run_metadata: 71046

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
71046	SRR21140656	SRX17152941	SRS14724786	SRP393052	PRJNA871254	Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 RNA seq and Ribo seq	GSE211652	Other	Purpose: To systematically investigate the molecular mechanisms resulting from Mycn loss of function. Methods: Approximately 30 mycn mutant or WT zebrafish embryos at 72 hpf were harvested . Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics PN 1000074 according to the manufacturer's protocol for 10000 cells recovery. Results: More than 3 000 genes showed reduced tranlation efficiency in Mycn mutant. Conclusions: mTOR signaling was reduced in Mycn mutant. Overall design: wild type or mycn zebrafish embryos at 72 hpf were harvested for RNA seq and Ribo seq.				wild type zebrafish embryos Ribo seq 72 hpf replicate 2	GSM6482083		source name:zebrafish cells\|strain:AB\|tissue:embryonic cells\|age:72 hpf	wild type zebrafish embryos Ribo seq 72 hpf replicate 2	The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by limma package. Assembly: GRCz11	zebrafish cells	WT and Mycn mutant zebrafish embryos were collected for RNA sequencing or Ribo seq at 72 hpf	For bulk RNA seq RNA libraries were prepared for sequencing using standard Illumina protocols. For Ribo seq WT and mycn mutant embryos were collected at 3 dpf digested with cold 0.5% trypsin to a single cell suspension and homogenized in lysis buffer for 20–50 times. The homogenate centrifuged at 12 000 g for 15 min at 4°C and the supernatants were digested with RNase for 30 mins and aborted by 1M EGTA followed by layering on top of a 10%–50% sucrose gradient solution. Ultracentrifugation was performed at 36 000 rpm for 2 hrs hours at 4°C. post centrifugation the fractions were collected according to the absorbance at optical density OD260 by a TRAIX detector. Then the RNA was purified and used to construct the library for sequencing.	embryos were cultured in a Petri dish filled with 0.3X Danieau buffer	strain:AB\|tissue:embryonic cells\|age:72 hpf	GSM6482083	GSM6482083: wild type zebrafish embryos Ribo seq 72 hpf replicate 2; Danio rerio; OTHER	GSM6482083 r1	GSM6482083	1	For bulk RNA seq RNA libraries were prepared for sequencing using standard Illumina protocols. For Ribo seq WT and mycn mutant embryos were collected at 3 dpf digested with cold 0.5% trypsin to a single cell suspension and homogenized in lysis buffer for 20–50 times. The homogenate centrifuged at 12 000 g for 15 min at 4°C and the supernatants were digested with RNase for 30 mins and aborted by 1M EGTA followed by layering on top of a 10%–50% sucrose gradient solution. Ultracentrifugation was performed at 36 000 rpm for 2 hrs hours at 4°C. post centrifugation the fractions were collected according to the absorbance at optical density OD260 by a TRAIX detector. Then the RNA was purified and used to construct the library for sequencing.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP393052			wt2-riboseq_1.clean.fq.gz wt2-riboseq_2.clean.fq.gz	fastq fastq	509843192.0	8545402.0	GSM6482083 r1	0:29.81 1:29.85	A:121579451;C:133424275;G:133469726;T:121359509;N:10231	29	29			121579451	133424275	133469726	121359509	10231	SRX17152941	SRS14724786	SRA1479247	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University	2	0.47779	0.47724	0.17114	0.17128	0.73296	0.73208	0.5655	0.56416	23	23	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	sc	bulk	bulk		China	2022-08-19	Larval	Larval	Embryo Imprecise	All anatomical structures