run_metadata: 34490

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
34490	SRR31790711	SRX27151924	SRS23606409	SRP552945	PRJNA1201093	Fine particulate matter PM2.5 induces microRNA 192–5p causing glomerular damage	GSE285038	Transcriptome Analysis	To unravel changes in gene expression due to exposure to PM2.5 we performed bulk RNA seq analyses of zebrafish larvae exposed to PM2.5 and controls. Among others PM2.5 increased oxoglutarate alpha ketoglutarate receptor 1a nitric oxide synthase arachidonate 5 lipoxygenase b immunity related GTPase family e1 sulfotransferase family 5A and macrophage expressed 1. NADPH oxidase organizer 1a and NADPH oxidase 1 were upregulated due to PM2.5 exposure. Furthermore protein tyrosine/serine/threonine phosphatase activity was decreased post exposure to PM2.5. GESA analysis showed that genes involved in proteasome complex formation inflammatory and immune response leucocyte mediated cytotoxicity peptidase activator activity protein folding and apoptotic signaling were upregulated post exposure to PM2.5. These results indicate that PM2.5 exposure caused the activation of immune inflammatory and oxidative stress pathways and lipid and metabolic dysregulation. Overall design: Zebrafish were mated at 28.5°C and larvae grew in standard E3 solution. Zebrafish larvae were exposed to 1.2 × 10^7 smog particles from 72 hpf till 120 hpf. Untreated zebrafish larvae served as controls. RNA was isolated from 5 7 zebrafish larvae in each group. RNA from whole zebrafish was isolated using the ReliaPrep™ RNA Miniprep System Promega Madison WI USA based on the manufacturer's protocol. The RNA quality of each sample was evaluated with a bioanalyzer and only samples with an RNA Integrity Number RIN greater than 7.8 were selected for sequencing. Libraries were prepared following Novogene's in house protocol. Sequencing was carried out using paired end reads of 150 base pairs on an Illumina Novaseq 6000 Illumina USA yielding an average of 20 million reads per sample.		pubmed:40373708		RNA zebrafish larvae control rep 1	GSM8695643		source name:larvea\|tissue:larvea\|treatment:control\|geo loc name:missing\|collection date:missing	RNA zebrafish larvae control rep 1	RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the Danio rerio reference genome GRCz11 using STAR version 2.6.1c. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample	larvea		RNA was isolated using the peqGold total RNA kit VWR Peqlab Erlangen Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated Illumina.		tissue:larvea\|treatment:control	GSM8695643	GSM8695643: RNA zebrafish larvae control rep 1; Danio rerio; RNA Seq	GSM8695643 r1	GSM8695643	1	RNA was isolated using the peqGold total RNA kit VWR Peqlab Erlangen Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated Illumina.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus		SRP552945			RNA_zebrafish_larvae_control_rep_1_R1.fq.gz RNA_zebrafish_larvae_control_rep_1_R2.fq.gz	fastq fastq	8152835100.0	27176117.0	GSM8695643 r1	0:150 1:150	A:2164487396;C:1922161762;G:1918935266;T:2142562884;N:4687792	150	150			2164487396	1922161762	1918935266	2142562884	4687792	SRX27151924	SRS23606409	SRA2123535	Institute for Stem Cell Biology, RWTH Aachen University Medical School	Institute for Stem Cell Biology, RWTH Aachen University Medical School												B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	unknown	bulk	bulk	bulk		Germany	2024-12-20	Larval	Larval	Undetermined	Undetermined