{"database": "metadata", "table": "run_metadata", "rows": [[32784, "SRR29438461", "SRX24951081", "SRS21654792", "SRP514388", "PRJNA1124950", "Deciphering the Toxic Effects of Polystyrene Nanoparticle on Erythropoiesis at Single Cell Resolution", "GSE270075", "Transcriptome Analysis", "The toxic effects of polystyrene nanoparticles on aquatic ecosystems have been predominantly studied  with a focus on oxidative stress and inflammatory responses. However  this study comprehensively examined the effects of polystyrene nanoparticles on the development of zebrafish embryos using single cell RNA sequencing analysis  explicitly investigating their effects on erythropoiesis. In vivo experiments were conducted using zebrafish embryos to validate the single cell RNA sequencing analysis. Exposure to polystyrene nanoparticles resulted in a decrease in the proportion of mature erythrocytes due to an increase in immature erythrocytes during the erythrocyte differentiation process. Additionally  heme synthesis was impaired  leading to a decrease in the proportion of erythrocytes. These findings indicated the toxic effects of polystyrene nanoparticles on hematopoiesis. Overall design: 120 hpf zebrafish embryos were pooled as a control groupwild type and 20 nm polystyrene nanoparticles PS20nm exposed group for single cell RNA sequencing.", null, "pubmed:39846194", null, "Zebra Control", "GSM8334031", null, "source name:embryos|tissue:embryos|Stage:120 hpf|treatment:Wild type|geo loc name:missing|collection date:missing", "Zebra Control", "First  the quality and basic statistics of raw sequencing data were checked through FastQC. post the quality control process  sequencing data were processed through a Cell Ranger v6.0.0 10X Genomics count pipeline using zebrafish genome GRCz11. The zebrafish genome and transcriptome information were downloaded from the Ensembl FTP server release 104  and the index was constructed by processing with the Cell Ranger mkref pipeline. The cellranger count pipeline produces gene expression matrices containing the unique molecular identifier UMI counts per gene  per barcode. Also  clusters with expression profiles and information on differential gene expression were generated from the pipeline. Downstream analysis was performed using Seurat version 4.3.0 in R version 4.2.2 to process data produced through 10x genomics. Assembly: GRCz11 Supplementary files format and content: Three types of processed data files are provided: barcode.tsv  features.tsv  matrix.mtx", "embryos", null, "The samples were carefully resuspended in a cold  calcium  and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7\u2122 Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems  catalog number F23001. Following this  the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech  catalog number 130 090 101 and MS columns Miltenyi Biotech  catalog number 130 042 201 in accordance with the manufacturer\u2019s guidelines. Following the guidelines of the 10x Chromium Single Cell 5\u2019 v2 protocol 10x Genomics  document number CG000331  Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell 5\u2019 Reagent v2 kits 10x Genomics  PN 1000244. In brief  the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5\u2032 Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics  PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs  RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction  where barcoded full length cDNA was synthesized from mRNA  the barcoded cDNA molecules were enriched with PCR. For the preparation of the 5\u2019 Gene Expression Library  the amplified cDNA underwent a series of steps  including enzymatic fragmentation  end repair  A tailing  adapter ligation  and index PCR.", null, "tissue:embryos|Stage:120 hpf|treatment:Wild type", "GSM8334031", "GSM8334031: Zebra Control; Danio rerio; RNA Seq", "GSM8334031 r1", "GSM8334031", "1", "The samples were carefully resuspended in a cold  calcium  and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7\u2122 Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems  catalog number F23001. Following this  the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech  catalog number 130 090 101 and MS columns Miltenyi Biotech  catalog number 130 042 201 in accordance with the manufacturer's guidelines. Following the guidelines of the 10x Chromium Single Cell five prime v2 protocol 10x Genomics  document number CG000331  Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell five prime Reagent v2 kits 10x Genomics  PN 1000244. In brief  the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5\u2032 Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics  PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs  RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction  where barcoded full length cDNA was synthesized from mRNA  the barcoded cDNA molecules were enriched with PCR. For the preparation of the five prime Gene Expression Library  the amplified cDNA underwent a series of steps  including enzymatic fragmentation  end repair  A tailing  adapter ligation  and index PCR.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP514388", null, null, "Zebra_Control_S1_L002_R1_001.fastq.gz Zebra_Control_S1_L002_R2_001.fastq.gz", "fastq fastq", 44451768632.0, 383204902.0, "GSM8334031 r1", "0:26 1:90", "A:10119968829;C:11732695259;G:10981098564;T:11603155786;N:14850194", 26, 90, null, null, 10119968829, 11732695259, 10981098564, 11603155786, 14850194, "SRX24951081", "SRS21654792", "SRA1904713", "Pusan National University", "Pusan National University", 2, 0.07283, 0.96543, 0.02838, 0.15165, 0.98052, 0.78464, 0.32149, 0.56384, 26, 90, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "5prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "South Korea", "2024-06-17", "Larval", "Larval", "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": ["32784"], "units": {}, "query_ms": 9.890657005598769}