run_metadata: 60049

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
60049	SRR12125398	SRX8646717	SRS6930260	SRP269528	PRJNA643503	Variability of an early developmental cell population underlies stochastic laterality defects	GSE153621	Transcriptome Analysis	Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.		pubmed:33440143		TL emb1 5.25hpf	GSM4648246		source name:Whole embryo\|strain:TL\|developmental stage:5.25hpf\|tissue:Whole embryo\|biological replicate id:1	TL emb1 5.25hpf	R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.	Whole embryo		RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.	Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.	strain:TL\|developmental stage:5.25hpf\|tissue:Whole embryo\|biological replicate id:1	GSM4648246	GSM4648246: TL emb1 5.25hpf; Danio rerio; RNA Seq	GSM4648246		1	RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.	GEO Accession:GSM4648246	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP269528			TL_emb1_5_25hpf.fastq	fastq	539868982.0	8057746.0	GSM4648246 r1	0:67	A:164876385;C:95791327;G:123943212;T:155156126;N:101932	67				164876385	95791327	123943212	155156126	101932	SRX8646717	SRS6930260	SRA1093450	GEO	Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine	1	0.83865		0.06636		0.78953		0.69934		67		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq		Germany	2020-07-01	Gastrula	Embryo	Whole Organism	All anatomical structures