{"database": "metadata", "table": "run_metadata", "rows": [[49594, "SRR7947906", "SRX4781860", "SRS3862052", "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, "sphere DMSO icSHAPE", "GSM3409384", null, "source name:sphere DMSO|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:4hpf", "sphere DMSO icSHAPE", "Library strategy: icSHAPE icSHAPE computational pipeline reference: PubMedID: 26766114  DOI: 10.1038/nprot.2016.011 trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.", "sphere DMSO", "For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5  C for 5min.", "The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol\u00ae Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37\u00b0C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/\u00b5l RiboLock  0.1 U/\u00b5l FastAP Life Technology  2 U/\u00b5l T4 PNKNEB before 3\u2019 adapter ligation with addition of 10 \u00b5l ligation mix 5mM DTT  0.5\u00b5M 5\u2019 adenylated and 3\u2019 blocked linker 3\u2019 bio for unmodified  3\u2019 ddc for modified  0.66 U/\u00b5l T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25\u00b0C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1\u00b5l FastAP  0.2\u00b5l SSB Promega  0.8\u00b5l Ribolock and 1\u00b5l 5\u2019 Deadenylase NEB in 1X NEB buffer 2 NEB at 30\u00b0C for 90 min. And then 1\u00b5l RecJf NEB was added with another incubation at 37\u00b0C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq\uff0c Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer\u2019s protocol.", "Zebrafish wild type strain AB was raised in system water at 28.5\u00b0C under standard conditions.", "strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:4hpf", "GSM3409384", "GSM3409384: sphere DMSO; Danio rerio; OTHER", "GSM3409384", null, "1", "The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol\u00ae Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37\u00b0C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/\u00b5l RiboLock  0.1 U/\u00b5l FastAP Life Technology  2 U/\u00b5l T4 PNKNEB before three prime adapter ligation with addition of 10 \u00b5l ligation mix 5mM DTT  0.5\u00b5M five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/\u00b5l T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25\u00b0C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1\u00b5l FastAP  0.2\u00b5l SSB Promega  0.8\u00b5l Ribolock and 1\u00b5l five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30\u00b0C for 90 min. And then 1\u00b5l RecJf NEB was added with another incubation at 37\u00b0C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq\uff0c Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.", "GEO Accession:GSM3409384", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP163087", null, null, "sphere_DMSO_rep2.fastq.gz", "fastq", 67804917750.0, 452032785.0, "GSM3409384 r2", "0:150 1:0", "A:18522337687;C:17556962469;G:15356031761;T:16361409956;N:8175877", 150, 0, null, null, 18522337687, 17556962469, 15356031761, 16361409956, 8175877, "SRX4781860", "SRS3862052", "SRA787572", "GEO", "Life Science, Tsinghua University", 1, 0.04269, null, 0.00601, null, 0.92652, null, 0.69825, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "clip", "iclip", null, "China", "2018-10-01", "Blastula", "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": ["49594"], "units": {}, "query_ms": 8.821183997497428}