{"database": "metadata", "table": "run_metadata", "rows": [[34090, "SRR31047785", "SRX26432304", "SRS22949544", "SRP539617", "PRJNA1175041", "6PPD induces cerebrovascular defects by triggering oxidative stress and ferroptosis in zebrafish", "GSE279887", "Transcriptome Analysis", "N 1 3 dimethylbutyl N' phenyl p phenylenediamine 6PPD  which is widely used as an antiozonant in rubber tires  has recently got much attention for its acute aquatic toxicity. However  the developmental toxicity of 6PPD in cerebrovascular network remains unknown. Here  we investigated the effects of 6PPD exposure in cerebral vascular using the larvae of zebrafish. 6PPD would not affect the body length and shape of zebrafish larvae at the concentrations ranging from 20 \u00b5g/L to 1000 \u00b5g/L. 6PPD induced developmental defects in the brain in a concentration dependent manner. The trunk vascular development would not be affected while the cerebrovascular network was disrupted upon 6PPD exposure. 6PPD would trigger excessive Reactive Oxygen Species ROS in the brain  indicating abnormal oxidative stress. Mechanistically  brain specific transcriptome analysis showed that 6PPD could potentially cause the blockage of arachidonic acid AA metabolism related genes and the upregulation of ferroptosis related genes. Besides  treatment with ferroptosis inhibitor N Acetyl L cysteine NAC attenuated oxidative damage and improved the construction of cerebrovascular network upon 6PPD exposure. Moreover  using a human vascular endothelial cell line  we further confirmed that 6PPD could trigger abnormal oxidative stress and defective expansion capacity  implying the conserved toxicity cross species. These findings are useful for the elucidation of toxicity underlying 6PPD in cerebrovascular systems of both zebrafish and humans. Overall design: To investigate the effects of 6PPD on zebrafish development  embryos were treated with 500 \u00b5g/L 6PPD from 10 hpf until 2 dpf dpf. For transcriptomic analysis  three biological replicates were prepared for both the 6PPD treatment group and the DMSO control group. For each replicate  the heads of 150 embryos at 2 dpf were dissected  flash frozen in liquid nitrogen  and sent for transcriptomic sequencing. The raw data analysis was performed to identify differentially expressed genes between the 6PPD treated and control groups.", null, null, null, "6PPD 1", "GSM8582551", null, "source name:Brain|tissue:Brain|treatment:6PPD|geo loc name:missing|collection date:missing", "6PPD 1", "Self house pipeline Sequence reads were trimmed for adaptor sequence/low quality seguence using fastp parameter  Quality limit: 20 Trimmed sequence reads were mapped to GRCz11.109 use HISAT2 Read count extraction and normalization were performed using featureCounts and StringTie Assembly: GRCz11.109 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "Brain", "For transcriptomic analysis  three biological replicates were prepared for both the 500 \u03bcg/L 6PPD treatment group and the DMSO control group. The embryos were treated from 10 hpf to 2dpf.For each replicate  the heads of 150 embryos at 2 dpf were dissected  flash frozen in liquid nitrogen.", "Total RNA was isolated and purified using TRIzol reagent Invitrogen  Carlsbad  CA  USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop  Wilmington  DE  USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent  CA  USA with RIN number >7.0  and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA\uff09. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec  annealing at 60\u2103 for 15 sec  and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last  we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO.  Ltd.  Hangzhou  China following the vendor's recommended protocol.", "Embryos were collected and cultured in egg water 0.06 mg/mL sea salt  0.5 mg/L methylene blue and incubated  before 24 hpf at 28\u00b0C. To inhibit pigmentation  embryos were treated with 0.003% 1 phenyl 2 thiourea PTU  Aladdin starting at 24 hpf.", "tissue:Brain|treatment:6PPD", "GSM8582551", "GSM8582551: 6PPD 1; Danio rerio; RNA Seq", "GSM8582551 r1", "GSM8582551", "1", "Total RNA was isolated and purified using TRIzol reagent Invitrogen  Carlsbad  CA  USA following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND 1000 NanoDrop  Wilmington  DE  USA. The RNA integrity was assessed by Bioanalyzer 2100 Agilent  CA  USA with RIN number >7.0  and confirmed by electrophoresis with denaturing agarose gel. Poly A RNA is purified from 1\u03bcg total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94\u2103 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA\uff09. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95\u2103 for 3 min; 8 cycles of denaturation at 98\u2103 for 15 sec  annealing at 60\u2103 for 15 sec  and extension at 72\u2103 for 30 sec; and then final extension at 72\u2103 for 5 min. The average insert size for the final cDNA library was 300\u00b150 bp. At last  we performed the 2\u00d7150bp paired end sequencing PE150 on an illumina Novaseq\u2122 6000 LC Bio Technology CO.  Ltd.  Hangzhou  China following the vendor's recommended protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539617", null, null, "6PPD1head_Clean_Data1.fq.gz 6PPD1head_Clean_Data2.fq.gz", "fastq fastq", 5412472152.0, 18274114.0, "GSM8582551 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26432304", "SRS22949544", "SRA1994053", "Guizhou Medical University", "Guizhou Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-10-19", "Multi-stage", "Embryo", "Brain", "Nervous System"]], "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": ["34090"], "units": {}, "query_ms": 13.25106099830009}