run_metadata: 60879

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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
60879	SRR12623498	SRX9106224	SRS7349641	SRP282042	PRJNA662909	Nanoplastics and sunscreens contained in personal care products induce neurotoxicity in early zebrafish embryos	GSE157816	Transcriptome Analysis	Nanoplastics with small particle size and high surface area/volume ratio make them easy to absorb environmental pollutants and affect their bioavailability. In this study polystyrene nanoplastic beads PS NPBs with a particle size of 100nm and sunscreen butyl methoxydibenzoylmethane BMDBM contained in personal care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryo. The exposure period was 2 hpf 12 hpf. The BMDBM and PS NPBs significantly upregulated the genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases but the influenced genes were not exactly the same and the combined exposure reduced the adverse effects on the expression of all genes. With the help of single cell RNA sequencing technology the neural mid cells were identified as the target cells of both pollutants and brain development head development and notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS NPBs were identified. The BMDBM mainly affect the differentiation and fate of neurons in central nervous system through the regulation of her5 her6 her11 lfng pax2a and fgfr4. The PS NPBs regulated the expression of olig2 foxg1a fzd8b six3a rx1 lhx2b nkx2.1a and sfrp5 to alter nervous system development retinal development and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested and significant inhibition of locomotor activity was found indicating that early disrupting effect on central nervous system would have a sustained impact on the behavior of zebrafish. Overall design: mRNA profiles of 12 hpf wild type zebrafish embryos				MPs	GSM4775401		tissue:emberyo\|treatment:exposed to MPs\|age:12 hpf\|genotype:wild type	MPs	Seurat package in R version 3.5.2 was used to analyze the sequenced reads. Principal component analysis PCA was used for dimensionality reduction and a graph based clustering was applied to cluster in PCA space. UMAP was used for the visualization of the clusters. The marker genes of each cluster were identified by FindMarkers function in the Seurat package. The clusters were annotated to a known cell type according to the Zebrafish Information Network ZFIN database and current literature Genome build: mm10 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell	emberyo		post exposure forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology Shanghai China at 37 °C for 5 min 100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics Pleasanton USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead Chip and Library Kits 10× Genomics Pleasanton USA.		treatment:exposed to MPs\|age:12 hpf\|genotype:wild type	GSM4775401	GSM4775401: MPs; Danio rerio; RNA Seq	GSM4775401		1	post exposure forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology Shanghai China at 37 °C for 5 min 100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics Pleasanton USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead Chip and Library Kits 10× Genomics Pleasanton USA.	GEO Accession:GSM4775401	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP282042			MPs_S2_L006_R1_001.fastq.gz	fastq	69080874938.0	457489238.0	GSM4775401 r2	0:151 1:0	A:16058446984;C:10537982472;G:9566377499;T:32913863031;N:4204952	151	0			16058446984	10537982472	9566377499	32913863031	4204952	SRX9106224	SRS7349641	SRA1123780	GEO	HOHAI	1	0.10674		0.01242		0.96621		0.50529		151		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only		China	2020-09-11	Segmentation	Embryo	Embryo Imprecise	All anatomical structures