{"database": "metadata", "table": "run_metadata", "rows": [[74038, "SRR23340949", "SRX19282955", "SRS16684619", "SRP420989", "PRJNA931595", "The effects of atorvastatin AVS and afidopyropen on developing zebrafish", "GSE224522", "Transcriptome Analysis", "For RNA seq experiments  20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf  fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments:  ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.", null, null, null, "Afid L1", "GSM7025513", null, "tissue:larvae|cell line:whole larvae|treatment:Afid low dose|geo loc name:missing|collection date:missing", "Afid L1", "Raw data raw reads of FASTQ format were firstly processed through fastp. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene  including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count  fpkm  log2 fold change  p value Supplementary files format and content: Afid vs ERM excel files containing read count  fpkm  log2 fold change  p value", "larvae", null, "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "cell line:whole larvae|treatment:Afid low dose", "GSM7025513", "GSM7025513: Afid L1; Danio rerio; RNA Seq", "GSM7025513 r1", "GSM7025513", "1", "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420989", null, "loader:fastq load.py", "Afid_L1_1.fq.gz Afid_L1_2.fq.gz", "fastq fastq", 5457503400.0, 18191678.0, "GSM7025513 r1", "0:150 1:150", "A:1458403365;C:1284463142;G:1280545664;T:1434027335;N:63894", 150, 150, null, null, 1458403365, 1284463142, 1280545664, 1434027335, 63894, "SRX19282955", "SRS16684619", "SRA1723725", "University of Florida", "University of Florida", 2, 0.96498, 0.96638, 0.12145, 0.12064, 0.67487, 0.67483, 0.47846, 0.47908, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-02-04", "Larval", "Larval", "Cell Line", "Cell Line"]], "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": ["74038"], "units": {}, "query_ms": 12.920551998831797}