run_metadata: 49575

This data as json

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
49575	SRR10434660	SRX7130630	SRS5639974	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.		pubmed:32423473		sphere Flag Elavl1a iCLIP rep2	GSM4157937		tissue:zebrafish embryos\|strain:zebrafish embryos\|cell type:normal zebrafish embryos cells\|age:4hpf	sphere 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’ 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		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 °C. 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°C under standard conditions.	strain:zebrafish embryos\|cell type:normal zebrafish embryos cells\|age:4hpf	GSM4157937	GSM4157937: sphere Flag Elavl1a iCLIP rep2; Danio rerio; OTHER	GSM4157937		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 °C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc	GEO Accession:GSM4157937	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten		SRP163087			Sphere_Elavl1a_iCLIP_rep2.R1.fq.gz Sphere_Elavl1a_iCLIP_rep2.R2.fq.gz	fastq fastq	22090855200.0	73636184.0	GSM4157937 r1	0:150 1:150	A:5631298996;C:5114935575;G:5742247735;T:5600647498;N:1725396	150	150			5631298996	5114935575	5742247735	5600647498	1725396	SRX7130630	SRS5639974	SRA787572	GEO	Life Science, Tsinghua University	2	0.23476	0.17586	0.06861	0.08859	0.99563	0.98873	0.95465	0.79994	150	150	B	B	mate2-mate1 similar by mapping diff	illumina	hiseq_era	full_length	poly_a	smarter	bulk	clip	iclip		China	2019-11-12	Blastula	Embryo	Embryo Imprecise	All anatomical structures