metadata: run_metadata: 45 rows where experiment.library_selection = "RANDOM PCR", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation

45 rows where experiment.library_selection = "RANDOM PCR", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation_coarse = "Nervous System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
44934	44934	SRR6308292	SRX3408680	SRS2701476	SRP125291	PRJNA419036	Danio rerio strain:ASWT Transcriptome or Gene expression	PRJNA419036	Other	A genome wide map of circular RNA in adult zebrafish.	Zf brain	Zf brain	strain:ASWT\|age:1year\|sex:male\|tissue:Brain\|BioSampleModel:Model organism or animal	A genome wide map of circular RNA in adult zebrafish	Zf brain	Zf brain	Tissue were isolated from adult zebrafish anaesthetized using 0.004% Tricaine Sigma USA. Extreme care was taken to avoid contamination to obtain pure homogenous tissue samples. The tissues were repeatedly washed in PBS to remove contaminating debris. The tissue samples were homogenized in Trizol for cell lysis Invitrogen USA. RNA was isolated from the homogenized tissue samples using RNeasy kit Qiagen USA. Sample preparation for sequencing was carried out using Truseq stranded RNA sample preparation kit Illumina USA as per supplier's instructions. In order to remove the ribosomal RNA rRNA one microgram of total RNA was hybridised with Ribo zero gold rRNA removal probe. Upon removing rRNA the samples were processed for fragmentation in the presence of ionic cations at 37 degree Celcius. First stranded complementary DNA cDNA was prepared by random hexamers and superscript II reverse transcriptase Invitrogen USA in presence of Actinomycin D to facilitate RNA dependent synthesis for improving strand specificity. The second strand was synthesised with second strand cDNA mix containing dUTP instead of dTTP and subjected to A base addition followed by adapter ligation. Final libraries were prepared by amplifying adapter ligated double strand cDNA. Clusters were generated on Hiseq flow cell v3 Illumina in cBot according to standard protocol Illumina USA.	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP125291	Zf_brain_R1.fastq Zf_brain_R2.fastq	fastq fastq	3103065297.0	16700545.0	Zf brain R2.fastq	0:97.29 1:88.52	A:832854751;C:721391526;G:701229714;T:847395346;N:193960	97	88	832854751	721391526	701229714	847395346	193960	SRX3408680	SRS2701476	SRA631861	CSIR-Institute of Genomics and Integrative Biology\|Genomic Medicine	CSIR-Institute of Genomics and Integrative Biology	2	0.91265	0.91134	0.39205	0.38961	0.7778	0.78094	0.69798	0.67369	90	45	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	ribozero	bulk	unknown	unknown	India	2017-11-20	Adult	Adult	Brain	Nervous System
51055	51055	SRR8457160	SRX5263759	SRS4264535	SRP180326	PRJNA515927	Effects of acrylamide on zebrafish brain	PRJNA515927	Other	Here we used a multi omics approach with proteomic and transcriptomic methodologies to identify the main key events involved in the development of neurotoxicity in zebrafish brain post acute exposure to 0.75 mM acrylamide for 72h.		ACR6	isolate:ACRYLAMIDE 6\|dev stage:ADULT\|sex:male\|tissue:BRAIN\|treatment:ACRYLAMIDE 0 75 mM\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult brain acrylamide	RL BACR6	RL BACR6	Libraries were made with TruSeq Stranded mRNA Library Prep Kit	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP180326	RL_BACR6_USPD16083281-D709-AK1544_H33JJDMXX_L1_1.fq.gz RL_BACR6_USPD16083281-D709-AK1544_H33JJDMXX_L1_2.fq.gz RL_BACR6_USPD16083281-D709-AK1544_H33JJDMXX_L2_1.fq.gz RL_BACR6_USPD16083281-D709-AK1544_H33JJDMXX_L2_2.fq.gz	fastq fastq fastq fastq	13321079400.0	44403598.0	RL BACR6 USPD16083281 D709 AK1544 H33JJDMXX L1 1.fq.gz	0:150 1:150	A:4077561492;C:2577657837;G:2772399063;T:3893433204;N:27804	150	150	4077561492	2577657837	2772399063	3893433204	27804	SRX5263759	SRS4264535	SRA836494	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.90801	0.90784	0.21763	0.21551	0.71177	0.71374	0.52257	0.51151	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2019-09-16	Adult	Adult	Brain	Nervous System
51056	51056	SRR8457161	SRX5263758	SRS4264534	SRP180326	PRJNA515927	Effects of acrylamide on zebrafish brain	PRJNA515927	Other	Here we used a multi omics approach with proteomic and transcriptomic methodologies to identify the main key events involved in the development of neurotoxicity in zebrafish brain post acute exposure to 0.75 mM acrylamide for 72h.		ACR7	isolate:ACRYLAMIDE 7\|dev stage:ADULT\|sex:male\|tissue:BRAIN\|treatment:ACRYLAMIDE 0 75 mM\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult brain acrylamide	RL BACR7	RL BACR7	Libraries were made with TruSeq Stranded mRNA Library Prep Kit	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP180326	RL_BACR7_USPD16083281-D710-AK1544_H33JJDMXX_L1_1.fq.gz RL_BACR7_USPD16083281-D710-AK1544_H33JJDMXX_L1_2.fq.gz RL_BACR7_USPD16083281-D710-AK1544_H33JJDMXX_L2_1.fq.gz RL_BACR7_USPD16083281-D710-AK1544_H33JJDMXX_L2_2.fq.gz	fastq fastq fastq fastq	14964908100.0	49883027.0	RL BACR7 USPD16083281 D710 AK1544 H33JJDMXX L1 1.fq.gz	0:150 1:150	A:4619040923;C:2862579619;G:3088698171;T:4394558323;N:31064	150	150	4619040923	2862579619	3088698171	4394558323	31064	SRX5263758	SRS4264534	SRA836494	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.90465	0.90353	0.22082	0.21768	0.71421	0.71737	0.52176	0.51638	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2019-09-16	Adult	Adult	Brain	Nervous System
51057	51057	SRR8457162	SRX5263757	SRS4264533	SRP180326	PRJNA515927	Effects of acrylamide on zebrafish brain	PRJNA515927	Other	Here we used a multi omics approach with proteomic and transcriptomic methodologies to identify the main key events involved in the development of neurotoxicity in zebrafish brain post acute exposure to 0.75 mM acrylamide for 72h.		ACR4	isolate:ACRYLAMIDE 4\|dev stage:ADULT\|sex:male\|tissue:BRAIN\|treatment:ACRYLAMIDE 0 75 mM\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult brain acrylamide	RL BACR4	RL BACR4	Libraries were made with TruSeq Stranded mRNA Library Prep Kit	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP180326	RL_BACR4_USPD16083281-D707-AK1544_H33JJDMXX_L1_1.fq.gz RL_BACR4_USPD16083281-D707-AK1544_H33JJDMXX_L1_2.fq.gz RL_BACR4_USPD16083281-D707-AK1544_H33JJDMXX_L2_1.fq.gz RL_BACR4_USPD16083281-D707-AK1544_H33JJDMXX_L2_2.fq.gz	fastq fastq fastq fastq	15097965600.0	50326552.0	RL BACR4 USPD16083281 D707 AK1544 H33JJDMXX L1 1.fq.gz	0:150 1:150	A:4648189490;C:2894934169;G:3114634101;T:4440176432;N:31408	150	150	4648189490	2894934169	3114634101	4440176432	31408	SRX5263757	SRS4264533	SRA836494	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.90938	0.90906	0.22046	0.2176	0.7162	0.71843	0.53806	0.53612	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2019-09-16	Adult	Adult	Brain	Nervous System
51058	51058	SRR8457163	SRX5263756	SRS4264532	SRP180326	PRJNA515927	Effects of acrylamide on zebrafish brain	PRJNA515927	Other	Here we used a multi omics approach with proteomic and transcriptomic methodologies to identify the main key events involved in the development of neurotoxicity in zebrafish brain post acute exposure to 0.75 mM acrylamide for 72h.		ACR5	isolate:ACRYLAMIDE 5\|dev stage:ADULT\|sex:male\|tissue:BRAIN\|treatment:ACRYLAMIDE 0 75 mM\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult brain acrylamide	RL BACR5	RL BACR5	Libraries were made with TruSeq Stranded mRNA Library Prep Kit	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP180326	RL_BACR5_USPD16083281-D708-AK1544_H33JJDMXX_L1_1.fq.gz RL_BACR5_USPD16083281-D708-AK1544_H33JJDMXX_L1_2.fq.gz RL_BACR5_USPD16083281-D708-AK1544_H33JJDMXX_L2_1.fq.gz RL_BACR5_USPD16083281-D708-AK1544_H33JJDMXX_L2_2.fq.gz	fastq fastq fastq fastq	13706450700.0	45688169.0	RL BACR5 USPD16083281 D708 AK1544 H33JJDMXX L1 1.fq.gz	0:150 1:150	A:4135905547;C:2716663467;G:2914788685;T:3939064139;N:28862	150	150	4135905547	2716663467	2914788685	3939064139	28862	SRX5263756	SRS4264532	SRA836494	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91293	0.91331	0.2028	0.20076	0.70461	0.70646	0.52084	0.52041	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2019-09-16	Adult	Adult	Brain	Nervous System
51059	51059	SRR8457164	SRX5263755	SRS4264531	SRP180326	PRJNA515927	Effects of acrylamide on zebrafish brain	PRJNA515927	Other	Here we used a multi omics approach with proteomic and transcriptomic methodologies to identify the main key events involved in the development of neurotoxicity in zebrafish brain post acute exposure to 0.75 mM acrylamide for 72h.		C3	isolate:CONTROL 3\|dev stage:ADULT\|sex:male\|tissue:BRAIN\|treatment:CONTROL\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult brain control	RL BCN3	RL BCN3	Libraries were made with TruSeq Stranded mRNA Library Prep Kit	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP180326	RL_BCN3_USPD16083281-D711-AK1543_H33JJDMXX_L1_1.fq.gz RL_BCN3_USPD16083281-D711-AK1543_H33JJDMXX_L1_2.fq.gz RL_BCN3_USPD16083281-D711-AK1543_H33JJDMXX_L2_1.fq.gz RL_BCN3_USPD16083281-D711-AK1543_H33JJDMXX_L2_2.fq.gz	fastq fastq fastq fastq	13441183500.0	44803945.0	RL BCN3 USPD16083281 D711 AK1543 H33JJDMXX L1 1.fq.gz	0:150 1:150	A:4029296236;C:2693075506;G:2817037913;T:3901745880;N:27965	150	150	4029296236	2693075506	2817037913	3901745880	27965	SRX5263755	SRS4264531	SRA836494	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91679	0.91699	0.21534	0.2127	0.70715	0.70857	0.53894	0.5356	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2019-09-16	Adult	Adult	Brain	Nervous System
51060	51060	SRR8457165	SRX5263754	SRS4264530	SRP180326	PRJNA515927	Effects of acrylamide on zebrafish brain	PRJNA515927	Other	Here we used a multi omics approach with proteomic and transcriptomic methodologies to identify the main key events involved in the development of neurotoxicity in zebrafish brain post acute exposure to 0.75 mM acrylamide for 72h.		C4	isolate:CONTROL 4\|dev stage:ADULT\|sex:male\|tissue:BRAIN\|treatment:CONTROL\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult brain control	RL BCN4	RL BCN4	Libraries were made with TruSeq Stranded mRNA Library Prep Kit	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP180326	RL_BCN4_USPD16083281-D712-AK1543_H33JJDMXX_L1_1.fq.gz RL_BCN4_USPD16083281-D712-AK1543_H33JJDMXX_L1_2.fq.gz RL_BCN4_USPD16083281-D712-AK1543_H33JJDMXX_L2_1.fq.gz RL_BCN4_USPD16083281-D712-AK1543_H33JJDMXX_L2_2.fq.gz	fastq fastq fastq fastq	13681781400.0	45605938.0	RL BCN4 USPD16083281 D712 AK1543 H33JJDMXX L1 1.fq.gz	0:150 1:150	A:4120928931;C:2729479678;G:2852424176;T:3978920008;N:28607	150	150	4120928931	2729479678	2852424176	3978920008	28607	SRX5263754	SRS4264530	SRA836494	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.92338	0.92298	0.19958	0.19716	0.71364	0.71396	0.53724	0.53847	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2019-09-16	Adult	Adult	Brain	Nervous System
51061	51061	SRR8457166	SRX5263753	SRS4264529	SRP180326	PRJNA515927	Effects of acrylamide on zebrafish brain	PRJNA515927	Other	Here we used a multi omics approach with proteomic and transcriptomic methodologies to identify the main key events involved in the development of neurotoxicity in zebrafish brain post acute exposure to 0.75 mM acrylamide for 72h.		C1	isolate:CONTROL 1\|dev stage:ADULT\|sex:male\|tissue:BRAIN\|treatment:CONTROL\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult brain control	RL BCN1	RL BCN1	Libraries were made with TruSeq Stranded mRNA Library Prep Kit	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP180326	RL_BCN1_USPD16083281-D709-AK1543_H33JJDMXX_L1_1.fq.gz RL_BCN1_USPD16083281-D709-AK1543_H33JJDMXX_L1_2.fq.gz RL_BCN1_USPD16083281-D709-AK1543_H33JJDMXX_L2_1.fq.gz RL_BCN1_USPD16083281-D709-AK1543_H33JJDMXX_L2_2.fq.gz	fastq fastq fastq fastq	13492877400.0	44976258.0	RL BCN1 USPD16083281 D709 AK1543 H33JJDMXX L1 1.fq.gz	0:150 1:150	A:4152227077;C:2599207484;G:2709335522;T:4032079300;N:28017	150	150	4152227077	2599207484	2709335522	4032079300	28017	SRX5263753	SRS4264529	SRA836494	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91166	0.91152	0.21688	0.21367	0.71498	0.71626	0.52504	0.52566	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2019-09-16	Adult	Adult	Brain	Nervous System
51062	51062	SRR8457167	SRX5263752	SRS4264528	SRP180326	PRJNA515927	Effects of acrylamide on zebrafish brain	PRJNA515927	Other	Here we used a multi omics approach with proteomic and transcriptomic methodologies to identify the main key events involved in the development of neurotoxicity in zebrafish brain post acute exposure to 0.75 mM acrylamide for 72h.		C2	isolate:CONTROL 2\|dev stage:ADULT\|sex:male\|tissue:BRAIN\|treatment:CONTROL\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult brain control	RL BCN2	RL BCN2	Libraries were made with TruSeq Stranded mRNA Library Prep Kit	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP180326	RL_BCN2_USPD16083281-D710-AK1543_H33JJDMXX_L1_1.fq.gz RL_BCN2_USPD16083281-D710-AK1543_H33JJDMXX_L1_2.fq.gz RL_BCN2_USPD16083281-D710-AK1543_H33JJDMXX_L2_1.fq.gz RL_BCN2_USPD16083281-D710-AK1543_H33JJDMXX_L2_2.fq.gz	fastq fastq fastq fastq	15973375800.0	53244586.0	RL BCN2 USPD16083281 D710 AK1543 H33JJDMXX L1 1.fq.gz	0:150 1:150	A:4721295230;C:3278709896;G:3425972319;T:4547364912;N:33443	150	150	4721295230	3278709896	3425972319	4547364912	33443	SRX5263752	SRS4264528	SRA836494	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.92491	0.92533	0.16191	0.15951	0.71037	0.71127	0.53492	0.53627	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2019-09-16	Adult	Adult	Brain	Nervous System
51063	51063	SRR8457168	SRX5263751	SRS4264527	SRP180326	PRJNA515927	Effects of acrylamide on zebrafish brain	PRJNA515927	Other	Here we used a multi omics approach with proteomic and transcriptomic methodologies to identify the main key events involved in the development of neurotoxicity in zebrafish brain post acute exposure to 0.75 mM acrylamide for 72h.		C7	isolate:CONTROL 7\|dev stage:ADULT\|sex:male\|tissue:BRAIN\|treatment:CONTROL\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult brain control	RL BCN7	RL BCN7	Libraries were made with TruSeq Stranded mRNA Library Prep Kit	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP180326	RL_BCN7_USPD16083281-D703-AK1544_H33JJDMXX_L1_1.fq.gz RL_BCN7_USPD16083281-D703-AK1544_H33JJDMXX_L1_2.fq.gz RL_BCN7_USPD16083281-D703-AK1544_H33JJDMXX_L2_1.fq.gz RL_BCN7_USPD16083281-D703-AK1544_H33JJDMXX_L2_2.fq.gz	fastq fastq fastq fastq	16214703900.0	54049013.0	RL BCN7 USPD16083281 D703 AK1544 H33JJDMXX L1 1.fq.gz	0:150 1:150	A:4706043702;C:3391758892;G:3607961912;T:4508905693;N:33701	150	150	4706043702	3391758892	3607961912	4508905693	33701	SRX5263751	SRS4264527	SRA836494	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.9242	0.9255	0.1763	0.1751	0.7021	0.7026	0.53332	0.53169	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2019-09-16	Adult	Adult	Brain	Nervous System
51064	51064	SRR8457169	SRX5263750	SRS4264526	SRP180326	PRJNA515927	Effects of acrylamide on zebrafish brain	PRJNA515927	Other	Here we used a multi omics approach with proteomic and transcriptomic methodologies to identify the main key events involved in the development of neurotoxicity in zebrafish brain post acute exposure to 0.75 mM acrylamide for 72h.		ACR1	isolate:ACRYLAMIDE 1\|dev stage:ADULT\|sex:male\|tissue:BRAIN\|treatment:ACRYLAMIDE 0 75 mM\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult brain acrylamide	RL BACR1	RL BACR1	Libraries were made with TruSeq Stranded mRNA Library Prep Kit	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP180326	RL_BACR1_USPD16083281-D704-AK1544_H33JJDMXX_L1_1.fq.gz RL_BACR1_USPD16083281-D704-AK1544_H33JJDMXX_L1_2.fq.gz RL_BACR1_USPD16083281-D704-AK1544_H33JJDMXX_L2_1.fq.gz RL_BACR1_USPD16083281-D704-AK1544_H33JJDMXX_L2_2.fq.gz	fastq fastq fastq fastq	12780426900.0	42601423.0	RL BACR1 USPD16083281 D704 AK1544 H33JJDMXX L1 1.fq.gz	0:150 1:150	A:4077162301;C:2317979412;G:2520736024;T:3864523131;N:26032	150	150	4077162301	2317979412	2520736024	3864523131	26032	SRX5263750	SRS4264526	SRA836494	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.89328	0.88998	0.24952	0.24527	0.72391	0.72636	0.52842	0.51597	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2019-09-16	Adult	Adult	Brain	Nervous System
51065	51065	SRR8457170	SRX5263749	SRS4264525	SRP180326	PRJNA515927	Effects of acrylamide on zebrafish brain	PRJNA515927	Other	Here we used a multi omics approach with proteomic and transcriptomic methodologies to identify the main key events involved in the development of neurotoxicity in zebrafish brain post acute exposure to 0.75 mM acrylamide for 72h.		C5	isolate:CONTROL 5\|dev stage:ADULT\|sex:male\|tissue:BRAIN\|treatment:CONTROL\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult brain control	RL BCN5	RL BCN5	Libraries were made with TruSeq Stranded mRNA Library Prep Kit	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP180326	RL_BCN5_USPD16083281-D701-AK1544_H33JJDMXX_L1_1.fq.gz RL_BCN5_USPD16083281-D701-AK1544_H33JJDMXX_L1_2.fq.gz RL_BCN5_USPD16083281-D701-AK1544_H33JJDMXX_L2_1.fq.gz RL_BCN5_USPD16083281-D701-AK1544_H33JJDMXX_L2_2.fq.gz	fastq fastq fastq fastq	15313482000.0	51044940.0	RL BCN5 USPD16083281 D701 AK1544 H33JJDMXX L1 1.fq.gz	0:150 1:150	A:4425126782;C:3218321935;G:3420657633;T:4249343523;N:32127	150	150	4425126782	3218321935	3420657633	4249343523	32127	SRX5263749	SRS4264525	SRA836494	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.92744	0.92914	0.16483	0.16311	0.69921	0.70072	0.52488	0.52792	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2019-09-16	Adult	Adult	Brain	Nervous System
51066	51066	SRR8457171	SRX5263748	SRS4264524	SRP180326	PRJNA515927	Effects of acrylamide on zebrafish brain	PRJNA515927	Other	Here we used a multi omics approach with proteomic and transcriptomic methodologies to identify the main key events involved in the development of neurotoxicity in zebrafish brain post acute exposure to 0.75 mM acrylamide for 72h.		C6	isolate:CONTROL 6\|dev stage:ADULT\|sex:male\|tissue:BRAIN\|treatment:CONTROL\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult brain control	RL BCN6	RL BCN6	Libraries were made with TruSeq Stranded mRNA Library Prep Kit	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP180326	RL_BCN6_USPD16083281-D702-AK1544_H33JJDMXX_L1_1.fq.gz RL_BCN6_USPD16083281-D702-AK1544_H33JJDMXX_L1_2.fq.gz RL_BCN6_USPD16083281-D702-AK1544_H33JJDMXX_L2_1.fq.gz RL_BCN6_USPD16083281-D702-AK1544_H33JJDMXX_L2_2.fq.gz	fastq fastq fastq fastq	16909535400.0	56365118.0	RL BCN6 USPD16083281 D702 AK1544 H33JJDMXX L1 1.fq.gz	0:150 1:150	A:4904345120;C:3532094778;G:3785408104;T:4687652027;N:35371	150	150	4904345120	3532094778	3785408104	4687652027	35371	SRX5263748	SRS4264524	SRA836494	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.92452	0.92481	0.17231	0.17011	0.70236	0.70504	0.53595	0.53186	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2019-09-16	Adult	Adult	Brain	Nervous System
51067	51067	SRR8457172	SRX5263747	SRS4264522	SRP180326	PRJNA515927	Effects of acrylamide on zebrafish brain	PRJNA515927	Other	Here we used a multi omics approach with proteomic and transcriptomic methodologies to identify the main key events involved in the development of neurotoxicity in zebrafish brain post acute exposure to 0.75 mM acrylamide for 72h.		ACR2	isolate:ACRYLAMIDE 2\|dev stage:ADULT\|sex:male\|tissue:BRAIN\|treatment:ACRYLAMIDE 0 75 mM\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult brain acrylamide	RL BACR2	RL BACR2	Libraries were made with TruSeq Stranded mRNA Library Prep Kit	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP180326	RL_BACR2_USPD16083281-D705-AK1544_H33JJDMXX_L1_1.fq.gz RL_BACR2_USPD16083281-D705-AK1544_H33JJDMXX_L1_2.fq.gz RL_BACR2_USPD16083281-D705-AK1544_H33JJDMXX_L2_1.fq.gz RL_BACR2_USPD16083281-D705-AK1544_H33JJDMXX_L2_2.fq.gz	fastq fastq fastq fastq	13318002300.0	44393341.0	RL BACR2 USPD16083281 D705 AK1544 H33JJDMXX L1 1.fq.gz	0:150 1:150	A:4118509656;C:2543378236;G:2731612441;T:3924474226;N:27741	150	150	4118509656	2543378236	2731612441	3924474226	27741	SRX5263747	SRS4264522	SRA836494	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.90772	0.90665	0.21245	0.20943	0.71303	0.71628	0.53042	0.53048	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2019-09-16	Adult	Adult	Brain	Nervous System
51068	51068	SRR8457173	SRX5263746	SRS4264523	SRP180326	PRJNA515927	Effects of acrylamide on zebrafish brain	PRJNA515927	Other	Here we used a multi omics approach with proteomic and transcriptomic methodologies to identify the main key events involved in the development of neurotoxicity in zebrafish brain post acute exposure to 0.75 mM acrylamide for 72h.		ACR3	isolate:ACRYLAMIDE 3\|dev stage:ADULT\|sex:male\|tissue:BRAIN\|treatment:ACRYLAMIDE 0 75 mM\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult brain acrylamide	RL BACR3	RL BACR3	Libraries were made with TruSeq Stranded mRNA Library Prep Kit	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP180326	RL_BACR3_USPD16083281-D706-AK1544_H33JJDMXX_L1_1.fq.gz RL_BACR3_USPD16083281-D706-AK1544_H33JJDMXX_L1_2.fq.gz RL_BACR3_USPD16083281-D706-AK1544_H33JJDMXX_L2_1.fq.gz RL_BACR3_USPD16083281-D706-AK1544_H33JJDMXX_L2_2.fq.gz	fastq fastq fastq fastq	12902854200.0	43009514.0	RL BACR3 USPD16083281 D706 AK1544 H33JJDMXX L1 1.fq.gz	0:150 1:150	A:4024812887;C:2425575563;G:2599539399;T:3852899449;N:26902	150	150	4024812887	2425575563	2599539399	3852899449	26902	SRX5263746	SRS4264523	SRA836494	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.89966	0.89949	0.23529	0.2328	0.71593	0.71758	0.52131	0.52766	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2019-09-16	Adult	Adult	Brain	Nervous System
51142	51142	SRR8560600	SRX5362099	SRS4352686	SRP185448	PRJNA521037	Danio rerio Raw sequence reads	PRJNA521037	Other	These samples were obtained from the brain tissues of Zebrafish.	Model organism or animal sample from zebrafish transcriptome	Zebrafish Brain Female 2	breed:WUHAN Zebrafish\|age:6 month\|sex:female\|tissue:Brain\|BioSampleModel:Model organism or animal	L8 M b 3	S514 03B CHG022895	S514 03B CHG022895	Total RNA	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	HiSeq X Ten	SRP185448	forward_paired_S514_03B_CHG022895-L8-M-b-3-TGACCA_L004_R1.fastq.gz reverse_paired_S514_03B_CHG022895-L8-M-b-3-TGACCA_L004_R2.fastq.gz	fastq fastq	7628485402.0	25511585.0	forward paired S514 03B CHG022895 L8 M b 3 TGACCA L004 R1.fastq.gz	0:149.51 1:149.51	A:2091284668;C:1702731096;G:1731364829;T:2102370951;N:733858	149	149	2091284668	1702731096	1731364829	2102370951	733858	SRX5362099	SRS4352686	SRA848347	Shanghai Ocean University\|Developmental Biology	Shanghai Ocean University	2	0.92762	0.9327	0.12346	0.1232	0.70914	0.72308	0.40633	0.39971	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-03-11	Adult	Adult	Brain	Nervous System
51143	51143	SRR8560011	SRX5361510	SRS4352098	SRP185448	PRJNA521037	Danio rerio Raw sequence reads	PRJNA521037	Other	These samples were obtained from the brain tissues of Zebrafish.	Model organism or animal sample from zebrafish transcriptome	Zebrafish Brain Female 3	breed:WUHAN Zebrafish\|age:6 month\|sex:female\|tissue:Brain\|BioSampleModel:Model organism or animal	L8 M b 2	S514 03B CHG022895	S514 03B CHG022895	Total RNA	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	HiSeq X Ten	SRP185448	reverse_paired_S514_03B_CHG022895-L8-M-b-2-TTAGGC_L004_R2.fastq.gz forward_paired_S514_03B_CHG022895-L8-M-b-2-TTAGGC_L004_R1.fastq.gz	fastq fastq	7336543582.0	24532541.0	forward paired S514 03B CHG022895 L8 M b 2 TTAGGC L004 R1.fastq.gz	0:149.53 1:149.53	A:2051683174;C:1600158179;G:1625061539;T:2058934658;N:706032	149	149	2051683174	1600158179	1625061539	2058934658	706032	SRX5361510	SRS4352098	SRA848345	Shanghai Ocean University\|Developmental Biology	Shanghai Ocean University	2	0.91391	0.91599	0.16011	0.16199	0.70502	0.72301	0.51597	0.51246	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-02-11	Adult	Adult	Brain	Nervous System
51144	51144	SRR8559986	SRX5361485	SRS4352015	SRP185448	PRJNA521037	Danio rerio Raw sequence reads	PRJNA521037	Other	These samples were obtained from the brain tissues of Zebrafish.	Model organism or animal sample from zebrafish transcriptome	Zebrafish Brain Female 1	breed:WUHAN Zebrafish\|age:6 month\|sex:female\|tissue:Brain\|BioSampleModel:Model organism or animal	L8 M b 1	S514 03B CHG022895	S514 03B CHG022895	Total RNA	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	HiSeq X Ten	SRP185448	reverse_paired_S514_03B_CHG022895-L8-M-b-1-CGATGT_L004_R2.fastq.gz forward_paired_S514_03B_CHG022895-L8-M-b-1-CGATGT_L004_R1.fastq.gz	fastq fastq	8240697150.0	27526762.0	forward paired S514 03B CHG022895 L8 M b 1 CGATGT L004 R1.fastq.gz	0:149.69 1:149.69	A:2319163482;C:1782124375;G:1804779286;T:2333828773;N:801234	149	149	2319163482	1782124375	1804779286	2333828773	801234	SRX5361485	SRS4352015	SRA848339	Shanghai Ocean University\|Developmental Biology	Shanghai Ocean University	2	0.91542	0.91676	0.16201	0.16315	0.7025	0.71472	0.49212	0.53014	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-02-11	Adult	Adult	Brain	Nervous System
51145	51145	SRR8559050	SRX5360563	SRS4351135	SRP185448	PRJNA521037	Danio rerio Raw sequence reads	PRJNA521037	Other	These samples were obtained from the brain tissues of Zebrafish.	Model organism or animal sample from zebrafish transcriptome	Zebrafish Brain Male 3	breed:WUHAN Zebrafish\|age:6 month\|sex:male\|tissue:Brain\|BioSampleModel:Model organism or animal	L5 F b 2	S514 03A CHG022892	S514 03A CHG022892	Total RNA	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	HiSeq X Ten	SRP185448	forward_paired_S514_03A_CHG022892-L5-F-b-2-GATCAG_L008_R1.fastq.gz reverse_paired_S514_03A_CHG022892-L5-F-b-2-GATCAG_L008_R2.fastq.gz	fastq fastq	9641784182.0	32223361.0	forward paired S514 03A CHG022892 L5 F b 2 GATCAG L008 R1.fastq.gz	0:149.61 1:149.61	A:2692586270;C:2100635383;G:2134009452;T:2713885084;N:667993	149	149	2692586270	2100635383	2134009452	2713885084	667993	SRX5360563	SRS4351135	SRA848314	Shanghai Ocean University\|Developmental Biology	Shanghai Ocean University	2	0.90518	0.90831	0.14842	0.14748	0.69976	0.70824	0.51783	0.52198	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-03-11	Adult	Adult	Brain	Nervous System
51146	51146	SRR8558589	SRX5360216	SRS4350804	SRP185448	PRJNA521037	Danio rerio Raw sequence reads	PRJNA521037	Other	These samples were obtained from the brain tissues of Zebrafish.	Model organism or animal sample from zebrafish transcriptome	Zebrafish Brain Male 2	breed:WUHAN Zebrafish\|age:6 month\|sex:male\|tissue:Brain\|BioSampleModel:Model organism or animal	L1 F b 3	S514 03A CHG022888	S514 03A CHG022888	Total RNA	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	HiSeq X Ten	SRP185448	reverse_paired_S514_03A_CHG022888-L1-F-b-3-TAGCTT_L004_R2.fastq.gz forward_paired_S514_03A_CHG022888-L1-F-b-3-TAGCTT_L004_R1.fastq.gz	fastq fastq	11155488410.0	37300230.0	forward paired S514 03A CHG022888 L1 F b 3 TAGCTT L004 R1.fastq.gz	0:149.54 1:149.54	A:3115393522;C:2430838355;G:2464586732;T:3143761507;N:908294	149	149	3115393522	2430838355	2464586732	3143761507	908294	SRX5360216	SRS4350804	SRA848281	Shanghai Ocean University\|Developmental Biology	Shanghai Ocean University	2	0.91537	0.91755	0.1702	0.16846	0.70421	0.71104	0.49272	0.49841	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-02-11	Adult	Adult	Brain	Nervous System
51147	51147	SRR8556702	SRX5358431	SRS4349238	SRP185448	PRJNA521037	Danio rerio Raw sequence reads	PRJNA521037	Other	These samples were obtained from the brain tissues of Zebrafish.	Model organism or animal sample from zebrafish transcriptome	Zebrafish Brain Male 1	breed:WUHAN Zebrafish\|age:6 month\|sex:male\|tissue:Brain\|BioSampleModel:Model organism or animal	L1 F b 1	S514 03A CHG022888	S514 03A CHG022888	Total RNA	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	HiSeq X Ten	SRP185448	forward_paired_S514_03A_CHG022888-L1-F-b-1-ACTTGA_L004_R1.fastq.gz reverse_paired_S514_03A_CHG022888-L1-F-b-1-ACTTGA_L004_R2.fastq.gz	fastq fastq	10399806328.0	34872944.0	forward paired S514 03A CHG022888 L1 F b 1 ACTTGA L004 R1.fastq.gz	0:149.11 1:149.11	A:2940878200;C:2248395647;G:2269209495;T:2940413594;N:909392	149	149	2940878200	2248395647	2269209495	2940413594	909392	SRX5358431	SRS4349238	SRA848115	Shanghai Ocean University\|Developmental Biology	Shanghai Ocean University	2	0.87255	0.87878	0.1256	0.12457	0.72756	0.73182	0.52994	0.53177	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-02-11	Adult	Adult	Brain	Nervous System
52344	52344	SRR9182350	SRX5954864	SRS4865355	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain NAC.ACR NV 22	NV 22	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:N acetyl L cysteine – Acrylamide replicate 6\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: NAC ACR treatment adult male brain	NV 22	NV 22	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-22-TTACGTGC-AGACCTTG_S370_R1_001.fastq.gz 2465-NV-22-TTACGTGC-AGACCTTG_S370_R2_001.fastq.gz	fastq fastq	11819786100.0	39399287.0	2465 NV 22 TTACGTGC AGACCTTG S370 R1 001.fastq.gz	0:150 1:150	A:3380503046;C:2495962964;G:2656047304;T:3270872050;N:16400736	150	150	3380503046	2495962964	2656047304	3270872050	16400736	SRX5954864	SRS4865355	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91494	0.91128	0.18909	0.18574	0.71108	0.71137	0.48868	0.499	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52345	52345	SRR9182351	SRX5954863	SRS4865356	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain NAC.ACR NV 21	NV 21	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:N acetyl L cysteine – Acrylamide replicate 5\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: NAC ACR treatment adult male brain	NV 21	NV 21	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-21-CACAGACT-CTGTACCA_S369_R1_001.fastq.gz 2465-NV-21-CACAGACT-CTGTACCA_S369_R2_001.fastq.gz	fastq fastq	10663919700.0	35546399.0	2465 NV 21 CACAGACT CTGTACCA S369 R1 001.fastq.gz	0:150 1:150	A:3044142401;C:2256718117;G:2404580970;T:2943582444;N:14895768	150	150	3044142401	2256718117	2404580970	2943582444	14895768	SRX5954863	SRS4865356	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91165	0.91549	0.18677	0.18546	0.71127	0.71112	0.49855	0.50317	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52346	52346	SRR9182352	SRX5954862	SRS4865354	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain NAC.ACR NV 24	NV 24	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:N acetyl L cysteine – Acrylamide replicate 8\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: NAC ACR treatment adult male brain	NV 24	NV 24	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-24-CACGCAAT-CCTTCCAT_S372_R1_001.fastq.gz 2465-NV-24-CACGCAAT-CCTTCCAT_S372_R2_001.fastq.gz	fastq fastq	13721223900.0	45737413.0	2465 NV 24 CACGCAAT CCTTCCAT S372 R1 001.fastq.gz	0:150 1:150	A:3890225027;C:2875058260;G:3195515732;T:3741344065;N:19080816	150	150	3890225027	2875058260	3195515732	3741344065	19080816	SRX5954862	SRS4865354	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.90192	0.90137	0.19497	0.19179	0.7138	0.71141	0.49776	0.4936	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52347	52347	SRR9182353	SRX5954861	SRS4865353	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain NAC.ACR NV 23	NV 23	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:N acetyl L cysteine – Acrylamide replicate 7\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: NAC ACR treatment adult male brain	NV 23	NV 23	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-23-CCAAGGTT-AGGATAGC_S371_R1_001.fastq.gz 2465-NV-23-CCAAGGTT-AGGATAGC_S371_R2_001.fastq.gz	fastq fastq	14683576200.0	48945254.0	2465 NV 23 CCAAGGTT AGGATAGC S371 R1 001.fastq.gz	0:150 1:150	A:4153451869;C:3142795551;G:3335897512;T:4030892485;N:20538783	150	150	4153451869	3142795551	3335897512	4030892485	20538783	SRX5954861	SRS4865353	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91115	0.91565	0.18214	0.18219	0.70804	0.70676	0.49259	0.50002	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52348	52348	SRR9182354	SRX5954860	SRS4865352	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain NAC.ACR NV 19	NV 19	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:N acetyl L cysteine – Acrylamide replicate 3\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: NAC ACR treatment adult male brain	NV 19	NV 19	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-19-GTCCTTGA-TCGTCTGA_S367_R1_001.fastq.gz 2465-NV-19-GTCCTTGA-TCGTCTGA_S367_R2_001.fastq.gz	fastq fastq	10887194400.0	36290648.0	2465 NV 19 GTCCTTGA TCGTCTGA S367 R1 001.fastq.gz	0:150 1:150	A:3100889552;C:2293240625;G:2475143574;T:3002632683;N:15287966	150	150	3100889552	2293240625	2475143574	3002632683	15287966	SRX5954860	SRS4865352	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91599	0.91172	0.19536	0.19246	0.70806	0.70798	0.50256	0.50214	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52349	52349	SRR9182355	SRX5954859	SRS4865351	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain NAC.ACR NV 20	NV 20	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:N acetyl L cysteine – Acrylamide replicate 4\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: NAC ACR treatment adult male brain	NV 20	NV 20	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-20-TGCGTAAC-AGCCTATC_S368_R1_001.fastq.gz 2465-NV-20-TGCGTAAC-AGCCTATC_S368_R2_001.fastq.gz	fastq fastq	8599848000.0	28666160.0	2465 NV 20 TGCGTAAC AGCCTATC S368 R1 001.fastq.gz	0:150 1:150	A:2459848462;C:1811876909;G:1935013502;T:2381063714;N:12045413	150	150	2459848462	1811876909	1935013502	2381063714	12045413	SRX5954859	SRS4865351	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.90829	0.91168	0.1888	0.18778	0.71052	0.70974	0.50265	0.50128	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52350	52350	SRR9182356	SRX5954858	SRS4865350	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain ACR NV 15	NV 15	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Acrylamide replicate 7\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: ACR treatment adult male brain	NV 15	NV 15	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-15-CTGTACCA-CACAGACT_S363_R1_001.fastq.gz 2465-NV-15-CTGTACCA-CACAGACT_S363_R2_001.fastq.gz	fastq fastq	12883881000.0	42946270.0	2465 NV 15 CTGTACCA CACAGACT S363 R1 001.fastq.gz	0:150 1:150	A:3671918368;C:2718517333;G:2919934921;T:3555514010;N:17996368	150	150	3671918368	2718517333	2919934921	3555514010	17996368	SRX5954858	SRS4865350	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.90841	0.90853	0.19392	0.19141	0.70587	0.70654	0.49326	0.49205	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52351	52351	SRR9182357	SRX5954857	SRS4865349	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain ACR NV 16	NV 16	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Acrylamide replicate 8\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: ACR treatment adult male brain	NV 16	NV 16	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-16-AGACCTTG-TTACGTGC_S364_R1_001.fastq.gz 2465-NV-16-AGACCTTG-TTACGTGC_S364_R2_001.fastq.gz	fastq fastq	9547257000.0	31824190.0	2465 NV 16 AGACCTTG TTACGTGC S364 R1 001.fastq.gz	0:150 1:150	A:2727492613;C:2021687582;G:2149525733;T:2635174423;N:13376649	150	150	2727492613	2021687582	2149525733	2635174423	13376649	SRX5954857	SRS4865349	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91935	0.91466	0.19454	0.19179	0.70692	0.70749	0.49886	0.5096	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52352	52352	SRR9182358	SRX5954856	SRS4865348	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain NAC.ACR NV 17	NV 17	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:N acetyl L cysteine – Acrylamide replicate 1\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: NAC ACR treatment adult male brain	NV 17	NV 17	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-17-AGGATAGC-CCAAGGTT_S365_R1_001.fastq.gz 2465-NV-17-AGGATAGC-CCAAGGTT_S365_R2_001.fastq.gz	fastq fastq	10214864100.0	34049547.0	2465 NV 17 AGGATAGC CCAAGGTT S365 R1 001.fastq.gz	0:150 1:150	A:2930759198;C:2153599072;G:2292844182;T:2823524324;N:14137324	150	150	2930759198	2153599072	2292844182	2823524324	14137324	SRX5954856	SRS4865348	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.90601	0.9096	0.1939	0.19302	0.71153	0.71058	0.4986	0.49859	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52353	52353	SRR9182359	SRX5954855	SRS4865346	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain NAC.ACR NV 18	NV 18	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:N acetyl L cysteine – Acrylamide replicate 2\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: NAC ACR treatment adult male brain	NV 18	NV 18	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-18-CCTTCCAT-CACGCAAT_S366_R1_001.fastq.gz 2465-NV-18-CCTTCCAT-CACGCAAT_S366_R2_001.fastq.gz	fastq fastq	11525333100.0	38417777.0	2465 NV 18 CCTTCCAT CACGCAAT S366 R1 001.fastq.gz	0:150 1:150	A:3270678875;C:2451086000;G:2608740654;T:3178621310;N:16206261	150	150	3270678875	2451086000	2608740654	3178621310	16206261	SRX5954855	SRS4865346	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.90965	0.91093	0.19965	0.19785	0.70707	0.70751	0.50506	0.50301	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52354	52354	SRR9182360	SRX5954854	SRS4865347	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain ACR NV 11	NV 11	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Acrylamide replicate 3\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: ACR treatment adult male brain	NV 11	NV 11	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-11-GTACACCT-TCCTCATG_S359_R1_001.fastq.gz 2465-NV-11-GTACACCT-TCCTCATG_S359_R2_001.fastq.gz	fastq fastq	9189461700.0	30631539.0	2465 NV 11 GTACACCT TCCTCATG S359 R1 001.fastq.gz	0:150 1:150	A:2648852788;C:1939379177;G:1999011312;T:2589230521;N:12987902	150	150	2648852788	1939379177	1999011312	2589230521	12987902	SRX5954854	SRS4865347	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91673	0.91678	0.19869	0.19589	0.71279	0.71108	0.48443	0.48705	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52355	52355	SRR9182361	SRX5954853	SRS4865345	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain ACR NV 12	NV 12	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Acrylamide replicate 4\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: ACR treatment adult male brain	NV 12	NV 12	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-12-CGGCATTA-GTCAGTCA_S360_R1_001.fastq.gz 2465-NV-12-CGGCATTA-GTCAGTCA_S360_R2_001.fastq.gz	fastq fastq	9866562000.0	32888540.0	2465 NV 12 CGGCATTA GTCAGTCA S360 R1 001.fastq.gz	0:150 1:150	A:2801381823;C:2096538504;G:2245280379;T:2709477444;N:13883850	150	150	2801381823	2096538504	2245280379	2709477444	13883850	SRX5954853	SRS4865345	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91095	0.91237	0.19276	0.1915	0.71212	0.71147	0.49114	0.49659	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52356	52356	SRR9182362	SRX5954852	SRS4865343	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain ACR NV 13	NV 13	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Acrylamide replicate 5\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: ACR treatment adult male brain	NV 13	NV 13	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-13-TCGTCTGA-GTCCTTGA_S361_R1_001.fastq.gz 2465-NV-13-TCGTCTGA-GTCCTTGA_S361_R2_001.fastq.gz	fastq fastq	10306052700.0	34353509.0	2465 NV 13 TCGTCTGA GTCCTTGA S361 R1 001.fastq.gz	0:150 1:150	A:2914600925;C:2190104547;G:2374390393;T:2812694857;N:14261978	150	150	2914600925	2190104547	2374390393	2812694857	14261978	SRX5954852	SRS4865343	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.90694	0.90932	0.18903	0.18749	0.70968	0.70891	0.49997	0.50056	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52357	52357	SRR9182363	SRX5954851	SRS4865344	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain ACR NV 14	NV 14	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Acrylamide replicate 6\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: ACR treatment adult male brain	NV 14	NV 14	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-14-AGCCTATC-TGCGTAAC_S362_R1_001.fastq.gz 2465-NV-14-AGCCTATC-TGCGTAAC_S362_R2_001.fastq.gz	fastq fastq	10331273100.0	34437577.0	2465 NV 14 AGCCTATC TGCGTAAC S362 R1 001.fastq.gz	0:150 1:150	A:2924091961;C:2225839714;G:2343478200;T:2823411001;N:14452224	150	150	2924091961	2225839714	2343478200	2823411001	14452224	SRX5954851	SRS4865344	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91523	0.91836	0.18722	0.18606	0.70926	0.70989	0.4901	0.49001	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52358	52358	SRR9182364	SRX5954850	SRS4865342	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain ACR NV 9	NV 9	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Acrylamide replicate 1\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: ACR treatment adult male brain	NV 9	NV 9	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-9-CGCAACTA-TCGGATTC_S357_R1_001.fastq.gz 2465-NV-9-CGCAACTA-TCGGATTC_S357_R2_001.fastq.gz	fastq fastq	11301892800.0	37672976.0	2465 NV 9 CGCAACTA TCGGATTC S357 R1 001.fastq.gz	0:150 1:150	A:3243365605;C:2381322574;G:2546823051;T:3114598680;N:15782890	150	150	3243365605	2381322574	2546823051	3114598680	15782890	SRX5954850	SRS4865342	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.90022	0.90704	0.20495	0.20403	0.71577	0.71528	0.49285	0.5029	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52359	52359	SRR9182365	SRX5954849	SRS4865341	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain ACR NV 10	NV 10	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Acrylamide replicate 2\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: ACR treatment adult male brain	NV 10	NV 10	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-10-CGTATCTC-CAAGGTAC_S358_R1_001.fastq.gz 2465-NV-10-CGTATCTC-CAAGGTAC_S358_R2_001.fastq.gz	fastq fastq	8971546500.0	29905155.0	2465 NV 10 CGTATCTC CAAGGTAC S358 R1 001.fastq.gz	0:150 1:150	A:2536960465;C:1929843661;G:2029563929;T:2462734724;N:12443721	150	150	2536960465	1929843661	2029563929	2462734724	12443721	SRX5954849	SRS4865341	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91207	0.91692	0.1843	0.1845	0.71187	0.71185	0.49886	0.49928	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52360	52360	SRR9182366	SRX5954848	SRS4865340	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain Control NV 1	NV 1	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Control replicate 1\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: control adult male brain	NV 1	NV 1	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-1-TTACCGAC-CGAATACG_S349_R1_001.fastq.gz 2465-NV-1-TTACCGAC-CGAATACG_S349_R2_001.fastq.gz	fastq fastq	10273535700.0	34245119.0	2465 NV 1 TTACCGAC CGAATACG S349 R1 001.fastq.gz	0:150 1:150	A:2928554067;C:2159492430;G:2335266656;T:2835786931;N:14435616	150	150	2928554067	2159492430	2335266656	2835786931	14435616	SRX5954848	SRS4865340	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.9087	0.90313	0.19787	0.19441	0.71756	0.71709	0.51109	0.50869	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52361	52361	SRR9182367	SRX5954847	SRS4865339	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain Control NV 2	NV 2	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Control replicate 2\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: control adult male brain	NV 2	NV 2	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-2-AGTGACCT-TCTAGGAG_S350_R1_001.fastq.gz 2465-NV-2-AGTGACCT-TCTAGGAG_S350_R2_001.fastq.gz	fastq fastq	11207097900.0	37356993.0	2465 NV 2 AGTGACCT TCTAGGAG S350 R1 001.fastq.gz	0:150 1:150	A:3148284817;C:2423396873;G:2587025230;T:3032822731;N:15568249	150	150	3148284817	2423396873	2587025230	3032822731	15568249	SRX5954847	SRS4865339	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91551	0.91538	0.17481	0.17281	0.70556	0.70487	0.48335	0.48786	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52362	52362	SRR9182368	SRX5954846	SRS4865338	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain Control NV 3	NV 3	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Control replicate 3\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: control adult male brain	NV 3	NV 3	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-3-TCGGATTC-CGCAACTA_S351_R1_001.fastq.gz 2465-NV-3-TCGGATTC-CGCAACTA_S351_R2_001.fastq.gz	fastq fastq	12058574400.0	40195248.0	2465 NV 3 TCGGATTC CGCAACTA S351 R1 001.fastq.gz	0:150 1:150	A:3459397409;C:2538226914;G:2686587266;T:3357533701;N:16829110	150	150	3459397409	2538226914	2686587266	3357533701	16829110	SRX5954846	SRS4865338	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91597	0.90969	0.20272	0.19926	0.71683	0.71705	0.50712	0.51001	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52363	52363	SRR9182369	SRX5954845	SRS4865337	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain Control NV 4	NV 4	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Control replicate 4\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: control adult male brain	NV 4	NV 4	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-4-CAAGGTAC-CGTATCTC_S352_R1_001.fastq.gz 2465-NV-4-CAAGGTAC-CGTATCTC_S352_R2_001.fastq.gz	fastq fastq	9553550700.0	31845169.0	2465 NV 4 CAAGGTAC CGTATCTC S352 R1 001.fastq.gz	0:150 1:150	A:2651658029;C:2055962954;G:2305916565;T:2526800154;N:13212998	150	150	2651658029	2055962954	2305916565	2526800154	13212998	SRX5954845	SRS4865337	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.90798	0.91396	0.17694	0.17825	0.71033	0.70922	0.50819	0.50573	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52364	52364	SRR9182370	SRX5954844	SRS4865336	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain Control NV 5	NV 5	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Control replicate 5\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: control adult male brain	NV 5	NV 5	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-5-TCCTCATG-GTACACCT_S353_R1_001.fastq.gz 2465-NV-5-TCCTCATG-GTACACCT_S353_R2_001.fastq.gz	fastq fastq	11521424700.0	38404749.0	2465 NV 5 TCCTCATG GTACACCT S353 R1 001.fastq.gz	0:150 1:150	A:3258562339;C:2467727220;G:2627261408;T:3152030777;N:15842956	150	150	3258562339	2467727220	2627261408	3152030777	15842956	SRX5954844	SRS4865336	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91092	0.91441	0.18002	0.17856	0.70881	0.70903	0.4941	0.48795	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52365	52365	SRR9182371	SRX5954843	SRS4865335	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain Control NV 6	NV 6	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Control replicate 6\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: control adult male brain	NV 6	NV 6	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-6-GTCAGTCA-CGGCATTA_S354_R1_001.fastq.gz 2465-NV-6-GTCAGTCA-CGGCATTA_S354_R2_001.fastq.gz	fastq fastq	9803104500.0	32677015.0	2465 NV 6 GTCAGTCA CGGCATTA S354 R1 001.fastq.gz	0:150 1:150	A:2779645686;C:2103402652;G:2218294150;T:2688098948;N:13663064	150	150	2779645686	2103402652	2218294150	2688098948	13663064	SRX5954843	SRS4865335	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.9114	0.91625	0.1819	0.18102	0.70611	0.70644	0.48862	0.48985	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52366	52366	SRR9182372	SRX5954842	SRS4865334	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain Control NV 7	NV 7	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Control replicate 7\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: control adult male brain	NV 7	NV 7	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-7-CGAATACG-TTACCGAC_S355_R1_001.fastq.gz 2465-NV-7-CGAATACG-TTACCGAC_S355_R2_001.fastq.gz	fastq fastq	9872477100.0	32908257.0	2465 NV 7 CGAATACG TTACCGAC S355 R1 001.fastq.gz	0:150 1:150	A:2786558009;C:2110864680;G:2279325984;T:2682111265;N:13617162	150	150	2786558009	2110864680	2279325984	2682111265	13617162	SRX5954842	SRS4865334	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.90855	0.91239	0.1835	0.18248	0.7125	0.7108	0.49696	0.49654	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System
52367	52367	SRR9182373	SRX5954841	SRS4865333	SRP200180	PRJNA545942	Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain	PRJNA545942	Other	Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical transcriptomic proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis to MALDI TOF mass spectrometry for proteome analysis and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules thioredoxin related proteins transmembrane transport redox metabolism and catalytic activity as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects like the dysregulation of genes related to microtubules presynaptic vesicle alteration and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity connecting the different toxic effects across different levels of organization from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.	ZF Brain Control NV 8	NV 8	strain:WT\|dev stage:Adult\|sex:male\|tissue:Brain\|treatment:Control replicate 8\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: control adult male brain	NV 8	NV 8	Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University Nashville TN for library preparation and sequencing on the Illumina Novaseq platform	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP200180	2465-NV-8-TCTAGGAG-AGTGACCT_S356_R1_001.fastq.gz 2465-NV-8-TCTAGGAG-AGTGACCT_S356_R2_001.fastq.gz	fastq fastq	8271516900.0	27571723.0	2465 NV 8 TCTAGGAG AGTGACCT S356 R1 001.fastq.gz	0:150 1:150	A:2342223288;C:1770487584;G:1884385861;T:2263052869;N:11367298	150	150	2342223288	1770487584	1884385861	2263052869	11367298	SRX5954841	SRS4865333	SRA893242	Mississippi State University\|Institute for Genomics, Biocomputing & Biotechnolo	Mississippi State University	2	0.91345	0.91392	0.17601	0.17437	0.70985	0.70962	0.49294	0.49772	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-06-03	Adult	Adult	Brain	Nervous System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;