run_metadata: 29255

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
29255	SRR27489772	SRX23160937	SRS20111098	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.			polysome fraction	HMW fraction 6hpf replica A	MPRA repA fractions 8 9 6hpf		strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:12\|replicate:replicate A\|BioSampleModel:Model organism or animal									HMW fraction 6hpf replica A	Library 12	Library 12	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.			OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112			BSSE_QGF_206647_HGWLYDSX3_3_MPRA_repA_fractions_8_9_6hpf_TTGGACTC_GGAAGCAG_S12_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206647_HGWLYDSX3_3_MPRA_repA_fractions_8_9_6hpf_TTGGACTC_GGAAGCAG_S12_L003_R2_001_MM_1.fastq.gz	fastq fastq	14724761980.0	48757490.0	BSSE QGF 206647 HGWLYDSX3 3 MPRA repA fractions 8 9 6hpf TTGGACTC GGAAGCAG S12 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3711442998;C:3830334531;G:3642299006;T:3539948266;N:737179	151	151			3711442998	3830334531	3642299006	3539948266	737179	SRX23160937	SRS20111098	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01161	8e-05	0.0002	1e-05	0.99214	0.99985	0.4529	0.3	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown		Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures