{"database": "metadata", "table": "run_metadata", "rows": [[49573, "SRR10434662", "SRX7130632", "SRS5639976", "SRP163087", "PRJNA494251", "Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis", "GSE120724", "Other", "We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.", null, "pubmed:32423473", null, "shield Flag Elavl1a iCLIP rep2", "GSM4157939", null, "tissue:zebrafish embryos|strain:zebrafish embryos|cell type:normal zebrafish embryos cells|age:6hpf", "shield Flag Elavl1a iCLIP rep2", "The proceesing procedure is similar to CTK toolhttps://zhanglab.c2b2.columbia.edu/index.php/ICLIP data analysis using CTK. First  we trimmed three prime adaptor from reads by cutadapt collapsed duplicated reads by fastq2collapse.pl in CTK tool stripped  5\u2019 degenerated barcode mapped clean reads to zebrafish reference genomez10 by bwav0.7.17. data from replicates was merged for peak calling We use CTK tool CITS mode to call the peaks. Reads were clustered using tag2cluster.pl with parameters  big  s  maxgap \" 1\" peaks are identified using tag2peak.pl with parameters  big  ss  v   prefix \"CITS\"  gap 25  p 0.05 Genome build: z10 Supplementary files format and content: iCLIP peaks identified by CTK tool were provided in bed file format. The first three columns represent the 0 based location of the peak in the genome and the last column represents the strand.The fourth column reprents the peak ID and describes the gene locus  peak heightPH  expected PH/backgroundPH0 and pvalueP. The fifth  column represents the peak height.", "zebrafish embryos", null, "iCLIP seq was carried out as previously described Despic et al.  2017. Breifly  flag elavl1a mRNA injected embryos were collected at xxx h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed  and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h.p.f. and 6 h.p.f. at 4 \u00b0C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc", "Zebrafish wild type strain AB was raised in system water at 28.5\u00b0C under standard conditions.", "strain:zebrafish embryos|cell type:normal zebrafish embryos cells|age:6hpf", "GSM4157939", "GSM4157939: shield Flag Elavl1a iCLIP rep2; Danio rerio; OTHER", "GSM4157939", null, "1", "iCLIP seq was carried out as previously described Despic et al.  2017. Breifly  flag elavl1a mRNA injected embryos were collected at xxx h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed  and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h.p.f. and 6 h.p.f. at 4 \u00b0C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc", "GEO Accession:GSM4157939", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP163087", null, null, "Shield_Elavl1a_iCLIP_rep2.R2.fq.gz Shield_Elavl1a_iCLIP_rep2.R1.fq.gz", "fastq fastq", 23879342400.0, 79597808.0, "GSM4157939 r1", "0:150 1:150", "A:6335254303;C:5166953187;G:6017120995;T:6358132998;N:1880917", 150, 150, null, null, 6335254303, 5166953187, 6017120995, 6358132998, 1880917, "SRX7130632", "SRS5639976", "SRA787572", "GEO", "Life Science, Tsinghua University", 2, 0.14294, 0.15151, 0.03583, 0.08959, 0.99397, 0.98269, 0.96727, 0.75507, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "clip", "iclip", null, "China", "2019-11-12", "Gastrula", "Embryo", "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": ["49573"], "units": {}, "query_ms": 13.404732999333646}