{"database": "metadata", "table": "run_metadata", "rows": [[60886, "SRR12623493", "SRX9106222", "SRS7349638", "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", null, null, null, "control", "GSM4775399", null, "tissue:emberyo|treatment:untreated|age:12 hpf|genotype:wild type", "control", "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", null, "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 \u00b0C for 5 min  100 \u00b5L of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 \u00b5m 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\u00d7 Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3\u2032 Gel Bead  Chip and Library Kits 10\u00d7 Genomics  Pleasanton  USA.", null, "treatment:untreated|age:12 hpf|genotype:wild type", "GSM4775399", "GSM4775399: control; Danio rerio; RNA Seq", "GSM4775399", null, "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 \u00b0C for 5 min  100 \u00b5L of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 \u00b5m 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\u00d7 Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3\u2032 Gel Bead  Chip and Library Kits 10\u00d7 Genomics  Pleasanton  USA.", "GEO Accession:GSM4775399", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP282042", null, null, "Control_S4_L008_R2_001.fastq.gz", "fastq", 68429323981.0, 453174331.0, "GSM4775399 r3", "0:0 1:151", "A:19629507419;C:13923809144;G:15473487376;T:19395858693;N:6661349", 0, 151, null, null, 19629507419, 13923809144, 15473487376, 19395858693, 6661349, "SRX9106222", "SRS7349638", "SRA1123780", "GEO", "HOHAI", 1, 0.90437, null, 0.12406, null, 0.79076, null, 0.50621, null, 151, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2020-09-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["60886"], "units": {}, "query_ms": 7.517430000007153}