run_metadata: 69678

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
69678	SRR19094455	SRX15162537	SRS12904064	SRP373785	PRJNA835404	Proteostasis governs differential temperature sensitivity across embryonic cell types	GSE202294	Other	The genetic program of embryonic development is remarkably robust but temperature stress can degrade its ability to generate animals with invariant anatomy. While the stereotyped consistent phenotypes associated with environmental stress during vertebrate development suggest that some cell types are more sensitive to stress than others the basis of this sensitivity is unknown. Here we characterize hundreds of individual zebrafish embryos under temperature stress using whole animal single cell RNA seq to identify cell types and molecular programs within them that drive phenotypic variability. We find that temperature perturbs the normal proportions and gene expression programs of numerous cell types and also introduces asynchrony in their development. The notochord is particularly sensitive to temperature stress which we show is due to a specialized cell type sheath cells. Further analyses show that sheath cells accumulate misfolded protein at elevated temperature leading to a cascading structural failure of the notochord and irreversible anatomic defects in the embryo. Our study demonstrates that whole animal single cell RNA seq can characterize mechanisms important for developmental robustness and pinpoint molecular programs within specific cell types that constitute key failure points. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to temperature perturbations 28C 32C 34C with sci RNA seq3.		pubmed:37949057		Hotfish	GSM6107905		source name:Whole embryo\|tissue:Whole embryo\|developmental stage:24 30 36 hpf\|strain:AB\|genotype:wild type\|treatment:temperature perturbation experiment controls treated\|temperature:28C 32C 34C\|fraction:nuclear polyA RNA	Hotfish	The demultiplexing barcoded processing gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: hotfish.cds monocle3 object Supplementary files format and content: HF4 counts.RDS gene by cell counts sparse matrix Supplementary files format and content: HF4 cell metadata.txt cell metadata tab separated Supplementary files format and content: HF4 gene metadata.txt gene metadata tab separated Supplementary files format and content: HF4 hash sampleSheet.txt hash sample table tab separated Supplementary files format and content: HF4 processed hashTable.csv hash count table tab separated	Whole embryo		Embryos were transferred one by one into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS 5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq	Zebrafish embryos were raised in embryo media at 28.5 32 and 34C.	tissue:Whole embryo\|developmental stage:24 30 36 hpf\|strain:AB\|genotype:wild type\|treatment:temperature perturbation experiment controls treated\|temperature:28C 32C 34C\|fraction:nuclear polyA RNA	GSM6107905	GSM6107905: Hotfish; Danio rerio; RNA Seq	GSM6107905 r1	GSM6107905	1	Embryos were transferred one by one into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS 5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP373785		loader:fastq load.py\|options: appendBCtoName	HF4-L002.fastq.gz	fastq	64445114000.0	644451140.0	GSM6107905 r2	0:100	A:21755385809;C:12837761861;G:14651336119;T:15197372623;N:3257588	100				21755385809	12837761861	14651336119	15197372623	3257588	SRX15162537	SRS12904064	SRA1415795	University of Washington	University of Washington	1	0.73455		0.40204		0.84153		0.56626		100		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_plate	scirnaseq		United States	2022-05-05	Pharyngula	Embryo	Whole Organism	All anatomical structures