metadata: run_metadata: 75 rows where experiment.library_strategy = "ssRNA-seq", experiment.platform = "ILLUMINA" and technology = "unknown"

75 rows where experiment.library_strategy = "ssRNA-seq", experiment.platform = "ILLUMINA" and technology = "unknown"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
9343	9343	ERR2935792	ERX2938586	ERS2922622	ERP112367	PRJEB30004	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E-MTAB-7464	Transcriptome Analysis	Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Cnt mRNA ML 4	SAMEA5138255	Izmir Biomedicine and Genome Center / Turkey	ENA FIRST PUBLIC:2020 11 28T04:04:08Z\|ENA LAST UPDATE:2018 11 28T11:38:53Z\|External Id:SAMEA5138255\|INSDC center name:Izmir Biomedicine and Genome Center / Turkey\|INSDC first public:2020 11 28T04:04:08Z\|INSDC last update:2018 11 28T11:38:53Z\|INSDC status:public\|Submitter Id:E MTAB 7464:Cnt mRNA ML 4\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:Chemical ablation\|organism part:caudal fin\|sample name:E MTAB 7464:Cnt mRNA ML 4\|scientific name:Danio rerio\|sex:male\|strain:AB	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E MTAB 7464:Cnt mRNA ML 4 p	Cnt mRNA ML 4 p	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Experimental Factor: compound:neocuproine\|Experimental Factor: dose:1\|Experimental Factor: injury:chemical ablation\|Experimental Factor: time:0\|Experimental Factor: organism part:caudal fin	ssRNA-seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP112367	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Cnt-mRNA-ML-4_2.fastq.gz Cnt-mRNA-ML-4_1.fastq.gz	fastq fastq	12134105440.0	75838159.0	E MTAB 7464:Cnt mRNA ML 4	0:80 1:80	A:3262023701;C:2677095735;G:2964643096;T:3227367048;N:2975860	80	80	3262023701	2677095735	2964643096	3227367048	2975860	ERX2938586	ERS2922622	ERA1667271	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	2	0.91144	0.90945	0.31692	0.30691	0.75203	0.75722	0.51882	0.5197	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	other	trueseq	bulk	unknown	unknown	Turkey	2018-11-28	Adult	Adult	Multi-tissue	Multi-system
9344	9344	ERR2935791	ERX2938585	ERS2922621	ERP112367	PRJEB30004	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E-MTAB-7464	Transcriptome Analysis	Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Cnt mRNA ML 3	SAMEA5138254	Izmir Biomedicine and Genome Center / Turkey	ENA FIRST PUBLIC:2020 11 28T04:04:08Z\|ENA LAST UPDATE:2018 11 28T11:38:53Z\|External Id:SAMEA5138254\|INSDC center name:Izmir Biomedicine and Genome Center / Turkey\|INSDC first public:2020 11 28T04:04:08Z\|INSDC last update:2018 11 28T11:38:53Z\|INSDC status:public\|Submitter Id:E MTAB 7464:Cnt mRNA ML 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:Chemical ablation\|organism part:caudal fin\|sample name:E MTAB 7464:Cnt mRNA ML 3\|scientific name:Danio rerio\|sex:male\|strain:AB	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E MTAB 7464:Cnt mRNA ML 3 p	Cnt mRNA ML 3 p	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Experimental Factor: compound:neocuproine\|Experimental Factor: dose:1\|Experimental Factor: injury:chemical ablation\|Experimental Factor: time:0\|Experimental Factor: organism part:caudal fin	ssRNA-seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP112367	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Cnt-mRNA-ML-3_1.fastq.gz Cnt-mRNA-ML-3_2.fastq.gz	fastq fastq	10198941920.0	63743387.0	E MTAB 7464:Cnt mRNA ML 3	0:80 1:80	A:2707258482;C:2295053882;G:2521099885;T:2673029444;N:2500227	80	80	2707258482	2295053882	2521099885	2673029444	2500227	ERX2938585	ERS2922621	ERA1667271	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	2	0.88029	0.87951	0.30611	0.30513	0.76189	0.7685	0.52656	0.52076	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	other	trueseq	bulk	unknown	unknown	Turkey	2018-11-28	Adult	Adult	Multi-tissue	Multi-system
9345	9345	ERR2935790	ERX2938584	ERS2922620	ERP112367	PRJEB30004	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E-MTAB-7464	Transcriptome Analysis	Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Cnt mRNA ML 2	SAMEA5138253	Izmir Biomedicine and Genome Center / Turkey	ENA FIRST PUBLIC:2020 11 28T04:04:08Z\|ENA LAST UPDATE:2018 11 28T11:38:53Z\|External Id:SAMEA5138253\|INSDC center name:Izmir Biomedicine and Genome Center / Turkey\|INSDC first public:2020 11 28T04:04:08Z\|INSDC last update:2018 11 28T11:38:53Z\|INSDC status:public\|Submitter Id:E MTAB 7464:Cnt mRNA ML 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:Chemical ablation\|organism part:caudal fin\|sample name:E MTAB 7464:Cnt mRNA ML 2\|scientific name:Danio rerio\|sex:female\|strain:AB	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E MTAB 7464:Cnt mRNA ML 2 p	Cnt mRNA ML 2 p	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Experimental Factor: compound:neocuproine\|Experimental Factor: dose:1\|Experimental Factor: injury:chemical ablation\|Experimental Factor: time:0\|Experimental Factor: organism part:caudal fin	ssRNA-seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP112367	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Cnt-mRNA-ML-2_1.fastq.gz Cnt-mRNA-ML-2_2.fastq.gz	fastq fastq	13001272960.0	81257956.0	E MTAB 7464:Cnt mRNA ML 2	0:80 1:80	A:3429977204;C:2902807573;G:3288394622;T:3376870832;N:3222729	80	80	3429977204	2902807573	3288394622	3376870832	3222729	ERX2938584	ERS2922620	ERA1667271	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	2	0.89439	0.89378	0.3049	0.30551	0.75771	0.76761	0.52718	0.52248	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	other	trueseq	bulk	unknown	unknown	Turkey	2018-11-28	Adult	Adult	Multi-tissue	Multi-system
9346	9346	ERR2935789	ERX2938583	ERS2922619	ERP112367	PRJEB30004	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E-MTAB-7464	Transcriptome Analysis	Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Cnt mRNA ML 1	SAMEA5138252	Izmir Biomedicine and Genome Center / Turkey	ENA FIRST PUBLIC:2020 11 28T04:04:08Z\|ENA LAST UPDATE:2018 11 28T11:38:53Z\|External Id:SAMEA5138252\|INSDC center name:Izmir Biomedicine and Genome Center / Turkey\|INSDC first public:2020 11 28T04:04:08Z\|INSDC last update:2018 11 28T11:38:53Z\|INSDC status:public\|Submitter Id:E MTAB 7464:Cnt mRNA ML 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:Chemical ablation\|organism part:caudal fin\|sample name:E MTAB 7464:Cnt mRNA ML 1\|scientific name:Danio rerio\|sex:female\|strain:AB	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E MTAB 7464:Cnt mRNA ML 1 p	Cnt mRNA ML 1 p	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Experimental Factor: compound:neocuproine\|Experimental Factor: dose:1\|Experimental Factor: injury:chemical ablation\|Experimental Factor: time:0\|Experimental Factor: organism part:caudal fin	ssRNA-seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP112367	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Cnt-mRNA-ML-1_2.fastq.gz Cnt-mRNA-ML-1_1.fastq.gz	fastq fastq	10689399040.0	66808744.0	E MTAB 7464:Cnt mRNA ML 1	0:80 1:80	A:2897858681;C:2320332197;G:2613694217;T:2854881563;N:2632382	80	80	2897858681	2320332197	2613694217	2854881563	2632382	ERX2938583	ERS2922619	ERA1667271	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	2	0.87118	0.87075	0.30823	0.30776	0.74673	0.75692	0.49822	0.50666	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	other	trueseq	bulk	unknown	unknown	Turkey	2018-11-28	Adult	Adult	Multi-tissue	Multi-system
9347	9347	ERR2935788	ERX2938582	ERS2922618	ERP112367	PRJEB30004	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E-MTAB-7464	Transcriptome Analysis	Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	7dpa mRNA ML 4	SAMEA5138251	Izmir Biomedicine and Genome Center / Turkey	ENA FIRST PUBLIC:2020 11 28T04:04:08Z\|ENA LAST UPDATE:2018 11 28T11:38:53Z\|External Id:SAMEA5138251\|INSDC center name:Izmir Biomedicine and Genome Center / Turkey\|INSDC first public:2020 11 28T04:04:08Z\|INSDC last update:2018 11 28T11:38:53Z\|INSDC status:public\|Submitter Id:E MTAB 7464:7dpa mRNA ML 4\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:Chemical ablation\|organism part:caudal fin\|sample name:E MTAB 7464:7dpa mRNA ML 4\|scientific name:Danio rerio\|sex:male\|strain:AB	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E MTAB 7464:7dpa mRNA ML 4 p	7dpa mRNA ML 4 p	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Experimental Factor: compound:neocuproine\|Experimental Factor: dose:1\|Experimental Factor: injury:chemical ablation\|Experimental Factor: time:7\|Experimental Factor: organism part:caudal fin	ssRNA-seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP112367	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	7dpa-mRNA-ML-4_1.fastq.gz 7dpa-mRNA-ML-4_2.fastq.gz	fastq fastq	11636085120.0	72725532.0	E MTAB 7464:7dpa mRNA ML 4	0:80 1:80	A:3154141550;C:2591688923;G:2792349992;T:3095216690;N:2687965	80	80	3154141550	2591688923	2792349992	3095216690	2687965	ERX2938582	ERS2922618	ERA1667271	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	2	0.8808	0.88291	0.28917	0.2893	0.73377	0.74097	0.50493	0.4989	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	other	trueseq	bulk	unknown	unknown	Turkey	2018-11-28	Adult	Adult	Multi-tissue	Multi-system
9348	9348	ERR2935787	ERX2938581	ERS2922617	ERP112367	PRJEB30004	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E-MTAB-7464	Transcriptome Analysis	Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	7dpa mRNA ML 3	SAMEA5138250	Izmir Biomedicine and Genome Center / Turkey	ENA FIRST PUBLIC:2020 11 28T04:04:08Z\|ENA LAST UPDATE:2018 11 28T11:38:53Z\|External Id:SAMEA5138250\|INSDC center name:Izmir Biomedicine and Genome Center / Turkey\|INSDC first public:2020 11 28T04:04:08Z\|INSDC last update:2018 11 28T11:38:53Z\|INSDC status:public\|Submitter Id:E MTAB 7464:7dpa mRNA ML 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:Chemical ablation\|organism part:caudal fin\|sample name:E MTAB 7464:7dpa mRNA ML 3\|scientific name:Danio rerio\|sex:male\|strain:AB	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E MTAB 7464:7dpa mRNA ML 3 p	7dpa mRNA ML 3 p	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Experimental Factor: compound:neocuproine\|Experimental Factor: dose:1\|Experimental Factor: injury:chemical ablation\|Experimental Factor: time:7\|Experimental Factor: organism part:caudal fin	ssRNA-seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP112367	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	7dpa-mRNA-ML-3_1.fastq.gz 7dpa-mRNA-ML-3_2.fastq.gz	fastq fastq	9873881440.0	61711759.0	E MTAB 7464:7dpa mRNA ML 3	0:80 1:80	A:2682240945;C:2177286149;G:2380282226;T:2631847017;N:2225103	80	80	2682240945	2177286149	2380282226	2631847017	2225103	ERX2938581	ERS2922617	ERA1667271	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	2	0.83715	0.84278	0.34243	0.34676	0.73764	0.75041	0.50878	0.49819	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	other	trueseq	bulk	unknown	unknown	Turkey	2018-11-28	Adult	Adult	Multi-tissue	Multi-system
9349	9349	ERR2935786	ERX2938580	ERS2922616	ERP112367	PRJEB30004	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E-MTAB-7464	Transcriptome Analysis	Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	7dpa mRNA ML 2	SAMEA5138249	Izmir Biomedicine and Genome Center / Turkey	ENA FIRST PUBLIC:2020 11 28T04:04:08Z\|ENA LAST UPDATE:2018 11 28T11:38:53Z\|External Id:SAMEA5138249\|INSDC center name:Izmir Biomedicine and Genome Center / Turkey\|INSDC first public:2020 11 28T04:04:08Z\|INSDC last update:2018 11 28T11:38:53Z\|INSDC status:public\|Submitter Id:E MTAB 7464:7dpa mRNA ML 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:Chemical ablation\|organism part:caudal fin\|sample name:E MTAB 7464:7dpa mRNA ML 2\|scientific name:Danio rerio\|sex:female\|strain:AB	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E MTAB 7464:7dpa mRNA ML 2 p	7dpa mRNA ML 2 p	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Experimental Factor: compound:neocuproine\|Experimental Factor: dose:1\|Experimental Factor: injury:chemical ablation\|Experimental Factor: time:7\|Experimental Factor: organism part:caudal fin	ssRNA-seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP112367	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	7dpa-mRNA-ML-2_2.fastq.gz 7dpa-mRNA-ML-2_1.fastq.gz	fastq fastq	12193073280.0	76206708.0	E MTAB 7464:7dpa mRNA ML 2	0:80 1:80	A:3333326821;C:2692186511;G:2887657057;T:3277111703;N:2791188	80	80	3333326821	2692186511	2887657057	3277111703	2791188	ERX2938580	ERS2922616	ERA1667271	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	2	0.8495	0.851	0.36393	0.36549	0.72466	0.73582	0.50377	0.4964	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	other	trueseq	bulk	unknown	unknown	Turkey	2018-11-28	Adult	Adult	Multi-tissue	Multi-system
9350	9350	ERR2935785	ERX2938579	ERS2922615	ERP112367	PRJEB30004	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E-MTAB-7464	Transcriptome Analysis	Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	7dpa mRNA ML 1	SAMEA5138248	Izmir Biomedicine and Genome Center / Turkey	ENA FIRST PUBLIC:2020 11 28T04:04:08Z\|ENA LAST UPDATE:2018 11 28T11:38:53Z\|External Id:SAMEA5138248\|INSDC center name:Izmir Biomedicine and Genome Center / Turkey\|INSDC first public:2020 11 28T04:04:08Z\|INSDC last update:2018 11 28T11:38:53Z\|INSDC status:public\|Submitter Id:E MTAB 7464:7dpa mRNA ML 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:Chemical ablation\|organism part:caudal fin\|sample name:E MTAB 7464:7dpa mRNA ML 1\|scientific name:Danio rerio\|sex:female\|strain:AB	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E MTAB 7464:7dpa mRNA ML 1 p	7dpa mRNA ML 1 p	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Experimental Factor: compound:neocuproine\|Experimental Factor: dose:1\|Experimental Factor: injury:chemical ablation\|Experimental Factor: time:7\|Experimental Factor: organism part:caudal fin	ssRNA-seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP112367	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	7dpa-mRNA-ML-1_1.fastq.gz 7dpa-mRNA-ML-1_2.fastq.gz	fastq fastq	11533139040.0	72082119.0	E MTAB 7464:7dpa mRNA ML 1	0:80 1:80	A:3069170319;C:2575356466;G:2889466424;T:2996503729;N:2642102	80	80	3069170319	2575356466	2889466424	2996503729	2642102	ERX2938579	ERS2922615	ERA1667271	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	2	0.86529	0.86845	0.33913	0.34252	0.72928	0.74194	0.50425	0.50214	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	other	trueseq	bulk	unknown	unknown	Turkey	2018-11-28	Adult	Adult	Multi-tissue	Multi-system
9351	9351	ERR2935784	ERX2938578	ERS2922614	ERP112367	PRJEB30004	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E-MTAB-7464	Transcriptome Analysis	Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	1dpa mRNA ML 4	SAMEA5138247	Izmir Biomedicine and Genome Center / Turkey	ENA FIRST PUBLIC:2020 11 28T04:04:08Z\|ENA LAST UPDATE:2018 11 28T11:38:53Z\|External Id:SAMEA5138247\|INSDC center name:Izmir Biomedicine and Genome Center / Turkey\|INSDC first public:2020 11 28T04:04:08Z\|INSDC last update:2018 11 28T11:38:53Z\|INSDC status:public\|Submitter Id:E MTAB 7464:1dpa mRNA ML 4\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:Chemical ablation\|organism part:caudal fin\|sample name:E MTAB 7464:1dpa mRNA ML 4\|scientific name:Danio rerio\|sex:male\|strain:AB	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E MTAB 7464:1dpa mRNA ML 4 p	1dpa mRNA ML 4 p	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Experimental Factor: compound:neocuproine\|Experimental Factor: dose:1\|Experimental Factor: injury:chemical ablation\|Experimental Factor: time:1\|Experimental Factor: organism part:caudal fin	ssRNA-seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP112367	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	1dpa-mRNA-ML-4_1.fastq.gz 1dpa-mRNA-ML-4_2.fastq.gz	fastq fastq	13728291840.0	85801824.0	E MTAB 7464:1dpa mRNA ML 4	0:80 1:80	A:3747242594;C:3041779368;G:3248651209;T:3687437813;N:3180856	80	80	3747242594	3041779368	3248651209	3687437813	3180856	ERX2938578	ERS2922614	ERA1667271	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	2	0.90774	0.91111	0.34968	0.34939	0.72809	0.73472	0.50073	0.49547	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	other	trueseq	bulk	unknown	unknown	Turkey	2018-11-28	Adult	Adult	Multi-tissue	Multi-system
9352	9352	ERR2935783	ERX2938577	ERS2922613	ERP112367	PRJEB30004	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E-MTAB-7464	Transcriptome Analysis	Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	1dpa mRNA ML 3	SAMEA5138246	Izmir Biomedicine and Genome Center / Turkey	ENA FIRST PUBLIC:2020 11 28T04:04:08Z\|ENA LAST UPDATE:2018 11 28T11:38:53Z\|External Id:SAMEA5138246\|INSDC center name:Izmir Biomedicine and Genome Center / Turkey\|INSDC first public:2020 11 28T04:04:08Z\|INSDC last update:2018 11 28T11:38:53Z\|INSDC status:public\|Submitter Id:E MTAB 7464:1dpa mRNA ML 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:Chemical ablation\|organism part:caudal fin\|sample name:E MTAB 7464:1dpa mRNA ML 3\|scientific name:Danio rerio\|sex:male\|strain:AB	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E MTAB 7464:1dpa mRNA ML 3 p	1dpa mRNA ML 3 p	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Experimental Factor: compound:neocuproine\|Experimental Factor: dose:1\|Experimental Factor: injury:chemical ablation\|Experimental Factor: time:1\|Experimental Factor: organism part:caudal fin	ssRNA-seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP112367	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	1dpa-mRNA-ML-3_2.fastq.gz 1dpa-mRNA-ML-3_1.fastq.gz	fastq fastq	12524780320.0	78279877.0	E MTAB 7464:1dpa mRNA ML 3	0:80 1:80	A:3452368285;C:2754592593;G:2905324477;T:3409605329;N:2889636	80	80	3452368285	2754592593	2905324477	3409605329	2889636	ERX2938577	ERS2922613	ERA1667271	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	2	0.90778	0.91013	0.32736	0.3259	0.73724	0.74251	0.51117	0.51031	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	other	trueseq	bulk	unknown	unknown	Turkey	2018-11-28	Adult	Adult	Multi-tissue	Multi-system
9353	9353	ERR2935782	ERX2938576	ERS2922612	ERP112367	PRJEB30004	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E-MTAB-7464	Transcriptome Analysis	Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	1dpa mRNA ML 2	SAMEA5138245	Izmir Biomedicine and Genome Center / Turkey	ENA FIRST PUBLIC:2020 11 28T04:04:08Z\|ENA LAST UPDATE:2018 11 28T11:38:53Z\|External Id:SAMEA5138245\|INSDC center name:Izmir Biomedicine and Genome Center / Turkey\|INSDC first public:2020 11 28T04:04:08Z\|INSDC last update:2018 11 28T11:38:53Z\|INSDC status:public\|Submitter Id:E MTAB 7464:1dpa mRNA ML 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:Chemical ablation\|organism part:caudal fin\|sample name:E MTAB 7464:1dpa mRNA ML 2\|scientific name:Danio rerio\|sex:female\|strain:AB	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E MTAB 7464:1dpa mRNA ML 2 p	1dpa mRNA ML 2 p	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Experimental Factor: compound:neocuproine\|Experimental Factor: dose:1\|Experimental Factor: injury:chemical ablation\|Experimental Factor: time:1\|Experimental Factor: organism part:caudal fin	ssRNA-seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP112367	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	1dpa-mRNA-ML-2_1.fastq.gz 1dpa-mRNA-ML-2_2.fastq.gz	fastq fastq	15395445120.0	96221532.0	E MTAB 7464:1dpa mRNA ML 2	0:80 1:80	A:4187891415;C:3447519966;G:3632085998;T:4124408897;N:3538844	80	80	4187891415	3447519966	3632085998	4124408897	3538844	ERX2938576	ERS2922612	ERA1667271	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	2	0.90197	0.90707	0.33526	0.33624	0.7371	0.74479	0.51163	0.50652	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	other	trueseq	bulk	unknown	unknown	Turkey	2018-11-28	Adult	Adult	Multi-tissue	Multi-system
9354	9354	ERR2935781	ERX2938575	ERS2922611	ERP112367	PRJEB30004	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E-MTAB-7464	Transcriptome Analysis	Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	1dpa mRNA ML 1	SAMEA5138244	Izmir Biomedicine and Genome Center / Turkey	ENA FIRST PUBLIC:2020 11 28T04:04:08Z\|ENA LAST UPDATE:2018 11 28T11:38:53Z\|External Id:SAMEA5138244\|INSDC center name:Izmir Biomedicine and Genome Center / Turkey\|INSDC first public:2020 11 28T04:04:08Z\|INSDC last update:2018 11 28T11:38:53Z\|INSDC status:public\|Submitter Id:E MTAB 7464:1dpa mRNA ML 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:Chemical ablation\|organism part:caudal fin\|sample name:E MTAB 7464:1dpa mRNA ML 1\|scientific name:Danio rerio\|sex:female\|strain:AB	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	E MTAB 7464:1dpa mRNA ML 1 p	1dpa mRNA ML 1 p	RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 µM for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy® Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina	Experimental Factor: compound:neocuproine\|Experimental Factor: dose:1\|Experimental Factor: injury:chemical ablation\|Experimental Factor: time:1\|Experimental Factor: organism part:caudal fin	ssRNA-seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP112367	NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model	ENA FIRST PUBLIC:2023 08 24\|ENA LAST UPDATE:2023 08 24	1dpa-mRNA-ML-1_2.fastq.gz 1dpa-mRNA-ML-1_1.fastq.gz	fastq fastq	9835056000.0	61469100.0	E MTAB 7464:1dpa mRNA ML 1	0:80 1:80	A:2673004774;C:2192168640;G:2335585327;T:2632030261;N:2266998	80	80	2673004774	2192168640	2335585327	2632030261	2266998	ERX2938575	ERS2922611	ERA1667271	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	Izmir Biomedicine and Genome Center / Turkey\|European Nucleotide Archive	2	0.89673	0.89924	0.33937	0.33954	0.72342	0.73032	0.49857	0.48103	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	other	trueseq	bulk	unknown	unknown	Turkey	2018-11-28	Adult	Adult	Multi-tissue	Multi-system
15557	15557	ERR12916374	ERX12288721	ERS18989008	ERP159620	PRJEB75017	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E-MTAB-14020	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 4	SAMEA115497325	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14020:Sample 4\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14020:Sample 4\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T12	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E MTAB 14020:Sample 4 p	Sample 4 p	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159620	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32227_R2068_dre_nc_fulvestrant_lib661348_10164_3_1.fastq.gz NG-32227_R2068_dre_nc_fulvestrant_lib661348_10164_3_2.fastq.gz	fastq fastq	12187177686.0	40354893.0	E MTAB 14020:NG 32227 R2068 dre nc fulvestrant lib661348 10164 3	0:151 1:151	A:3305078518;C:2786935079;G:2833891750;T:3261092784;N:179555	151	151	3305078518	2786935079	2833891750	3261092784	179555	ERX12288721	ERS18989008	ERA29606970	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15558	15558	ERR12916378	ERX12288725	ERS18989012	ERP159620	PRJEB75017	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E-MTAB-14020	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 8	SAMEA115497329	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14020:Sample 8\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14020:Sample 8\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T18	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E MTAB 14020:Sample 8 p	Sample 8 p	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159620	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32227_R2075_dre_C2_fulvestrant_lib661353_10164_3_1.fastq.gz NG-32227_R2075_dre_C2_fulvestrant_lib661353_10164_3_2.fastq.gz	fastq fastq	11901620680.0	39409340.0	E MTAB 14020:NG 32227 R2075 dre C2 fulvestrant lib661353 10164 3	0:151 1:151	A:3237613547;C:2714994048;G:2755289588;T:3193549887;N:173610	151	151	3237613547	2714994048	2755289588	3193549887	173610	ERX12288725	ERS18989012	ERA29606970	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15559	15559	ERR12916373	ERX12288720	ERS18989007	ERP159620	PRJEB75017	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E-MTAB-14020	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 3	SAMEA115497324	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14020:Sample 3\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14020:Sample 3\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T8	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E MTAB 14020:Sample 3 p	Sample 3 p	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159620	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32542_R2066_dre_C3_fulvestrant_lib672119_10184_2_1.fastq.gz NG-32542_R2066_dre_C3_fulvestrant_lib672119_10184_2_2.fastq.gz	fastq fastq	10934088784.0	36205592.0	E MTAB 14020:NG 32542 R2066 dre C3 fulvestrant lib672119 10184 2	0:151 1:151	A:2998030197;C:2488169576;G:2491574541;T:2956054160;N:260310	151	151	2998030197	2488169576	2491574541	2956054160	260310	ERX12288720	ERS18989007	ERA29606970	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15560	15560	ERR12916376	ERX12288723	ERS18989010	ERP159620	PRJEB75017	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E-MTAB-14020	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 6	SAMEA115497327	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14020:Sample 6\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14020:Sample 6\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T12	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E MTAB 14020:Sample 6 p	Sample 6 p	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159620	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32542_R2071_dre_C3_fulvestrant_lib672120_10184_1_1.fastq.gz NG-32542_R2071_dre_C3_fulvestrant_lib672120_10184_1_2.fastq.gz	fastq fastq	10332415392.0	34213296.0	E MTAB 14020:NG 32542 R2071 dre C3 fulvestrant lib672120 10184 1	0:151 1:151	A:2830892520;C:2350292883;G:2358159763;T:2792844342;N:225884	151	151	2830892520	2350292883	2358159763	2792844342	225884	ERX12288723	ERS18989010	ERA29606970	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15561	15561	ERR12916375	ERX12288722	ERS18989009	ERP159620	PRJEB75017	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E-MTAB-14020	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 5	SAMEA115497326	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14020:Sample 5\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14020:Sample 5\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T12	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E MTAB 14020:Sample 5 p	Sample 5 p	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159620	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32227_R2070_dre_C2_fulvestrant_lib661350_10164_3_1.fastq.gz NG-32227_R2070_dre_C2_fulvestrant_lib661350_10164_3_2.fastq.gz	fastq fastq	11003883400.0	36436700.0	E MTAB 14020:NG 32227 R2070 dre C2 fulvestrant lib661350 10164 3	0:151 1:151	A:2994383363;C:2510974240;G:2552484598;T:2945879588;N:161611	151	151	2994383363	2510974240	2552484598	2945879588	161611	ERX12288722	ERS18989009	ERA29606970	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15562	15562	ERR12916372	ERX12288719	ERS18989006	ERP159620	PRJEB75017	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E-MTAB-14020	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 2	SAMEA115497323	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14020:Sample 2\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14020:Sample 2\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T8	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E MTAB 14020:Sample 2 p	Sample 2 p	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159620	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32227_R2065_dre_C2_fulvestrant_lib661347_10164_3_1.fastq.gz NG-32227_R2065_dre_C2_fulvestrant_lib661347_10164_3_2.fastq.gz	fastq fastq	11419243026.0	37812063.0	E MTAB 14020:NG 32227 R2065 dre C2 fulvestrant lib661347 10164 3	0:151 1:151	A:3111236492;C:2602474235;G:2639014496;T:3066349898;N:167905	151	151	3111236492	2602474235	2639014496	3066349898	167905	ERX12288719	ERS18989006	ERA29606970	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15563	15563	ERR12916379	ERX12288726	ERS18989013	ERP159620	PRJEB75017	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E-MTAB-14020	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 9	SAMEA115497330	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14020:Sample 9\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14020:Sample 9\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T18	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E MTAB 14020:Sample 9 p	Sample 9 p	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159620	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32542_R2076_dre_C3_fulvestrant_lib676805_10195_1_1.fastq.gz NG-32542_R2076_dre_C3_fulvestrant_lib676805_10195_1_2.fastq.gz	fastq fastq	13933360108.0	46136954.0	E MTAB 14020:NG 32542 R2076 dre C3 fulvestrant lib676805 10195 1	0:151 1:151	A:3755178070;C:3212497786;G:3265644027;T:3699709369;N:330856	151	151	3755178070	3212497786	3265644027	3699709369	330856	ERX12288726	ERS18989013	ERA29606970	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15564	15564	ERR12916371	ERX12288718	ERS18989005	ERP159620	PRJEB75017	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E-MTAB-14020	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 1	SAMEA115497322	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14020:Sample 1\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14020:Sample 1\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T8	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E MTAB 14020:Sample 1 p	Sample 1 p	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159620	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32227_R2063_dre_nc_fulvestrant_lib661345_10164_3_1.fastq.gz NG-32227_R2063_dre_nc_fulvestrant_lib661345_10164_3_2.fastq.gz	fastq fastq	9751334172.0	32289186.0	E MTAB 14020:NG 32227 R2063 dre nc fulvestrant lib661345 10164 3	0:151 1:151	A:2644860460;C:2230247028;G:2268943823;T:2607137645;N:145216	151	151	2644860460	2230247028	2268943823	2607137645	145216	ERX12288718	ERS18989005	ERA29606970	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15565	15565	ERR12916377	ERX12288724	ERS18989011	ERP159620	PRJEB75017	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E-MTAB-14020	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 7	SAMEA115497328	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14020:Sample 7\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14020:Sample 7\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T18	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E MTAB 14020:Sample 7 p	Sample 7 p	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159620	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32227_R2073_dre_nc_fulvestrant_lib661351_10164_3_1.fastq.gz NG-32227_R2073_dre_nc_fulvestrant_lib661351_10164_3_2.fastq.gz	fastq fastq	11826951482.0	39162091.0	E MTAB 14020:NG 32227 R2073 dre nc fulvestrant lib661351 10164 3	0:151 1:151	A:3220473968;C:2696879564;G:2734502253;T:3174923177;N:172520	151	151	3220473968	2696879564	2734502253	3174923177	172520	ERX12288724	ERS18989011	ERA29606970	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15566	15566	ERR12916383	ERX12288730	ERS18989113	ERP159621	PRJEB75018	mRNA Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups	E-MTAB-14022	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 4	SAMEA115497430	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14022:Sample 4\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14022:Sample 4\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T18	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	E MTAB 14022:Sample 4 p	Sample 4 p	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159621	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of 17Î² estradiol against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32544_R2128_dre_nc_estradiol_lib672208_10184_2_1.fastq.gz NG-32544_R2128_dre_nc_estradiol_lib672208_10184_2_2.fastq.gz	fastq fastq	11519262406.0	38143253.0	E MTAB 14022:NG 32544 R2128 dre nc estradiol lib672208 10184 2	0:151 1:151	A:3155893663;C:2615447205;G:2624126192;T:3123521216;N:274130	151	151	3155893663	2615447205	2624126192	3123521216	274130	ERX12288730	ERS18989113	ERA29607067	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15567	15567	ERR12916382	ERX12288729	ERS18989112	ERP159621	PRJEB75018	mRNA Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups	E-MTAB-14022	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 3	SAMEA115497429	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14022:Sample 3\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14022:Sample 3\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T8	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	E MTAB 14022:Sample 3 p	Sample 3 p	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159621	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of 17Î² estradiol against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32544_R2126_dre_C3_estradiol_lib672207_10184_2_1.fastq.gz NG-32544_R2126_dre_C3_estradiol_lib672207_10184_2_2.fastq.gz	fastq fastq	9989685860.0	33078430.0	E MTAB 14022:NG 32544 R2126 dre C3 estradiol lib672207 10184 2	0:151 1:151	A:2726397137;C:2282307054;G:2282386674;T:2698356730;N:238265	151	151	2726397137	2282307054	2282386674	2698356730	238265	ERX12288729	ERS18989112	ERA29607067	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15568	15568	ERR12916384	ERX12288731	ERS18989114	ERP159621	PRJEB75018	mRNA Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups	E-MTAB-14022	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 5	SAMEA115497431	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14022:Sample 5\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14022:Sample 5\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T18	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	E MTAB 14022:Sample 5 p	Sample 5 p	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159621	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of 17Î² estradiol against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32544_R2130_dre_C2_estradiol_lib672209_10184_2_1.fastq.gz NG-32544_R2130_dre_C2_estradiol_lib672209_10184_2_2.fastq.gz	fastq fastq	12577165386.0	41646243.0	E MTAB 14022:NG 32544 R2130 dre C2 estradiol lib672209 10184 2	0:151 1:151	A:3461907353;C:2843697550;G:2849814020;T:3421444968;N:301495	151	151	3461907353	2843697550	2849814020	3421444968	301495	ERX12288731	ERS18989114	ERA29607067	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15569	15569	ERR12916380	ERX12288727	ERS18989110	ERP159621	PRJEB75018	mRNA Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups	E-MTAB-14022	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 1	SAMEA115497427	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14022:Sample 1\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14022:Sample 1\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T8	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	E MTAB 14022:Sample 1 p	Sample 1 p	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159621	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of 17Î² estradiol against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32544_R2123_dre_nc_estradiol_lib676807_10195_2_1.fastq.gz NG-32544_R2123_dre_nc_estradiol_lib676807_10195_2_2.fastq.gz	fastq fastq	9678660288.0	32048544.0	E MTAB 14022:NG 32544 R2123 dre nc estradiol lib676807 10195 2	0:151 1:151	A:2651923654;C:2190605826;G:2231831230;T:2604055145;N:244433	151	151	2651923654	2190605826	2231831230	2604055145	244433	ERX12288727	ERS18989110	ERA29607067	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15570	15570	ERR12916381	ERX12288728	ERS18989111	ERP159621	PRJEB75018	mRNA Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups	E-MTAB-14022	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 2	SAMEA115497428	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14022:Sample 2\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14022:Sample 2\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T8	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	E MTAB 14022:Sample 2 p	Sample 2 p	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159621	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of 17Î² estradiol against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32544_R2125_dre_C2_estradiol_lib672206_10184_2_1.fastq.gz NG-32544_R2125_dre_C2_estradiol_lib672206_10184_2_2.fastq.gz	fastq fastq	11431327556.0	37852078.0	E MTAB 14022:NG 32544 R2125 dre C2 estradiol lib672206 10184 2	0:151 1:151	A:3138124320;C:2596000456;G:2590788209;T:3106140537;N:274034	151	151	3138124320	2596000456	2590788209	3106140537	274034	ERX12288728	ERS18989111	ERA29607067	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15571	15571	ERR12916386	ERX12288733	ERS18989116	ERP159621	PRJEB75018	mRNA Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups	E-MTAB-14022	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 7	SAMEA115497433	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14022:Sample 7\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14022:Sample 7\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T19	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	E MTAB 14022:Sample 7 p	Sample 7 p	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159621	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of 17Î² estradiol against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32544_R2133_dre_nc_estradiol_lib672211_10184_1_1.fastq.gz NG-32544_R2133_dre_nc_estradiol_lib672211_10184_1_2.fastq.gz	fastq fastq	13575436654.0	44951777.0	E MTAB 14022:NG 32544 R2133 dre nc estradiol lib672211 10184 1	0:151 1:151	A:3755208011;C:3052011499;G:3055003729;T:3712919528;N:293887	151	151	3755208011	3052011499	3055003729	3712919528	293887	ERX12288733	ERS18989116	ERA29607067	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15572	15572	ERR12916385	ERX12288732	ERS18989115	ERP159621	PRJEB75018	mRNA Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups	E-MTAB-14022	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 6	SAMEA115497432	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14022:Sample 6\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14022:Sample 6\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T18	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	E MTAB 14022:Sample 6 p	Sample 6 p	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159621	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of 17Î² estradiol against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32544_R2131_dre_C3_estradiol_lib672210_10184_1_1.fastq.gz NG-32544_R2131_dre_C3_estradiol_lib672210_10184_1_2.fastq.gz	fastq fastq	13579439362.0	44965031.0	E MTAB 14022:NG 32544 R2131 dre C3 estradiol lib672210 10184 1	0:151 1:151	A:3748627643;C:3057631445;G:3066968241;T:3705917099;N:294934	151	151	3748627643	3057631445	3066968241	3705917099	294934	ERX12288732	ERS18989115	ERA29607067	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15573	15573	ERR12916388	ERX12288735	ERS18989118	ERP159621	PRJEB75018	mRNA Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups	E-MTAB-14022	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 9	SAMEA115497435	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14022:Sample 9\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14022:Sample 9\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T19	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	E MTAB 14022:Sample 9 p	Sample 9 p	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159621	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of 17Î² estradiol against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32544_R2136_dre_C3_estradiol_lib672213_10184_1_1.fastq.gz NG-32544_R2136_dre_C3_estradiol_lib672213_10184_1_2.fastq.gz	fastq fastq	11908180120.0	39431060.0	E MTAB 14022:NG 32544 R2136 dre C3 estradiol lib672213 10184 1	0:151 1:151	A:3272028142;C:2696935524;G:2712854157;T:3226102684;N:259613	151	151	3272028142	2696935524	2712854157	3226102684	259613	ERX12288735	ERS18989118	ERA29607067	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15574	15574	ERR12916387	ERX12288734	ERS18989117	ERP159621	PRJEB75018	mRNA Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups	E-MTAB-14022	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 8	SAMEA115497434	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14022:Sample 8\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14022:Sample 8\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T19	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	E MTAB 14022:Sample 8 p	Sample 8 p	mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to 17β estradiol for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of 17β estradiol CAS 50 28 2 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159621	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of 17Î² estradiol against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32544_R2135_dre_C2_estradiol_lib672212_10184_2_1.fastq.gz NG-32544_R2135_dre_C2_estradiol_lib672212_10184_2_2.fastq.gz	fastq fastq	15738562088.0	52114444.0	E MTAB 14022:NG 32544 R2135 dre C2 estradiol lib672212 10184 2	0:151 1:151	A:4308214612;C:3581781339;G:3588099342;T:4260093303;N:373492	151	151	4308214612	3581781339	3588099342	4260093303	373492	ERX12288734	ERS18989117	ERA29607067	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15575	15575	ERR12916390	ERX12288737	ERS18989120	ERP159622	PRJEB75019	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E-MTAB-14023	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 2	SAMEA115497437	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14023:Sample 2\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14023:Sample 2\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T5	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E MTAB 14023:Sample 2 p	Sample 2 p	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159622	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-33234_R2197_dre_C2_bisphenola_lib692361_10227_1_1.fastq.gz NG-33234_R2197_dre_C2_bisphenola_lib692361_10227_1_2.fastq.gz	fastq fastq	16285232824.0	53924612.0	E MTAB 14023:NG 33234 R2197 dre C2 bisphenola lib692361 10227 1	0:151 1:151	A:4518199560;C:3645980414;G:3674232653;T:4446656777;N:163420	151	151	4518199560	3645980414	3674232653	4446656777	163420	ERX12288737	ERS18989120	ERA29607068	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15576	15576	ERR12916393	ERX12288740	ERS18989123	ERP159622	PRJEB75019	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E-MTAB-14023	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 5	SAMEA115497440	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14023:Sample 5\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14023:Sample 5\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T18	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E MTAB 14023:Sample 5 p	Sample 5 p	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159622	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-33234_R2202_dre_C2_bisphenola_lib692364_10224_3_1.fastq.gz NG-33234_R2202_dre_C2_bisphenola_lib692364_10224_3_2.fastq.gz	fastq fastq	14761516588.0	48879194.0	E MTAB 14023:NG 33234 R2202 dre C2 bisphenola lib692364 10224 3	0:151 1:151	A:4115762614;C:3282831633;G:3308598262;T:4054111375;N:212704	151	151	4115762614	3282831633	3308598262	4054111375	212704	ERX12288740	ERS18989123	ERA29607068	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15577	15577	ERR12916396	ERX12288743	ERS18989126	ERP159622	PRJEB75019	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E-MTAB-14023	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 8	SAMEA115497443	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14023:Sample 8\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14023:Sample 8\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T19	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E MTAB 14023:Sample 8 p	Sample 8 p	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159622	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-33234_R2207_dre_C2_bisphenola_lib692367_10227_1_1.fastq.gz NG-33234_R2207_dre_C2_bisphenola_lib692367_10227_1_2.fastq.gz	fastq fastq	13161143692.0	43579946.0	E MTAB 14023:NG 33234 R2207 dre C2 bisphenola lib692367 10227 1	0:151 1:151	A:3624299194;C:2976559804;G:2995115250;T:3565037596;N:131848	151	151	3624299194	2976559804	2995115250	3565037596	131848	ERX12288743	ERS18989126	ERA29607068	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15578	15578	ERR12916392	ERX12288739	ERS18989122	ERP159622	PRJEB75019	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E-MTAB-14023	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 4	SAMEA115497439	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14023:Sample 4\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14023:Sample 4\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T18	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E MTAB 14023:Sample 4 p	Sample 4 p	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159622	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-33234_R2200_dre_nc_bisphenola_lib692363_10227_2_1.fastq.gz NG-33234_R2200_dre_nc_bisphenola_lib692363_10227_2_2.fastq.gz	fastq fastq	26147833460.0	86582230.0	E MTAB 14023:NG 33234 R2200 dre nc bisphenola lib692363 10227 2	0:151 1:151	A:7258232055;C:5842879066;G:5902714067;T:7142264329;N:1743943	151	151	7258232055	5842879066	5902714067	7142264329	1743943	ERX12288739	ERS18989122	ERA29607068	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15579	15579	ERR12916394	ERX12288741	ERS18989124	ERP159622	PRJEB75019	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E-MTAB-14023	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 6	SAMEA115497441	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14023:Sample 6\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14023:Sample 6\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T18	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E MTAB 14023:Sample 6 p	Sample 6 p	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159622	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-33234_R2203_dre_C3_bisphenola_lib692365_10224_3_1.fastq.gz NG-33234_R2203_dre_C3_bisphenola_lib692365_10224_3_2.fastq.gz	fastq fastq	21922257010.0	72590255.0	E MTAB 14023:NG 33234 R2203 dre C3 bisphenola lib692365 10224 3	0:151 1:151	A:6045629984;C:4936064183;G:4974917873;T:5965326250;N:318720	151	151	6045629984	4936064183	4974917873	5965326250	318720	ERX12288741	ERS18989124	ERA29607068	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15580	15580	ERR12916397	ERX12288744	ERS18989127	ERP159622	PRJEB75019	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E-MTAB-14023	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 9	SAMEA115497444	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14023:Sample 9\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14023:Sample 9\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T19	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E MTAB 14023:Sample 9 p	Sample 9 p	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159622	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-33234_R2208_dre_C3_bisphenola_lib692368_10227_2_1.fastq.gz NG-33234_R2208_dre_C3_bisphenola_lib692368_10227_2_2.fastq.gz	fastq fastq	23881298998.0	79077149.0	E MTAB 14023:NG 33234 R2208 dre C3 bisphenola lib692368 10227 2	0:151 1:151	A:6507764646;C:5454501673;G:5496344023;T:6421103639;N:1585017	151	151	6507764646	5454501673	5496344023	6421103639	1585017	ERX12288744	ERS18989127	ERA29607068	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15581	15581	ERR12916391	ERX12288738	ERS18989121	ERP159622	PRJEB75019	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E-MTAB-14023	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 3	SAMEA115497438	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14023:Sample 3\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14023:Sample 3\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T5	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E MTAB 14023:Sample 3 p	Sample 3 p	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159622	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-33234_R2198_dre_C3_bisphenola_lib692362_10227_2_1.fastq.gz NG-33234_R2198_dre_C3_bisphenola_lib692362_10227_2_2.fastq.gz	fastq fastq	24214884272.0	80181736.0	E MTAB 14023:NG 33234 R2198 dre C3 bisphenola lib692362 10227 2	0:151 1:151	A:6702079295;C:5424413438;G:5474562552;T:6612208700;N:1620287	151	151	6702079295	5424413438	5474562552	6612208700	1620287	ERX12288738	ERS18989121	ERA29607068	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15582	15582	ERR12916389	ERX12288736	ERS18989119	ERP159622	PRJEB75019	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E-MTAB-14023	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 1	SAMEA115497436	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14023:Sample 1\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14023:Sample 1\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T5	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E MTAB 14023:Sample 1 p	Sample 1 p	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159622	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-33234_R2195_dre_nc_bisphenola_lib692360_10227_2_1.fastq.gz NG-33234_R2195_dre_nc_bisphenola_lib692360_10227_2_2.fastq.gz	fastq fastq	23247776686.0	76979393.0	E MTAB 14023:NG 33234 R2195 dre nc bisphenola lib692360 10227 2	0:151 1:151	A:6402000447;C:5235790040;G:5291162202;T:6317305100;N:1518897	151	151	6402000447	5235790040	5291162202	6317305100	1518897	ERX12288736	ERS18989119	ERA29607068	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
15583	15583	ERR12916395	ERX12288742	ERS18989125	ERP159622	PRJEB75019	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E-MTAB-14023	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to bisphenol A CAS 80 05 7. Zebrafish embryos were exposed to to bisphenol A according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 7	SAMEA115497442	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14023:Sample 7\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14023:Sample 7\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T19	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	E MTAB 14023:Sample 7 p	Sample 7 p	mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to bisphenol A for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of bisphenol A CAS 80 05 7 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159622	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Bisphenol A against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-33234_R2205_dre_nc_bisphenola_lib692366_10231_2_1.fastq.gz NG-33234_R2205_dre_nc_bisphenola_lib692366_10231_2_2.fastq.gz	fastq fastq	21053544346.0	69713723.0	E MTAB 14023:NG 33234 R2205 dre nc bisphenola lib692366 10231 2	0:151 1:151	A:5801431255;C:4747202786;G:4789489473;T:5713741720;N:1679112	151	151	5801431255	4747202786	4789489473	5713741720	1679112	ERX12288742	ERS18989125	ERA29607068	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures
16791	16791	ERR13300240	ERX12671102	ERS20278812	ERP161270	PRJEB76780	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E-MTAB-14184	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Methimazole CAS 60 56 0 a thyroid peroxidase inhibitor. Zebrafish embryos were exposed to methimazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 7	E MTAB 14184:Sample 7		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T12\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E MTAB 14184:Sample 7 p	Sample 7 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161270	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1986_dre_nc_metimazole_lib648391_10131_3_1.fastq.gz NG-31767_R1986_dre_nc_metimazole_lib648391_10131_3_2.fastq.gz	fastq fastq	11260667356.0	37286978.0	E MTAB 14184:NG 31767 R1986 dre nc metimazole lib648391 10131 3	0:151 1:151	A:3081176852;C:2552857390;G:2580624774;T:3045559228;N:449112	151	151	3081176852	2552857390	2580624774	3045559228	449112	ERX12671102	ERS20278812	ERA30642702	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16792	16792	ERR13300236	ERX12671098	ERS20278808	ERP161270	PRJEB76780	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E-MTAB-14184	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Methimazole CAS 60 56 0 a thyroid peroxidase inhibitor. Zebrafish embryos were exposed to methimazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 3	E MTAB 14184:Sample 3		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T3\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E MTAB 14184:Sample 3 p	Sample 3 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161270	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1980_dre_C2_metimazole_lib648387_10134_2_1.fastq.gz NG-31767_R1980_dre_C2_metimazole_lib648387_10134_2_2.fastq.gz	fastq fastq	10327728050.0	34197775.0	E MTAB 14184:NG 31767 R1980 dre C2 metimazole lib648387 10134 2	0:151 1:151	A:2799291910;C:2358529731;G:2393199259;T:2776615639;N:91511	151	151	2799291910	2358529731	2393199259	2776615639	91511	ERX12671098	ERS20278808	ERA30642702	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16793	16793	ERR13300237	ERX12671099	ERS20278809	ERP161270	PRJEB76780	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E-MTAB-14184	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Methimazole CAS 60 56 0 a thyroid peroxidase inhibitor. Zebrafish embryos were exposed to methimazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 4	E MTAB 14184:Sample 4		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T6\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E MTAB 14184:Sample 4 p	Sample 4 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161270	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1982_dre_nc_metimazole_lib648388_10131_3_1.fastq.gz NG-31767_R1982_dre_nc_metimazole_lib648388_10131_3_2.fastq.gz	fastq fastq	12475825058.0	41310679.0	E MTAB 14184:NG 31767 R1982 dre nc metimazole lib648388 10131 3	0:151 1:151	A:3409097477;C:2831943866;G:2867531242;T:3366748070;N:504403	151	151	3409097477	2831943866	2867531242	3366748070	504403	ERX12671099	ERS20278809	ERA30642702	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16794	16794	ERR13300235	ERX12671097	ERS20278807	ERP161270	PRJEB76780	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E-MTAB-14184	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Methimazole CAS 60 56 0 a thyroid peroxidase inhibitor. Zebrafish embryos were exposed to methimazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 2	E MTAB 14184:Sample 2		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T3\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E MTAB 14184:Sample 2 p	Sample 2 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161270	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1979_dre_C1_metimazole_lib648386_10131_3_1.fastq.gz NG-31767_R1979_dre_C1_metimazole_lib648386_10131_3_2.fastq.gz	fastq fastq	12056393264.0	39921832.0	E MTAB 14184:NG 31767 R1979 dre C1 metimazole lib648386 10131 3	0:151 1:151	A:3284811921;C:2746509095;G:2779390635;T:3245201332;N:480281	151	151	3284811921	2746509095	2779390635	3245201332	480281	ERX12671097	ERS20278807	ERA30642702	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16795	16795	ERR13300234	ERX12671096	ERS20278806	ERP161270	PRJEB76780	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E-MTAB-14184	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Methimazole CAS 60 56 0 a thyroid peroxidase inhibitor. Zebrafish embryos were exposed to methimazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 1	E MTAB 14184:Sample 1		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T3\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E MTAB 14184:Sample 1 p	Sample 1 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161270	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1978_dre_nc_metimazole_lib648385_10131_3_1.fastq.gz NG-31767_R1978_dre_nc_metimazole_lib648385_10131_3_2.fastq.gz	fastq fastq	13764936218.0	45579259.0	E MTAB 14184:NG 31767 R1978 dre nc metimazole lib648385 10131 3	0:151 1:151	A:3758304493;C:3129474937;G:3161322918;T:3715288378;N:545492	151	151	3758304493	3129474937	3161322918	3715288378	545492	ERX12671096	ERS20278806	ERA30642702	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16796	16796	ERR13300242	ERX12671104	ERS20278814	ERP161270	PRJEB76780	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E-MTAB-14184	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Methimazole CAS 60 56 0 a thyroid peroxidase inhibitor. Zebrafish embryos were exposed to methimazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 9	E MTAB 14184:Sample 9		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T12\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E MTAB 14184:Sample 9 p	Sample 9 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161270	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1988_dre_C2_metimazole_lib648393_10134_2_1.fastq.gz NG-31767_R1988_dre_C2_metimazole_lib648393_10134_2_2.fastq.gz	fastq fastq	13519918182.0	44767941.0	E MTAB 14184:NG 31767 R1988 dre C2 metimazole lib648393 10134 2	0:151 1:151	A:3699694563;C:3061675737;G:3096126907;T:3662301667;N:119308	151	151	3699694563	3061675737	3096126907	3662301667	119308	ERX12671104	ERS20278814	ERA30642702	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16797	16797	ERR13300239	ERX12671101	ERS20278811	ERP161270	PRJEB76780	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E-MTAB-14184	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Methimazole CAS 60 56 0 a thyroid peroxidase inhibitor. Zebrafish embryos were exposed to methimazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 6	E MTAB 14184:Sample 6		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T6\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E MTAB 14184:Sample 6 p	Sample 6 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161270	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1984_dre_C2_metimazole_lib648390_10131_3_1.fastq.gz NG-31767_R1984_dre_C2_metimazole_lib648390_10131_3_2.fastq.gz	fastq fastq	11682386498.0	38683399.0	E MTAB 14184:NG 31767 R1984 dre C2 metimazole lib648390 10131 3	0:151 1:151	A:3197033917;C:2653110640;G:2674567052;T:3157209187;N:465702	151	151	3197033917	2653110640	2674567052	3157209187	465702	ERX12671101	ERS20278811	ERA30642702	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16798	16798	ERR13300241	ERX12671103	ERS20278813	ERP161270	PRJEB76780	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E-MTAB-14184	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Methimazole CAS 60 56 0 a thyroid peroxidase inhibitor. Zebrafish embryos were exposed to methimazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 8	E MTAB 14184:Sample 8		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T12\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E MTAB 14184:Sample 8 p	Sample 8 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161270	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1987_dre_C1_metimazole_lib648392_10134_2_1.fastq.gz NG-31767_R1987_dre_C1_metimazole_lib648392_10134_2_2.fastq.gz	fastq fastq	14249559544.0	47183972.0	E MTAB 14184:NG 31767 R1987 dre C1 metimazole lib648392 10134 2	0:151 1:151	A:3912991191;C:3212312586;G:3257466757;T:3866663511;N:125499	151	151	3912991191	3212312586	3257466757	3866663511	125499	ERX12671103	ERS20278813	ERA30642702	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16799	16799	ERR13300238	ERX12671100	ERS20278810	ERP161270	PRJEB76780	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E-MTAB-14184	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Methimazole CAS 60 56 0 a thyroid peroxidase inhibitor. Zebrafish embryos were exposed to methimazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 5	E MTAB 14184:Sample 5		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T6\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	E MTAB 14184:Sample 5 p	Sample 5 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161270	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1983_dre_C1_metimazole_lib648389_10131_3_1.fastq.gz NG-31767_R1983_dre_C1_metimazole_lib648389_10131_3_2.fastq.gz	fastq fastq	12432697344.0	41167872.0	E MTAB 14184:NG 31767 R1983 dre C1 metimazole lib648389 10131 3	0:151 1:151	A:3393249603;C:2829226513;G:2854931342;T:3354793579;N:496307	151	151	3393249603	2829226513	2854931342	3354793579	496307	ERX12671100	ERS20278810	ERA30642702	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16800	16800	ERR13301113	ERX12671975	ERS20279263	ERP161271	PRJEB76781	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E-MTAB-14185	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 9	E MTAB 14185:Sample 9		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T12\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E MTAB 14185:Sample 9 p	Sample 9 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161271	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1977_dre_C3_iopanicacid_lib648384_10134_2_1.fastq.gz NG-31767_R1977_dre_C3_iopanicacid_lib648384_10134_2_2.fastq.gz	fastq fastq	14923903196.0	49416898.0	E MTAB 14185:NG 31767 R1977 dre C3 iopanicacid lib648384 10134 2	0:151 1:151	A:4052219773;C:3416033337;G:3452773871;T:4002745593;N:130622	151	151	4052219773	3416033337	3452773871	4002745593	130622	ERX12671975	ERS20279263	ERA30642739	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16801	16801	ERR13301105	ERX12671967	ERS20279255	ERP161271	PRJEB76781	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E-MTAB-14185	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 1	E MTAB 14185:Sample 1		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T3\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E MTAB 14185:Sample 1 p	Sample 1 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161271	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1966_dre_nc_iopanicacid_lib648376_10134_2_1.fastq.gz NG-31767_R1966_dre_nc_iopanicacid_lib648376_10134_2_2.fastq.gz	fastq fastq	14323093524.0	47427462.0	E MTAB 14185:NG 31767 R1966 dre nc iopanicacid lib648376 10134 2	0:151 1:151	A:3915028461;C:3251486078;G:3281494434;T:3874958216;N:126335	151	151	3915028461	3251486078	3281494434	3874958216	126335	ERX12671967	ERS20279255	ERA30642739	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16802	16802	ERR13301112	ERX12671974	ERS20279262	ERP161271	PRJEB76781	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E-MTAB-14185	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 8	E MTAB 14185:Sample 8		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T12\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E MTAB 14185:Sample 8 p	Sample 8 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161271	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1976_dre_C2_iopanicacid_lib648383_10131_3_1.fastq.gz NG-31767_R1976_dre_C2_iopanicacid_lib648383_10131_3_2.fastq.gz	fastq fastq	10961479882.0	36296291.0	E MTAB 14185:NG 31767 R1976 dre C2 iopanicacid lib648383 10131 3	0:151 1:151	A:2983032221;C:2502602193;G:2529591204;T:2945818101;N:436163	151	151	2983032221	2502602193	2529591204	2945818101	436163	ERX12671974	ERS20279262	ERA30642739	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16803	16803	ERR13301110	ERX12671972	ERS20279260	ERP161271	PRJEB76781	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E-MTAB-14185	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 6	E MTAB 14185:Sample 6		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T6\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E MTAB 14185:Sample 6 p	Sample 6 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161271	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1973_dre_C3_iopanicacid_lib648381_10134_2_1.fastq.gz NG-31767_R1973_dre_C3_iopanicacid_lib648381_10134_2_2.fastq.gz	fastq fastq	11098074784.0	36748592.0	E MTAB 14185:NG 31767 R1973 dre C3 iopanicacid lib648381 10134 2	0:151 1:151	A:3011128450;C:2542381325;G:2563170447;T:2981297586;N:96976	151	151	3011128450	2542381325	2563170447	2981297586	96976	ERX12671972	ERS20279260	ERA30642739	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16804	16804	ERR13301109	ERX12671971	ERS20279259	ERP161271	PRJEB76781	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E-MTAB-14185	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 5	E MTAB 14185:Sample 5		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T6\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E MTAB 14185:Sample 5 p	Sample 5 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161271	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1972_dre_C2_iopanicacid_lib648380_10131_3_1.fastq.gz NG-31767_R1972_dre_C2_iopanicacid_lib648380_10131_3_2.fastq.gz	fastq fastq	13552628708.0	44876254.0	E MTAB 14185:NG 31767 R1972 dre C2 iopanicacid lib648380 10131 3	0:151 1:151	A:3683544144;C:3104040164;G:3130331394;T:3634170005;N:543001	151	151	3683544144	3104040164	3130331394	3634170005	543001	ERX12671971	ERS20279259	ERA30642739	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16805	16805	ERR13301111	ERX12671973	ERS20279261	ERP161271	PRJEB76781	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E-MTAB-14185	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 7	E MTAB 14185:Sample 7		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T12\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E MTAB 14185:Sample 7 p	Sample 7 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161271	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1974_dre_nc_iopanicacid_lib648382_10134_2_1.fastq.gz NG-31767_R1974_dre_nc_iopanicacid_lib648382_10134_2_2.fastq.gz	fastq fastq	15020718054.0	49737477.0	E MTAB 14185:NG 31767 R1974 dre nc iopanicacid lib648382 10134 2	0:151 1:151	A:4067785748;C:3448087461;G:3475467669;T:4029245322;N:131854	151	151	4067785748	3448087461	3475467669	4029245322	131854	ERX12671973	ERS20279261	ERA30642739	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16806	16806	ERR13301106	ERX12671968	ERS20279256	ERP161271	PRJEB76781	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E-MTAB-14185	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 2	E MTAB 14185:Sample 2		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T3\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E MTAB 14185:Sample 2 p	Sample 2 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161271	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1968_dre_C2_iopanicacid_lib648377_10131_3_1.fastq.gz NG-31767_R1968_dre_C2_iopanicacid_lib648377_10131_3_2.fastq.gz	fastq fastq	11754494132.0	38922166.0	E MTAB 14185:NG 31767 R1968 dre C2 iopanicacid lib648377 10131 3	0:151 1:151	A:3200002137;C:2683120669;G:2711161374;T:3159741610;N:468342	151	151	3200002137	2683120669	2711161374	3159741610	468342	ERX12671968	ERS20279256	ERA30642739	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16807	16807	ERR13301107	ERX12671969	ERS20279257	ERP161271	PRJEB76781	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E-MTAB-14185	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 3	E MTAB 14185:Sample 3		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T3\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E MTAB 14185:Sample 3 p	Sample 3 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161271	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1969_dre_C3_iopanicacid_lib648378_10134_2_1.fastq.gz NG-31767_R1969_dre_C3_iopanicacid_lib648378_10134_2_2.fastq.gz	fastq fastq	12466152904.0	41278652.0	E MTAB 14185:NG 31767 R1969 dre C3 iopanicacid lib648378 10134 2	0:151 1:151	A:3383255890;C:2853477802;G:2880177719;T:3349132410;N:109083	151	151	3383255890	2853477802	2880177719	3349132410	109083	ERX12671969	ERS20279257	ERA30642739	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
16808	16808	ERR13301108	ERX12671970	ERS20279258	ERP161271	PRJEB76781	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E-MTAB-14185	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs.	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.	Sample 4	E MTAB 14185:Sample 4		strain:AB\|isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|tank:T6\|age:96\|developmental stage:embryo stage\|geographic location country and/or sea:not collected	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	E MTAB 14185:Sample 4 p	Sample 4 p	RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 1 min. Zebrafish embryos were exposed to Iopanoic acid CAS 96 83 3 for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of methimazole 6.25 and 12.5 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP161271	Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups	ENA FIRST PUBLIC:2024 09 01\|ENA LAST UPDATE:2024 09 01	NG-31767_R1970_dre_nc_iopanicacid_lib648379_10134_2_1.fastq.gz NG-31767_R1970_dre_nc_iopanicacid_lib648379_10134_2_2.fastq.gz	fastq fastq	12166326096.0	40285848.0	E MTAB 14185:NG 31767 R1970 dre nc iopanicacid lib648379 10134 2	0:151 1:151	A:3269774977;C:2810343720;G:2853693327;T:3232407966;N:106106	151	151	3269774977	2810343720	2853693327	3232407966	106106	ERX12671970	ERS20279258	ERA30642739	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2024-09-01	Larval	Larval	Whole Organism	All anatomical structures
19122	19122	ERR13769864	ERX13170665	ERS21155828	ERP165025	PRJEB81170	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E-MTAB-14534	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to epoxiconazole CAS 133855 98 8. Zebrafish embryos were exposed to epoxiconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 8	SAMEA116134545	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14534:Sample 8\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14534:Sample 8\|scientific name:Danio rerio\|strain:AB\|tank:18	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E MTAB 14534:Sample 8 p	Sample 8 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165025	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-A0241_R2358_dre_C2_Epoxyconazole_1.fastq.gz NG-A0241_R2358_dre_C2_Epoxyconazole_2.fastq.gz	fastq fastq	7341388336.0	24376917.0	E MTAB 14534:NG A0241 R2358 dre C2 Epoxyconazole	0:150.63 1:150.53	A:1774791178;C:1907646073;G:1798114071;T:1860811102;N:25912	150	150	1774791178	1907646073	1798114071	1860811102	25912	ERX13170665	ERS21155828	ERA30873013	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19123	19123	ERR13769858	ERX13170659	ERS21155821	ERP165025	PRJEB81170	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E-MTAB-14534	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to epoxiconazole CAS 133855 98 8. Zebrafish embryos were exposed to epoxiconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 2	SAMEA116134539	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14534:Sample 2\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14534:Sample 2\|scientific name:Danio rerio\|strain:AB\|tank:5	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E MTAB 14534:Sample 2 p	Sample 2 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165025	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-A0241_R2350_dre_C2_Epoxyconazole_1.fastq.gz NG-A0241_R2350_dre_C2_Epoxyconazole_2.fastq.gz	fastq fastq	4928314441.0	16363045.0	E MTAB 14534:NG A0241 R2350 dre C2 Epoxyconazole	0:150.64 1:150.55	A:1258708674;C:1228522249;G:1141520330;T:1299546598;N:16590	150	150	1258708674	1228522249	1141520330	1299546598	16590	ERX13170659	ERS21155821	ERA30873013	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19124	19124	ERR13769863	ERX13170664	ERS21155826	ERP165025	PRJEB81170	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E-MTAB-14534	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to epoxiconazole CAS 133855 98 8. Zebrafish embryos were exposed to epoxiconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 7	SAMEA116134544	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14534:Sample 7\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14534:Sample 7\|scientific name:Danio rerio\|strain:AB\|tank:18	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E MTAB 14534:Sample 7 p	Sample 7 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165025	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-A0241_R2356_dre_nc_Epoxyconazole_1.fastq.gz NG-A0241_R2356_dre_nc_Epoxyconazole_2.fastq.gz	fastq fastq	7401361830.0	24580354.0	E MTAB 14534:NG A0241 R2356 dre nc Epoxyconazole	0:150.63 1:150.48	A:1931695855;C:1796465634;G:1724622747;T:1948552491;N:25103	150	150	1931695855	1796465634	1724622747	1948552491	25103	ERX13170664	ERS21155826	ERA30873013	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19125	19125	ERR13769857	ERX13170658	ERS21155820	ERP165025	PRJEB81170	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E-MTAB-14534	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to epoxiconazole CAS 133855 98 8. Zebrafish embryos were exposed to epoxiconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 1	SAMEA116134538	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14534:Sample 1\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14534:Sample 1\|scientific name:Danio rerio\|strain:AB\|tank:5	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E MTAB 14534:Sample 1 p	Sample 1 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165025	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-A0241_R2348_dre_nc_Epoxyconazole_1.fastq.gz NG-A0241_R2348_dre_nc_Epoxyconazole_2.fastq.gz	fastq fastq	7902595509.0	26242638.0	E MTAB 14534:NG A0241 R2348 dre nc Epoxyconazole	0:150.60 1:150.54	A:1909826693;C:2059844949;G:1957422253;T:1975473886;N:27728	150	150	1909826693	2059844949	1957422253	1975473886	27728	ERX13170658	ERS21155820	ERA30873013	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19126	19126	ERR13769865	ERX13170666	ERS21155829	ERP165025	PRJEB81170	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E-MTAB-14534	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to epoxiconazole CAS 133855 98 8. Zebrafish embryos were exposed to epoxiconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 9	SAMEA116134546	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14534:Sample 9\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14534:Sample 9\|scientific name:Danio rerio\|strain:AB\|tank:18	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E MTAB 14534:Sample 9 p	Sample 9 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165025	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-A0241_R2359_dre_C3_Epoxyconazole_1.fastq.gz NG-A0241_R2359_dre_C3_Epoxyconazole_2.fastq.gz	fastq fastq	8612779844.0	28600206.0	E MTAB 14534:NG A0241 R2359 dre C3 Epoxyconazole	0:150.62 1:150.52	A:2216194427;C:2124565360;G:1960760572;T:2311192493;N:66992	150	150	2216194427	2124565360	1960760572	2311192493	66992	ERX13170666	ERS21155829	ERA30873013	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19127	19127	ERR13769862	ERX13170663	ERS21155825	ERP165025	PRJEB81170	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E-MTAB-14534	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to epoxiconazole CAS 133855 98 8. Zebrafish embryos were exposed to epoxiconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 6	SAMEA116134543	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14534:Sample 6\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14534:Sample 6\|scientific name:Danio rerio\|strain:AB\|tank:19	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E MTAB 14534:Sample 6 p	Sample 6 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165025	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-A0241_R2355_dre_C3_Epoxyconazole_1.fastq.gz NG-A0241_R2355_dre_C3_Epoxyconazole_2.fastq.gz	fastq fastq	7679419075.0	25506967.0	E MTAB 14534:NG A0241 R2355 dre C3 Epoxyconazole	0:150.54 1:150.54	A:2028698396;C:1826869096;G:1730945755;T:2092842481;N:63347	150	150	2028698396	1826869096	1730945755	2092842481	63347	ERX13170663	ERS21155825	ERA30873013	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19128	19128	ERR13769859	ERX13170660	ERS21155822	ERP165025	PRJEB81170	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E-MTAB-14534	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to epoxiconazole CAS 133855 98 8. Zebrafish embryos were exposed to epoxiconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 3	SAMEA116134540	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14534:Sample 3\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14534:Sample 3\|scientific name:Danio rerio\|strain:AB\|tank:5	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E MTAB 14534:Sample 3 p	Sample 3 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165025	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-A0241_R2351_dre_C3_Epoxyconazole_1.fastq.gz NG-A0241_R2351_dre_C3_Epoxyconazole_2.fastq.gz	fastq fastq	6474601667.0	21505790.0	E MTAB 14534:NG A0241 R2351 dre C3 Epoxyconazole	0:150.50 1:150.56	A:1706332998;C:1536842542;G:1460024450;T:1771349231;N:52446	150	150	1706332998	1536842542	1460024450	1771349231	52446	ERX13170660	ERS21155822	ERA30873013	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19129	19129	ERR13769861	ERX13170662	ERS21155824	ERP165025	PRJEB81170	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E-MTAB-14534	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to epoxiconazole CAS 133855 98 8. Zebrafish embryos were exposed to epoxiconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 5	SAMEA116134542	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14534:Sample 5\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14534:Sample 5\|scientific name:Danio rerio\|strain:AB\|tank:19	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E MTAB 14534:Sample 5 p	Sample 5 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165025	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-A0241_R2354_dre_C2_Epoxyconazole_1.fastq.gz NG-A0241_R2354_dre_C2_Epoxyconazole_2.fastq.gz	fastq fastq	6377733506.0	21175561.0	E MTAB 14534:NG A0241 R2354 dre C2 Epoxyconazole	0:150.64 1:150.54	A:1636745288;C:1571936335;G:1467391978;T:1701639518;N:20387	150	150	1636745288	1571936335	1467391978	1701639518	20387	ERX13170662	ERS21155824	ERA30873013	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19130	19130	ERR13769860	ERX13170661	ERS21155823	ERP165025	PRJEB81170	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E-MTAB-14534	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to epoxiconazole CAS 133855 98 8. Zebrafish embryos were exposed to epoxiconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 4	SAMEA116134541	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14534:Sample 4\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14534:Sample 4\|scientific name:Danio rerio\|strain:AB\|tank:19	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	E MTAB 14534:Sample 4 p	Sample 4 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to epoxiconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of epoxiconazole CAS 133855 98 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165025	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-A0241_R2352_dre_nc_Epoxyconazole_1.fastq.gz NG-A0241_R2352_dre_nc_Epoxyconazole_2.fastq.gz	fastq fastq	8036303276.0	26688809.0	E MTAB 14534:NG A0241 R2352 dre nc Epoxyconazole	0:150.65 1:150.47	A:2072292285;C:2015102230;G:1840115471;T:2108767785;N:25505	150	150	2072292285	2015102230	1840115471	2108767785	25505	ERX13170661	ERS21155823	ERA30873013	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19131	19131	ERR13769866	ERX13170667	ERS21155960	ERP165026	PRJEB81171	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E-MTAB-14535	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Tebuconazole CAS 107534 96 3. Zebrafish embryos were exposed to Tebuconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 1	SAMEA116134547	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14535:Sample 1\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14535:Sample 1\|scientific name:Danio rerio\|strain:AB\|tank:T6	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E MTAB 14535:Sample 1 p	Sample 1 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165026	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-31102_R1767_dre_nc_tebuconazole_lib625377_10093_2_1.fastq.gz NG-31102_R1767_dre_nc_tebuconazole_lib625377_10093_2_2.fastq.gz	fastq fastq	18564470614.0	61471757.0	E MTAB 14535:NG 31102 R1767 dre nc tebuconazole lib625377 10093 2	0:151 1:151	A:5041142316;C:4235450946;G:4302687288;T:4971755192;N:13434872	151	151	5041142316	4235450946	4302687288	4971755192	13434872	ERX13170667	ERS21155960	ERA30873014	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19132	19132	ERR13769871	ERX13170672	ERS21155966	ERP165026	PRJEB81171	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E-MTAB-14535	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Tebuconazole CAS 107534 96 3. Zebrafish embryos were exposed to Tebuconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 6	SAMEA116134552	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14535:Sample 6\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14535:Sample 6\|scientific name:Danio rerio\|strain:AB\|tank:T8	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E MTAB 14535:Sample 6 p	Sample 6 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165026	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-31102_R1773_dre_C2_tebuconazole_lib625382_10093_2_1.fastq.gz NG-31102_R1773_dre_C2_tebuconazole_lib625382_10093_2_2.fastq.gz	fastq fastq	18342059392.0	60735296.0	E MTAB 14535:NG 31102 R1773 dre C2 tebuconazole lib625382 10093 2	0:151 1:151	A:4977433285;C:4184472307;G:4256595742;T:4910358488;N:13199570	151	151	4977433285	4184472307	4256595742	4910358488	13199570	ERX13170672	ERS21155966	ERA30873014	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19133	19133	ERR13769872	ERX13170673	ERS21155967	ERP165026	PRJEB81171	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E-MTAB-14535	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Tebuconazole CAS 107534 96 3. Zebrafish embryos were exposed to Tebuconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 7	SAMEA116134553	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14535:Sample 7\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14535:Sample 7\|scientific name:Danio rerio\|strain:AB\|tank:T9	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E MTAB 14535:Sample 7 p	Sample 7 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165026	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-31102_R1775_dre_nc_tebuconazole_lib625383_10093_2_1.fastq.gz NG-31102_R1775_dre_nc_tebuconazole_lib625383_10093_2_2.fastq.gz	fastq fastq	15317243700.0	50719350.0	E MTAB 14535:NG 31102 R1775 dre nc tebuconazole lib625383 10093 2	0:151 1:151	A:4145722371;C:3510731502;G:3566518892;T:4083257831;N:11013104	151	151	4145722371	3510731502	3566518892	4083257831	11013104	ERX13170673	ERS21155967	ERA30873014	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19134	19134	ERR13769873	ERX13170674	ERS21155968	ERP165026	PRJEB81171	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E-MTAB-14535	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Tebuconazole CAS 107534 96 3. Zebrafish embryos were exposed to Tebuconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 8	SAMEA116134554	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14535:Sample 8\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14535:Sample 8\|scientific name:Danio rerio\|strain:AB\|tank:T9	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E MTAB 14535:Sample 8 p	Sample 8 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165026	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-31102_R1776_dre_C1_tebuconazole_lib625384_10093_2_1.fastq.gz NG-31102_R1776_dre_C1_tebuconazole_lib625384_10093_2_2.fastq.gz	fastq fastq	16917650118.0	56018709.0	E MTAB 14535:NG 31102 R1776 dre C1 tebuconazole lib625384 10093 2	0:151 1:151	A:4583668115;C:3876712213;G:3926360117;T:4518733127;N:12176546	151	151	4583668115	3876712213	3926360117	4518733127	12176546	ERX13170674	ERS21155968	ERA30873014	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19135	19135	ERR13769869	ERX13170670	ERS21155963	ERP165026	PRJEB81171	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E-MTAB-14535	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Tebuconazole CAS 107534 96 3. Zebrafish embryos were exposed to Tebuconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 4	SAMEA116134550	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14535:Sample 4\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14535:Sample 4\|scientific name:Danio rerio\|strain:AB\|tank:T8	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E MTAB 14535:Sample 4 p	Sample 4 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165026	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-31102_R1771_dre_nc_tebuconazole_lib625380_10093_2_1.fastq.gz NG-31102_R1771_dre_nc_tebuconazole_lib625380_10093_2_2.fastq.gz	fastq fastq	15091694094.0	49972497.0	E MTAB 14535:NG 31102 R1771 dre nc tebuconazole lib625380 10093 2	0:151 1:151	A:4105094759;C:3436348876;G:3489341654;T:4050085280;N:10823525	151	151	4105094759	3436348876	3489341654	4050085280	10823525	ERX13170670	ERS21155963	ERA30873014	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19136	19136	ERR13769867	ERX13170668	ERS21155961	ERP165026	PRJEB81171	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E-MTAB-14535	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Tebuconazole CAS 107534 96 3. Zebrafish embryos were exposed to Tebuconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 2	SAMEA116134548	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14535:Sample 2\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14535:Sample 2\|scientific name:Danio rerio\|strain:AB\|tank:T6	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E MTAB 14535:Sample 2 p	Sample 2 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165026	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-31102_R1768_dre_C1_tebuconazole_lib625378_10093_2_1.fastq.gz NG-31102_R1768_dre_C1_tebuconazole_lib625378_10093_2_2.fastq.gz	fastq fastq	15420402068.0	51060934.0	E MTAB 14535:NG 31102 R1768 dre C1 tebuconazole lib625378 10093 2	0:151 1:151	A:4170187223;C:3540628263;G:3586084856;T:4112404547;N:11097179	151	151	4170187223	3540628263	3586084856	4112404547	11097179	ERX13170668	ERS21155961	ERA30873014	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19137	19137	ERR13769870	ERX13170671	ERS21155964	ERP165026	PRJEB81171	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E-MTAB-14535	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Tebuconazole CAS 107534 96 3. Zebrafish embryos were exposed to Tebuconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 5	SAMEA116134551	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14535:Sample 5\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14535:Sample 5\|scientific name:Danio rerio\|strain:AB\|tank:T8	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E MTAB 14535:Sample 5 p	Sample 5 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165026	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-31102_R1772_dre_C1_tebuconazole_lib625381_10093_2_1.fastq.gz NG-31102_R1772_dre_C1_tebuconazole_lib625381_10093_2_2.fastq.gz	fastq fastq	21539825652.0	71323926.0	E MTAB 14535:NG 31102 R1772 dre C1 tebuconazole lib625381 10093 2	0:151 1:151	A:5838376307;C:4920633321;G:5004518589;T:5760852897;N:15444538	151	151	5838376307	4920633321	5004518589	5760852897	15444538	ERX13170671	ERS21155964	ERA30873014	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19138	19138	ERR13769868	ERX13170669	ERS21155962	ERP165026	PRJEB81171	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E-MTAB-14535	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Tebuconazole CAS 107534 96 3. Zebrafish embryos were exposed to Tebuconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 3	SAMEA116134549	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14535:Sample 3\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14535:Sample 3\|scientific name:Danio rerio\|strain:AB\|tank:T6	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E MTAB 14535:Sample 3 p	Sample 3 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165026	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-31102_R1769_dre_C2_tebuconazole_lib625379_10093_2_1.fastq.gz NG-31102_R1769_dre_C2_tebuconazole_lib625379_10093_2_2.fastq.gz	fastq fastq	14005704812.0	46376506.0	E MTAB 14535:NG 31102 R1769 dre C2 tebuconazole lib625379 10093 2	0:151 1:151	A:3814690471;C:3186800062;G:3233245385;T:3760940021;N:10028873	151	151	3814690471	3186800062	3233245385	3760940021	10028873	ERX13170669	ERS21155962	ERA30873014	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures
19139	19139	ERR13769874	ERX13170675	ERS21155969	ERP165026	PRJEB81171	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E-MTAB-14535	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Tebuconazole CAS 107534 96 3. Zebrafish embryos were exposed to Tebuconazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 9	SAMEA116134555	Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)	ENA first public:2025 04 30\|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14535:Sample 9\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14535:Sample 9\|scientific name:Danio rerio\|strain:AB\|tank:T9	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	E MTAB 14535:Sample 9 p	Sample 9 p	mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to tebuconazole for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations of Tebuconazole CAS 107534 96 3 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165026	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide tebuconazole against untreated control groups	ENA FIRST PUBLIC:2025 04 30\|ENA LAST UPDATE:2025 04 30	NG-31102_R1777_dre_C2_tebuconazole_lib625385_10093_2_1.fastq.gz NG-31102_R1777_dre_C2_tebuconazole_lib625385_10093_2_2.fastq.gz	fastq fastq	18304926076.0	60612338.0	E MTAB 14535:NG 31102 R1777 dre C2 tebuconazole lib625385 10093 2	0:151 1:151	A:4946094892;C:4197366058;G:4271966340;T:4876710265;N:12788521	151	151	4946094892	4197366058	4271966340	4876710265	12788521	ERX13170675	ERS21155969	ERA30873014	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2025-04-30	Undetermined	Embryo	Whole Organism	All anatomical structures

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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");;