{"database": "metadata", "table": "run_metadata", "rows": [[30205, "SRR27715730", "SRX23381949", "SRS20243483", "SRP485714", "PRJNA1068542", "The effects of HSP60 chaperone deficiency on zebrafish larvae", "GSE254091", "Transcriptome Analysis", "To understand the effects of Hsp60 deficiency in developing vertebrates  we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 /  larvae at 5dpf   were analyzed by RNASeq. For this purpose  3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.", null, "pubmed:39147275", null, "control 3", "GSM8033237", null, "source name:embryo|tissue:embryo|cell line:5 dpf|genotype:hspd1+/+|treatment:control|geo loc name:missing|collection date:missing", "control 3", "Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio  GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2   applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample", "embryo", null, "The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 \u00b5L TRIzol Invitrogen; #15596 018 and stored at  80\u00b0C until RNA extraction. According to the obtained genotyping results  bodies of hspd1+/+ and hspd1 /  larvae were pooled in groups of 5 larvae  and this process was repeated for 3 mating sets  resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol  including DNase treatment with DNA free Kit Ambion  AM1906 according to the manufacturer\u2019s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek  Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent  G2991AA  and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer\u2019s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at  80\u00b0C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.", "Adult hspd1+/  zebrafish lines were housed and maintained at 28\u00b0C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/  knockout line was in crossed and obtained embryos were maintained at 28.5\u00b0C in E3 buffer 5 mm NaCl  0.17 mm KCl  0.33 mm CaCl2  0.33 mm MgSO4  10\u22125% methylene blue  2 mM HEPES  pH 7.4 with daily replacements until 5 dpf.", "tissue:embryo|cell line:5 dpf|genotype:hspd1+/+|treatment:control", "GSM8033237", "GSM8033237: control 3; Danio rerio; RNA Seq", "GSM8033237 r1", "GSM8033237", "1", "The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 \u00b5L TRIzol Invitrogen; #15596 018 and stored at  80\u00b0C until RNA extraction. According to the obtained genotyping results  bodies of hspd1+/+ and hspd1 /  larvae were pooled in groups of 5 larvae  and this process was repeated for 3 mating sets  resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol  including DNase treatment with DNA free Kit Ambion  AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek  Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent  G2991AA  and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at  80\u00b0C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP485714", null, null, "14_1.fq.gz 14_2.fq.gz", "fastq fastq", 5020525200.0, 25102626.0, "GSM8033237 r1", "0:100 1:100", "A:1366975716;C:1129522599;G:1135845277;T:1388181608;N:0", 100, 100, null, null, 1366975716, 1129522599, 1135845277, 1388181608, 0, "SRX23381949", "SRS20243483", "SRA1791378", "Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital", "Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital", 2, 0.92923, 0.93091, 0.11899, 0.11908, 0.65117, 0.651, 0.48861, 0.48085, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2024-01-24", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"]], "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": ["30205"], "units": {}, "query_ms": 9.357458999147639}