{"database": "metadata", "table": "run_metadata", "rows": [[74621, "SRR23883665", "SRX19695587", "SRS17064513", "SRP427757", "PRJNA945489", "Transcriptomics analysis of a zebrafish model of Combined Saposin Deficiency", "GSE227551", "Transcriptome Analysis", "Combined Saposin Deficiency is a lysosomal storage disease with multiple organ pathologies that often involve neurodegeneration and early mortality.  To investigate the mechanisms driving saposin loss associated demyelination  the brains of psap /  zebrafish and wildtype siblings were analyzed via RNA seq. Overall design: A zebrafish model of Combined Saposin Deficiency was generated using CRISPR Cas9 targeting the prosaposin psap gene  which codes for saposins A D.  Mutagenized alleles were identified by DNA fragment analysis and Sanger sequencing  and fish carrying the mutations of interest were propagated to homozygosity.  RNA was isolated from the brains of four mpf psap /  zebrafish and wildtype siblings.", null, "pubmed:37183607", null, "Brain  psap knockout  4 mpf  replicate 4 [15628X8]", "GSM7102585", null, "source name:Brain 3 per sample|tissue:Brain 3 per sample|strain:TuAB|genotype:psap knockout|treatment:n1|time:4 mpf", "Brain  psap knockout  4 mpf  replicate 4 [15628X8]", "Reference database was created from zebrafish Zv10 genome and gene feature files Ensembl release 94 using STAR version 2.6.1b splice junctions optimized for 150 bp reads. Optical duplicates were removed using clumpify v38.34  reads were trimmed of adapters using cutadapt 1.16  alignment was performed with STAR two pass mode  and genes were assigned using featureCounts version 1.6.3. Output files cutadapt  FastQC  Picard CollectRnaSeqMetrics  STAR  and featureCounts were summarized using MultiQC to check for outliers. Differential expression analysis was performed in DESeq2 version 1.22.2 5% false discovery rate. Assembly: Zv10 Supplementary files format and content: DESeq2 generated .xlsx file containing raw and normalized counts annotated by Ensembl gene ID  and fold changes/adjusted p values annotated by gene name", "Brain 3 per sample", null, "RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.", null, "tissue:Brain 3 per sample|strain:TuAB|genotype:psap knockout|treatment:n1|time:4 mpf", "GSM7102585", "GSM7102585: Brain  psap knockout  4 mpf  replicate 4 [15628X8]; Danio rerio; RNA Seq", "GSM7102585 r1", "GSM7102585", "1", "RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit Qiagen following manufacturer's instructions; 3 brains 4 mpf were pooled for each sample. cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Kit Illumina following manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP427757", null, "loader:fastq load.py", "psap4_R1.fastq.gz psap4_R2.fastq.gz", "fastq fastq", 14570988714.0, 48248307.0, "GSM7102585 r1", "0:151 1:151", "A:4091189239;C:3187243752;G:3301025523;T:3991388289;N:141911", 151, 151, null, null, 4091189239, 3187243752, 3301025523, 3991388289, 141911, "SRX19695587", "SRS17064513", "SRA1606419", "Peterson, Pharmacology and Toxicology, University of Utah", "Peterson, Pharmacology and Toxicology, University of Utah", 2, 0.90366, 0.90563, 0.345, 0.34498, 0.67801, 0.67765, 0.49732, 0.49797, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United States", "2023-03-16", "Adult", "Adult", "Brain", "Nervous 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": ["74621"], "units": {}, "query_ms": 12.96037500287639}