "parent bioproject:PRJNA1047494", "pubmed:38984586", null, "Muller glia from WT retinas 2 xxx post injury dpi rep3 [5803 ML 6]", "GSM7926867", null, "source name:WT Muller glia injured retina|tissue:WT Muller glia injured retina|genotype:WT|treatment:injured|geo loc name:missing|collection date:missing", "Muller glia from WT retinas 2 xxx post injury dpi rep3 [5803 ML 6]", "University of Michigan Bioinformatics Core RNA seq pipeline \"Watermelon\" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample", "WT Muller glia injured retina", "Needle poke injury to retina.", "Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.", null, "tissue:WT Muller glia injured retina|genotype:WT|treatment:injured", "GSM7926867", "GSM7926867: Muller glia from WT retinas 2 xxx post injury dpi rep3 [5803 ML 6]; Danio rerio; RNA Seq", "GSM7926867 r1", "GSM7926867", "1", "Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475451", null, "loader:fastq load.py", "5803-ML-6_CTTGAAGG-TAGCGGAG_S219_R1_001.fastq.gz 5803-ML-6_CTTGAAGG-TAGCGGAG_S219_R2_001.fastq.gz", "fastq fastq", 39633900160.0, 131238080.0, "GSM7926867 r1", "0:151 1:151", "A:10574730340;C:8244722619;G:10678580933;T:10135778012;N:88256", 151, 151, null, null, 10574730340, 8244722619, 10678580933, 10135778012, 88256, "SRX22703635", "SRS19696110", "SRA1761648", "University of Michigan", "University of Michigan", 2, 0.82908, 0.8023, 0.08841, 0.07628, 0.72608, 0.73285, 0.53006, 0.52227, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-12-01", "Undetermined", "Undetermined", "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": ["29101"], "units": {}, "query_ms": 8.876953001163201}