run_metadata: 34089

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
34089	SRR31047784	SRX26432305	SRS22949545	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 µg/L to 1000 µg/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 µg/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.				6PPD 2	GSM8582552		source name:Brain\|tissue:Brain\|treatment:6PPD\|geo loc name:missing\|collection date:missing	6PPD 2	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 μg/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 1μg 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℃ 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ 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）. 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℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec annealing at 60℃ for 15 sec and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last we performed the 2×150bp paired end sequencing PE150 on an illumina Novaseq™ 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°C. To inhibit pigmentation embryos were treated with 0.003% 1 phenyl 2 thiourea PTU Aladdin starting at 24 hpf.	tissue:Brain\|treatment:6PPD	GSM8582552	GSM8582552: 6PPD 2; Danio rerio; RNA Seq	GSM8582552 r1	GSM8582552	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 1μg 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℃ 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ 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）. 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℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec annealing at 60℃ for 15 sec and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last we performed the 2×150bp paired end sequencing PE150 on an illumina Novaseq™ 6000 LC Bio Technology CO. Ltd. Hangzhou China following the vendor's recommended protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP539617			6PPD2head_Clean_Data1.fq.gz 6PPD2head_Clean_Data2.fq.gz	fastq fastq	6184525960.0	20877930.0	GSM8582552 r1												SRX26432305	SRS22949545	SRA1994053	Guizhou Medical University	Guizhou Medical University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		China	2024-10-19	Multi-stage	Embryo	Brain	Nervous System