{"database": "metadata", "table": "run_metadata", "rows": [[55737, "SRR10747734", "SRX7423116", "SRS5869236", "SRP238398", "PRJNA597022", "RNA seq analysis of gene regulation by miR 34a and expression changes induced by DNA damage in zebrafish", "GSE142440", "Transcriptome Analysis", "Li Fraumeni syndrome LFS is a disorder due to inherited mutations in the TP53 gene resulting in an increased risk of developing several types of cancer. MicroRNA miR 34a has been implicated downstream of p53 on the basis of being a direct transcriptional target and  when over expressed  having pro apoptotic phenotypes in cell lines. Moreover  miR 34a has been shown to be a modifier gene in the context of LFS  since its epigenetic silencing increases the likelihood of tumour development in patients with mutant TP53.  However  the in vivo consequences of miR 34 loss are still unclear. For example  mice lacking all three a b c miR 34 homologs show no detectable abnormalities in p53 responses. The relative expression of different miR 34 genes in zebrafish was studied using qRT PCR with specific assays. The miR 34a  miR 34b and miR 34c display unique onset of developmental expression and expression levels  with miR 34a being the most abundant and constant in expression. All of the miR 34 genes also showed clear induction by p53 when DNA damaging treatments are performed. Using CRISPR Cas9 technology  we generated a zebrafish miR 34a deletion mutant to further investigate the roles of miR 34a on its own and its association with the p53 pathway. Predictably  a miR 34a deletion mutant demonstrated absence of miR 34a  though without xxx 34b and miR 34c compensation beyond baseline expression levels. Mutants survive to maturity  show no overt phenotypes and have normal apoptotic responses to DNA damaging irradiation or camptothecin treatments. To further explore the effects of miR 34a  we performed gene expression profiling using RNA seq of wild type and miR 34a deletion mutant zebrafish embryos at 28 hpf with or without xxx with a DNA damaging drug camptothecin. The results of this RNA seq experiments showed that the loss of miR 34a does not strongly affect induction of genes by DNA damage. However  the overall pattern of gene expression is significantly different as shown by Principal Component Analysis and there is a group of about 100 genes which are differentially expressed due to loss of miR 34a. The dataset we present in this submission was used to reach these conclusions. Overall design: Zebrafish embryos at 24 hpf of wild type and miR 34a /  genotypes were dechorionated and the control DMSO or 1 uM camptothecin treatment for 4 hours was performed followed by RNA extraction from all samples.", null, null, null, "28 hpf miR 34a /  treated with 1\u03bcM CPT rep1", "GSM4227410", null, "tissue:whole embryo|genotype:miR 34a / |Stage:28 hpf|treatment:4 hours with 1\u03bcM camptothecin", "28 hpf miR 34a /  treated with 1\u03bcM CPT rep1", "Read trimming: the raw reads had the adapters \u201cATCACCGAC\u201d removed and filtered by the quality of 20 with the Trim Galore v0.4.4. Read mapping: The reads passed through the two step mapping for RNA Seq data from Ion proton: first with STAR v2.7 and then mapping the unmapped reads from the first alignment using bowtie2. The two mapped files were merged with Picard tools v2.5.0. Read counting: The counts were extracted using HTSeq V0.9.1. Genome build: danRer11 Supplementary files format and content: read counts", "whole embryo", "Camptothecin CPT treatments were performed by adding either DMSO control groups or the 2 mM stock CPT solution in DMSO to fish water for 1 \u00b5M concentration and incubating embryos for 4 hours.", "Each total RNA sample was extracted from 30 50 zebrafish embryos by homogenizing them in 500 \u00b5L Trizol reagent Thermo Fisher Scientific  15596026 using 1 mL syringe and 22G needle. Lysates were centrifuged at 12 000 g at 4\u00baC for 5 minutes and the supernatant was transferred to Phasemaker Tubes Thermo Fisher Scientific  A33248 and RNA was purified according to the Phasemaker Tubes protocol manual. Total RNA samples were measured and analyzed for integrity on Agilent Tape Station. Samples with RNA integration number \u22658 were selected for library preparation. Poly A enrichment was performed from 20 \u00b5g of total RNA to enrich for mRNA Dyna beads mRNA direct micro Kit. 100ng of poly A enriched RNA was fragmented using RNase III and purified using magnetic bead clean up module RNA Seq V2 kit  Life Technologies. The size distribution of the fragmented RNA was assessed on Agilent Tape Station using RNA HS screen tape assay and 50 ng of fragmented polyA enriched RNA was used to prepare whole transcriptome library RNA seq V2. Yield and size distribution of the library was analyzed on Agilent Tape Station using D1000 screen tape. Barcoded library was equally pooled and amplified onto Ion Sphere\u2122 Particles ISPs from Ion Pi HiQ OT2 kit Life Technologies. ISPs enriched with template library were loaded onto Ion PI chip V3 and sequenced on Ion Proton from Thermo Fisher.", "Zebrafish experiments and husbandry follows standard protocols in accordance with the standards of the University of Ottawa Animal Care Committee approval number: CHEOe 3168 A1. Zebrafish embryos were maintained at 28.5 \u00b0C during development and as adults. Embryos were grown in egg water 1x E3 prepared from 60x E3 stock.", "genotype:miR 34a / |Stage:28 hpf|treatment:4 hours with 1\u03bcM camptothecin", "GSM4227410", "GSM4227410: 28 hpf miR 34a /  treated with 1\u03bcM CPT rep1; Danio rerio; RNA Seq", "GSM4227410", null, "1", "Each total RNA sample was extracted from 30 50 zebrafish embryos by homogenizing them in 500 \u00b5L Trizol reagent Thermo Fisher Scientific  15596026 using 1 mL syringe and 22G needle. Lysates were centrifuged at 12 000 g at 4\u00baC for 5 minutes and the supernatant was transferred to Phasemaker Tubes Thermo Fisher Scientific  A33248 and RNA was purified according to the Phasemaker Tubes protocol manual. Total RNA samples were measured and analyzed for integrity on Agilent Tape Station. Samples with RNA integration number \u22658 were selected for library preparation. Poly A enrichment was performed from 20 \u00b5g of total RNA to enrich for mRNA Dyna beads mRNA direct micro Kit. 100ng of poly A enriched RNA was fragmented using RNase III and purified using magnetic bead clean up module RNA Seq V2 kit  Life Technologies. The size distribution of the fragmented RNA was assessed on Agilent Tape Station using RNA HS screen tape assay and 50 ng of fragmented polyA enriched RNA was used to prepare whole transcriptome library RNA seq V2. Yield and size distribution of the library was analyzed on Agilent Tape Station using D1000 screen tape. Barcoded library was equally pooled and amplified onto Ion Sphere\u2122 Particles ISPs from Ion Pi HiQ OT2 kit Life Technologies. ISPs enriched with template library were loaded onto Ion PI chip V3 and sequenced on Ion Proton from Thermo Fisher.", "GEO Accession:GSM4227410", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP238398", null, null, "28h_miR34a_CPT1.fastq.gz", "fastq", 3324553506.0, 48175746.0, "GSM4227410 r1", "0:69.01", "A:917927255;C:782740771;G:859994003;T:763891477;N:0", 69, null, null, null, 917927255, 782740771, 859994003, 763891477, 0, "SRX7423116", "SRS5869236", "SRA1014962", "GEO", "Berman Lab, CHEO Research Institute/University of Ottawa", 1, 0.76943, null, 0.06284, null, 0.7428, null, 0.47633, null, 115, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2019-12-20", "Pharyngula", "Embryo", "Whole Organism", "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": ["55737"], "units": {}, "query_ms": 9.650175001297612}