{"database": "metadata", "table": "run_metadata", "rows": [[76400, "SRR24921908", "SRX20682446", "SRS17977038", "SRP443822", "PRJNA983848", "Transcriptomic analysis of the liver from control sibling and mutant uhrf1 hi272 zebrafish larvae at 120 hpf treated with DMSO or Palbociclib PD", "GSE234993", "Transcriptome Analysis", "This study was carried out to compare the changes in gene expression in livers of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish larvae in response to treatment with  DMSO or Palbociclib PD Overall design: 48 hpf embryos from an incross of uhrf1 hi272+/   zebrafish adults with Tgfabp10a:CAAX EGFP to mark the livers  were treated with either 0.5% DMSO or 20 microM PD in 0.5% DMSO in 6 well plates. At  120 hpf  15  20 livers from were dissected from larvae treated with PD or DMSO treated and individual livers were immediately placed in TRIzol and stored at  80 while the carcass of each larvae was genotyped. The individual livers from uhrf1hi272 /   mutants and from WT in each treatment batch were pooled RNA was extracted per standard TRIzol/Chloroform method and concentrated  DNAse 1 treated and resuspended in DNase/RNase free water. For library preparation  high quality RNA was identified based on bioanalyzer analysis and quantified so that 100 ng of total RNA was used to initiate the library preparation using Ribo Zero rRNA Removal Kit Human/Mouse/Rat. The RNA sample was chemically fragmented and random primed for reverse transcription using Illumina TruSeq V2 RNA sample Prep Kit and first strand cDNA reverse transcribed using random primers. Following second strand cDNA synthesis  and end repair. TrueSeq adapter index was ligated to cDNA libraries  and PCR amplification of 12 cycles was done for enrichment  producing a 350 400?bp fragment including adapters. The fragment sizes and purity of the libraries were confirmed by analyzing on a Bioanalyzer 2100 and were sequenced using the Illumina NextSeq 550 system with a Paired end HO V2.5 kit  150 cycles.", null, "pubmed:38321933", null, "Liv 5 hi272 CDKI Mutant", "GSM7488254", null, "source name:embryo livers|strain:ABNYU|genotype:mutant uhrf1 hi272|treatment:CDKI|tissue:embryo livers|geo loc name:missing|collection date:missing", "Liv 5 hi272 CDKI Mutant", "Illumina Casava1.8 software used for basecalling Sequenced reads where first assessed for quality using FastQC v0.11.5. Trimmomatic v0.36 was used for quality trimming and adapter sequence removal  with the parameters ILLUMINACLIP: trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 The resulting transcripts from the raw counts were used for further downstream analysis Supplementary files format and content: txt containing raw counts", "embryo livers", "None", "TRIzol/Choloform Extraction RNA seq libraries were prepared with Ribo Zero kit  by the staff in the NYUAD genomics facility and quality controled by Bioanalyzer.", "Zebrafish larvae were kept in 6 well plate at a density of 2 larvae/ per 1 mL embyro medium in a 10:14 light/dark cycle", "strain:ABNYU|genotype:mutant uhrf1 hi272|treatment:CDKI|tissue:embryo livers", "GSM7488254", "GSM7488254: Liv 5 hi272 CDKI Mutant; Danio rerio; RNA Seq", "GSM7488254 r1", "GSM7488254", "1", "TRIzol/Choloform Extraction RNA seq libraries were prepared with Ribo Zero kit  by the staff in the NYUAD genomics facility and quality controled by Bioanalyzer.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP443822", null, "loader:fastq load.py", "Liv_5_hi272_CDKI_Mutant_S20_read1.fastq.gz Liv_5_hi272_CDKI_Mutant_S20_read2.fastq.gz", "fastq fastq", 3094376258.0, 10246279.0, "GSM7488254 r1", "0:151 1:151", "A:616434439;C:928229193;G:959244268;T:590421626;N:46732", 151, 151, null, null, 616434439, 928229193, 959244268, 590421626, 46732, "SRX20682446", "SRS17977038", "SRA1656736", "Biology, New York University Abu Dhabi", "Biology, New York University Abu Dhabi", 2, 0.40661, 0.40565, 0.03806, 0.03739, 0.82306, 0.82223, 0.67513, 0.64483, 151, 151, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2023-06-14", "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": ["76400"], "units": {}, "query_ms": 9.218943014275283}