run_metadata: 51709

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
51709	SRR8791415	SRX5581195	SRS4542776	SRP189574	PRJNA529372	miR 202 3p is important for the early development of zebrafish embryos.	PRJNA529372	Other	The expression level of miR 202 in embryos is very low. However when knocking out miR 202 using CRISPR/Cas9 it was found that homozygous embryos died early. Further experimental research found that miR 202 3p plays a crucial role. Therefore we selected wild type heterozygous and homozygous at 3.5hpf for RNA sequencing hoping to explain the important regulation of miR 202 3p on early development of embryo.				dre homozygous 2	sample 2		strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:3.5 hpf\|sex:not applicable\|tissue:embryo\|collected by:Haoyu RAN\|genotype:homozygous\|BioSampleModel:Model organism or animal									dre homozygous 2	202 Ho 2	202 Ho 2	The first step in the workflow involves purifying the poly A containing mRNA molecules using poly T oligo attached magnetic beads. Following purification the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by replacing dTTP with dUTP in the Second Strand Marking Mix SMM followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The incorporation of dUTP in second strand synthesis quenches the second strand during amplification because the polymerase used in the assay is not incorporated past this nucleotide. The addition of Actinomycin D to First Stand Synthesis Act D mix FSA prevents spurious DNA dependent synthesis while allowing RNA dependent synthesis improving strand specificity. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP189574			HOMO_3_5_2_S2_L001_R1_001.fastq.gz HOMO_3_5_2_S2_L001_R2_001.fastq.gz HOMO_3_5_2_S2_L002_R1_001.fastq.gz HOMO_3_5_2_S2_L002_R2_001.fastq.gz	fastq fastq fastq fastq	3565888981.0	17743517.0	HOMO 3 5 2 S2 L001 R1 001.fastq.gz	0:100.50 1:100.47	A:910268901;C:845993513;G:849351939;T:953522804;N:6751824	100	100			910268901	845993513	849351939	953522804	6751824	SRX5581195	SRS4542776	SRA866342	SHANGHAI OCEAN UNIVERSITY\|College of Fisheries and Life Science	SHANGHAI OCEAN UNIVERSITY	2	0.94565	0.93353	0.03202	0.03252	0.7402	0.7514	0.4884	0.48145	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		China	2020-04-01	Blastula	Embryo	Embryo Imprecise	All anatomical structures