{"database": "metadata", "table": "run_metadata", "rows": [[61805, "SRR13697040", "SRX10086233", "SRS8244021", "SRP290950", "PRJNA674050", "RNA Seq of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish livers", "GSE160710", "Transcriptome Analysis", "In this study  we performed RNA seq on 5 dpf livers of uhrf1 hi272 mutants and phenotypically wild type siblings collected at 120 hpf. Overall design: \"To perform RNA seq on pools of uhrf1 hi272 mutant and sibling livers at 5 dpf  we collected between 15 30 livers from 5 independent clutches of uhrf1 hi272 mutants and their phenotypically WT siblings which were sorted based on phenotype following immobilization using tricaine. We extracted total RNA from livers to generate libraries as per TRIzol protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2. Total RNA was DNAseI treated  depleted for ribosomal RNA by using RiboZero and used for Illumina Library prep. RNA was analyzed on an Agilent 2100 Bioanalyzer. Illumina TruSeq RNA sample preparation version 2 protocol with Ribo Zero Gold. cDNA libraries were sequenced on the Illumina NextSeq500 platform to obtain 75 bp single end reads.", "parent bioproject:PRJNA674302", "pubmed:33854502", null, "120hpf uhrf1 hi272 mutant livers clutch 1 22 livers", "GSM5077765", null, "source name:embryo livers|background:ABNYU|tissue:22 livers|developmental stage:120hpf|genotype:uhrf1 hi272 mutant|genotype:fabp10:CAAX EGFP transgenic liver", "120hpf uhrf1 hi272 mutant livers clutch 1 22 livers", "Illumina Casava  software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Trimmed read were mapped to GRCz10 whole genome using tophat2 with default parameters Alignment by HISTA2 with default parameters  only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of  ensemble gene annotation  TE quantification was taking the RepeatMasker annotation of danRer10 from UCSC table browser with HTseq  in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V3.12 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes and TEs", "embryo livers", null, "14  25 livers from 5 dpf 120 hpf zebrafish embryos were dissected  pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.", null, "background:ABNYU|tissue:22 livers|developmental stage:120hpf|genotype:uhrf1 hi272 mutant|genotype:fabp10:CAAX EGFP transgenic liver", "GSM5077765", "GSM5077765: 120hpf uhrf1 hi272 mutant livers clutch 1 22 livers; Danio rerio; RNA Seq", "GSM5077765", null, "1", "14  25 livers from 5 dpf 120 hpf zebrafish embryos were dissected  pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.", "GEO Accession:GSM5077765", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP290950", null, null, "Liv1_Hi272_Mut_S14_read1.fastq.gz Liv1_Hi272_Mut_S14_read2.fastq.gz", "fastq fastq", 3949222292.0, 13997773.0, "GSM5077765 r1", "0:140.79 1:141.34", "A:1045521928;C:936306390;G:944175682;T:1022498070;N:720222", 140, 141, null, null, 1045521928, 936306390, 944175682, 1022498070, 720222, "SRX10086233", "SRS8244021", "SRA1153151", "GEO", "Biology, New York University Abu Dhabi", 2, 0.88992, 0.89254, 0.18597, 0.18591, 0.82256, 0.83132, 0.46333, 0.55432, 113, 113, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2021-02-12", "Larval", "Larval", "Liver", "Liver and Biliary 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": ["61805"], "units": {}, "query_ms": 11.98126200324623}