run_metadata: 67135

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
67135	SRR17097013	SRX13284816	SRS11197573	SRP348912	PRJNA785573	Identifying key events from Per and Polyfluoroalkyl Substances exposure that influence larval zebrafish in light:dark assay using RNA sequencing analysis of perfluorohexane 1 sulfonate PFHxS	GSE190009	Transcriptome Analysis	Gene expression data from short term in vivo studies shows efficacy in quantifying concentration dependent effects that inform toxicity outcomes particularly for chemicals with limited toxicity data such as Per and Polyfluoroalkyl Substances PFAS. Automated behavioral assessments at non teratogenic concentrations reveal perfluorohexane 1 sulfonate PFHxS exposure causes hyperactivity in larval zebrafish 6 dpf dpf during the light phase of the light:dark assay compared to 0.4% dimethylsulfoxide DMSO vehicle control. To identify key events that drive this abnormal behavior zebrafish embryos were exposed to 7.87 25.1 µM PFHxS or 0.4% DMSO and RNA was isolated from pooled head tissue collected at 4 dpf and 5 dpf before the onset of hyperactivity for RNA sequencing NextSeq 500. Differentially expressed genes DEGs were identified using Gene Specific Analysis Partek Flow St. Louis MO and mapped to human orthologs for pathway analyses to inform modes of action. Overall design: At 0 dpf zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 µm nylon mesh filter Millipore Catalog No. MANMN4010 with 400µL of 10% Hanks' balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore Catalog No. MAMCS9610 containing 250µL of 10% HBSS Westerfield 2007 and 1µL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 or 1 dpf 5 dpf plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 µM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.				GRC350 D5 3F S10	GSM5711819		tissue:pooled heads collected anterior to swim bladder\|treatment:potassium perfluorohexane 1 sulfonate\|age:5 dpf stage:larvae\|strain:mixed wildtype	GRC350 D5 3F S10	Fastq files were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow v.8.0.19.0428; St. Louis MO. Gene counts were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation Gene features were offset to 0.0001 and those with geometric means across all samples ≤ 1 were filtered Sample gene counts were quantile normalized and log2 transformed Genome build: GRCz11 Ensembl version 93 gene annotation build Supplementary files format and content: tab delimited raw gene count matrix normalized gene count matrix	pooled heads collected anterior to swim bladder	At 0 dpf zebrafish embryos were bleached as previously described Tal et al. 2017. A single embryo at the dome to epib stages Kimmel et al. 1995 was placed into each individual well of a 96 well plate containing a 40 μm nylon mesh filter Millipore Catalog No. MANMN4010 with 400μL of 10% Hanks’ balanced salt solution HBSS per well. Filter inserts containing zebrafish embryos were transferred to 96 well culture trays Millipore Catalog No. MAMCS9610 containing 250μL of 10% HBSS Westerfield 2007 and 1μL of 250× working solutions per well. A final concentration of 0.4% DMSO was used for all exposure groups and as a vehicle control. Daily from 1–4 or 1 dpf 5 dpf plates underwent 100% media changes to refresh chemical dosing solutions by blotting Brandel; Catalog No. FPXLR 196 and transferring mesh inserts containing zebrafish to new bottom plates Millipore; Catalog No. MAMCS9610. To minimize evaporation plates were sealed Biorad; Catalog No. MSA5001 and wrapped with parafilm. Plates were maintained on a 14 h:10 h light cycle at 26.0°C and scored daily for death malformations hatching and swim bladder inflation. Zebrafish embryos were exposed to 7.87 25.1 μM PFHxS or 0.4% DMSO with targeting n=6 pooled replicates/treatment. Each pooled replicate consisted of 15 zebrafish heads collected anterior to the swim bladder/treatment.	Each pooled sample underwent RNA extraction using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix and they were run for 75 cycles single read.	All procedures involving zebrafish were approved by the U.S. Environmental Protection Agency EPA National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and carried out in accordance with the relevant guidelines and regulations. Embryos were obtained from a mixed wild type WT adult zebrafish line Danio rerio that was generated and maintained as previously described Phelps et al. 2017. Briefly to maintain genetic diversity a minimum of one WT line AB and/or Tupfel long fin WT strains was added one time per year. Zebrafish adults were housed in 6 L tanks at an approximate density of 8 fish/L. Adults were fed Gemma Micro 300 Skretting once daily and shell free E Z Egg Brine Shrimp Direct twice daily Mondays through Fridays. Both food sources were fed once daily on weekends. U.S. EPA WT zebrafish were maintained on a 14 h:10 h light cycle at 28.5°C and bred every 2–3 weeks. For embryo collection 60–100 adults were placed in 10 or 20 L angled static breeding tanks overnight. The following morning adults were transferred to new angled bottom tanks containing fish facility water and embryos were collected 30–40 min later.	treatment:potassium perfluorohexane 1 sulfonate\|concentration µm:7.87\|age:5 dpf stage:larvae\|strain:mixed wildtype	GSM5711819	GSM5711819: GRC350 D5 3F S10; Danio rerio; RNA Seq	GSM5711819		1	Each pooled sample underwent RNA extraction using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. The total RNA sample qualities were checked by Bioanalyzer and RNA concentrations were checked by Qubit RNA BR kit. The total RNA sample qualities were checked by Bioanalyzer and their concentrations were checked by Qubit RNA BR kit. All 48 total RNA 500 ng per sample selected by PI were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19. PCR amplification with 16 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library volume x concentration was pooled from 16 randomized libraries to make the sequencing library pools total 3 pools of 16 libraries each and the concentrations of the pooled libraries were checked by Qubit. The library pools were denatured and diluted according to Illmina NextSeq protocols. For PFHxS the final concentrations for sequencing were 2.8 3.0 pM + 2% Phix and they were run for 75 cycles single read.	GEO Accession:GSM5711819	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP348912			GRC350-D5-3F_S10_L003_R1_001.fastq.gz	fastq	450520125.0	6006935.0	GSM5711819 r3	0:75 1:0	A:119957953;C:101154236;G:109745090;T:119627796;N:35050	75	0			119957953	101154236	109745090	119627796	35050	SRX13284816	SRS11197573	SRA1337575	GEO	US EPA	1	0.94629		0.0931		0.70603		0.47769		75		B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	bulk	unknown	unknown		United States	2021-12-02	Larval	Larval	Multi-tissue	Multi-system