metadata: run_metadata: 287 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC" and tissue

287 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Head"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
10407	10407	ERR9077202	ERX8620336	ERS10857224	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT5S8	SAMEA13254181	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254181\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT5S8\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT5S8\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT5S8 s	Sv2aWT5S8 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT5S8L001-1.fastq.gz	fastq	652046291.0	8633105.0	E MTAB 11505:sv2aWT5S8L001	0:75.53 1:0	A:159570243;C:156420495;G:154853315;T:181073030;N:129208	75	0	159570243	156420495	154853315	181073030	129208	ERX8620336	ERS10857224	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95245	0.1148	0.65756	0.47011	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10408	10408	ERR9077203	ERX8620336	ERS10857224	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT5S8	SAMEA13254181	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254181\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT5S8\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT5S8\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT5S8 s	Sv2aWT5S8 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT5S8L002-1.fastq.gz	fastq	653840525.0	8656886.0	E MTAB 11505:sv2aWT5S8L002	0:75.53 1:0	A:159902458;C:156826842;G:155509070;T:181475104;N:127051	75	0	159902458	156826842	155509070	181475104	127051	ERX8620336	ERS10857224	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95226	0.1156	0.65792	0.4667	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10409	10409	ERR9077204	ERX8620336	ERS10857224	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT5S8	SAMEA13254181	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254181\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT5S8\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT5S8\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT5S8 s	Sv2aWT5S8 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT5S8L003-1.fastq.gz	fastq	659584196.0	8732885.0	E MTAB 11505:sv2aWT5S8L003	0:75.53 1:0	A:161257146;C:158299734;G:156793443;T:183128972;N:104901	75	0	161257146	158299734	156793443	183128972	104901	ERX8620336	ERS10857224	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95298	0.11485	0.65798	0.46853	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10410	10410	ERR9077205	ERX8620336	ERS10857224	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT5S8	SAMEA13254181	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254181\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT5S8\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT5S8\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT5S8 s	Sv2aWT5S8 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT5S8L004-1.fastq.gz	fastq	666627746.0	8826123.0	E MTAB 11505:sv2aWT5S8L004	0:75.53 1:0	A:162975131;C:159937258;G:158506242;T:185106149;N:102966	75	0	162975131	159937258	158506242	185106149	102966	ERX8620336	ERS10857224	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.9531	0.11425	0.65736	0.47309	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10411	10411	ERR9077198	ERX8620335	ERS10857223	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT4S7	SAMEA13254180	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254180\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT4S7\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT4S7\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT4S7 s	Sv2aWT4S7 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT4S7L001-1.fastq.gz	fastq	683751258.0	9051795.0	E MTAB 11505:sv2aWT4S7L001	0:75.54 1:0	A:162889923;C:167127644;G:164779384;T:188822907;N:131400	75	0	162889923	167127644	164779384	188822907	131400	ERX8620335	ERS10857223	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95739	0.0959	0.6606	0.46826	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10412	10412	ERR9077199	ERX8620335	ERS10857223	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT4S7	SAMEA13254180	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254180\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT4S7\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT4S7\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT4S7 s	Sv2aWT4S7 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT4S7L002-1.fastq.gz	fastq	684187711.0	9057591.0	E MTAB 11505:sv2aWT4S7L002	0:75.54 1:0	A:162923879;C:167246213;G:165071145;T:188818774;N:127700	75	0	162923879	167246213	165071145	188818774	127700	ERX8620335	ERS10857223	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95724	0.0959	0.66036	0.47026	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10413	10413	ERR9077200	ERX8620335	ERS10857223	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT4S7	SAMEA13254180	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254180\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT4S7\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT4S7\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT4S7 s	Sv2aWT4S7 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT4S7L003-1.fastq.gz	fastq	692320213.0	9165132.0	E MTAB 11505:sv2aWT4S7L003	0:75.54 1:0	A:164772792;C:169329920;G:166952052;T:191164422;N:101027	75	0	164772792	169329920	166952052	191164422	101027	ERX8620335	ERS10857223	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95786	0.09701	0.66131	0.47564	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10414	10414	ERR9077201	ERX8620335	ERS10857223	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT4S7	SAMEA13254180	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254180\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT4S7\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT4S7\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT4S7 s	Sv2aWT4S7 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT4S7L004-1.fastq.gz	fastq	697047881.0	9227702.0	E MTAB 11505:sv2aWT4S7L004	0:75.54 1:0	A:165881728;C:170388393;G:168105900;T:192572068;N:99792	75	0	165881728	170388393	168105900	192572068	99792	ERX8620335	ERS10857223	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.9584	0.09565	0.66115	0.46967	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10415	10415	ERR9077194	ERX8620334	ERS10857222	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT3S2	SAMEA13254179	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254179\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT3S2\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT3S2\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT3S2 s	Sv2aWT3S2 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT3S2L001-1.fastq.gz	fastq	723508205.0	9579193.0	E MTAB 11505:sv2aWT3S2L001	0:75.53 1:0	A:177832489;C:174193135;G:169978598;T:201360184;N:143799	75	0	177832489	174193135	169978598	201360184	143799	ERX8620334	ERS10857222	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95218	0.11732	0.65916	0.47955	71	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10416	10416	ERR9077195	ERX8620334	ERS10857222	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT3S2	SAMEA13254179	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254179\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT3S2\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT3S2\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT3S2 s	Sv2aWT3S2 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT3S2L002-1.fastq.gz	fastq	726190024.0	9614674.0	E MTAB 11505:sv2aWT3S2L002	0:75.53 1:0	A:178408224;C:174776263;G:170820745;T:202047224;N:137568	75	0	178408224	174776263	170820745	202047224	137568	ERX8620334	ERS10857222	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95093	0.11567	0.65865	0.46877	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10417	10417	ERR9077196	ERX8620334	ERS10857222	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT3S2	SAMEA13254179	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254179\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT3S2\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT3S2\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT3S2 s	Sv2aWT3S2 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT3S2L003-1.fastq.gz	fastq	735499955.0	9737845.0	E MTAB 11505:sv2aWT3S2L003	0:75.53 1:0	A:180659962;C:177141362;G:172905323;T:204678308;N:115000	75	0	180659962	177141362	172905323	204678308	115000	ERX8620334	ERS10857222	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95233	0.11614	0.65898	0.47114	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10418	10418	ERR9077197	ERX8620334	ERS10857222	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT3S2	SAMEA13254179	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254179\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT3S2\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT3S2\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT3S2 s	Sv2aWT3S2 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT3S2L004-1.fastq.gz	fastq	745285512.0	9867337.0	E MTAB 11505:sv2aWT3S2L004	0:75.53 1:0	A:183067487;C:179408382;G:175250814;T:207445912;N:112917	75	0	183067487	179408382	175250814	207445912	112917	ERX8620334	ERS10857222	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95245	0.11655	0.65857	0.47087	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10419	10419	ERR9077190	ERX8620333	ERS10857221	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT1S1	SAMEA13254178	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254178\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT1S1\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT1S1\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT1S1 s	Sv2aWT1S1 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT1S1L001-1.fastq.gz	fastq	647414748.0	8571883.0	E MTAB 11505:sv2aWT1S1L001	0:75.53 1:0	A:154593859;C:160498057;G:153809612;T:178389112;N:124108	75	0	154593859	160498057	153809612	178389112	124108	ERX8620333	ERS10857221	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95955	0.08686	0.65955	0.47406	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10420	10420	ERR9077191	ERX8620333	ERS10857221	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT1S1	SAMEA13254178	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254178\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT1S1\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT1S1\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT1S1 s	Sv2aWT1S1 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT1S1L002-1.fastq.gz	fastq	646657758.0	8561861.0	E MTAB 11505:sv2aWT1S1L002	0:75.53 1:0	A:154348044;C:160294625;G:153804048;T:178092212;N:118829	75	0	154348044	160294625	153804048	178092212	118829	ERX8620333	ERS10857221	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95942	0.08632	0.65991	0.47539	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10421	10421	ERR9077192	ERX8620333	ERS10857221	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT1S1	SAMEA13254178	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254178\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT1S1\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT1S1\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT1S1 s	Sv2aWT1S1 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT1S1L003-1.fastq.gz	fastq	654781451.0	8669333.0	E MTAB 11505:sv2aWT1S1L003	0:75.53 1:0	A:156252744;C:162396721;G:155681450;T:180352911;N:97625	75	0	156252744	162396721	155681450	180352911	97625	ERX8620333	ERS10857221	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95972	0.08498	0.66137	0.47457	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10422	10422	ERR9077193	ERX8620333	ERS10857221	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aWT1S1	SAMEA13254178	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254178\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aWT1S1\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/+\|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aWT1S1\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aWT1S1 s	Sv2aWT1S1 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aWT1S1L004-1.fastq.gz	fastq	659716937.0	8734618.0	E MTAB 11505:sv2aWT1S1L004	0:75.53 1:0	A:157367211;C:163585842;G:156911139;T:181757809;N:94936	75	0	157367211	163585842	156911139	181757809	94936	ERX8620333	ERS10857221	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95985	0.08585	0.65857	0.47349	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10423	10423	ERR9077186	ERX8620332	ERS10857220	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHO6S12	SAMEA13254177	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254177\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHO6S12\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a / \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHO6S12\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHO6S12 s	Sv2aHO6S12 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a /	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHO6S12L001-1.fastq.gz	fastq	675018261.0	8937958.0	E MTAB 11505:sv2aHO6S12L001	0:75.52 1:0	A:166564263;C:160539328;G:160003980;T:187773509;N:137181	75	0	166564263	160539328	160003980	187773509	137181	ERX8620332	ERS10857220	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.94964	0.13009	0.65413	0.47079	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10424	10424	ERR9077187	ERX8620332	ERS10857220	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHO6S12	SAMEA13254177	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254177\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHO6S12\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a / \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHO6S12\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHO6S12 s	Sv2aHO6S12 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a /	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHO6S12L002-1.fastq.gz	fastq	672995667.0	8911161.0	E MTAB 11505:sv2aHO6S12L002	0:75.52 1:0	A:165990319;C:160039398;G:159722501;T:187108781;N:134668	75	0	165990319	160039398	159722501	187108781	134668	ERX8620332	ERS10857220	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.94837	0.13029	0.65744	0.47959	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10425	10425	ERR9077188	ERX8620332	ERS10857220	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHO6S12	SAMEA13254177	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254177\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHO6S12\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a / \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHO6S12\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHO6S12 s	Sv2aHO6S12 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a /	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHO6S12L003-1.fastq.gz	fastq	683276767.0	9047147.0	E MTAB 11505:sv2aHO6S12L003	0:75.52 1:0	A:168501690;C:162583852;G:162063190;T:190018001;N:110034	75	0	168501690	162583852	162063190	190018001	110034	ERX8620332	ERS10857220	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.94983	0.13248	0.6565	0.47977	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10426	10426	ERR9077189	ERX8620332	ERS10857220	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHO6S12	SAMEA13254177	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254177\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHO6S12\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a / \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHO6S12\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHO6S12 s	Sv2aHO6S12 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a /	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHO6S12L004-1.fastq.gz	fastq	686469910.0	9089431.0	E MTAB 11505:sv2aHO6S12L004	0:75.52 1:0	A:169287189;C:163276361;G:162844724;T:190954218;N:107418	75	0	169287189	163276361	162844724	190954218	107418	ERX8620332	ERS10857220	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95061	0.13029	0.65389	0.48044	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10427	10427	ERR9077182	ERX8620331	ERS10857219	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHO4S10	SAMEA13254176	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254176\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHO4S10\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a / \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHO4S10\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHO4S10 s	Sv2aHO4S10 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a /	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHO4S10L001-1.fastq.gz	fastq	713858966.0	9452474.0	E MTAB 11505:sv2aHO4S10L001	0:75.52 1:0	A:177913695;C:169425317;G:167540012;T:198835532;N:144410	75	0	177913695	169425317	167540012	198835532	144410	ERX8620331	ERS10857219	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.94848	0.12981	0.6636	0.47772	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10428	10428	ERR9077183	ERX8620331	ERS10857219	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHO4S10	SAMEA13254176	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254176\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHO4S10\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a / \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHO4S10\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHO4S10 s	Sv2aHO4S10 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a /	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHO4S10L002-1.fastq.gz	fastq	717619593.0	9502301.0	E MTAB 11505:sv2aHO4S10L002	0:75.52 1:0	A:178830542;C:170284720;G:168594514;T:199773382;N:136435	75	0	178830542	170284720	168594514	199773382	136435	ERX8620331	ERS10857219	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.94812	0.12868	0.6645	0.47281	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10429	10429	ERR9077184	ERX8620331	ERS10857219	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHO4S10	SAMEA13254176	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254176\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHO4S10\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a / \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHO4S10\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHO4S10 s	Sv2aHO4S10 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a /	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHO4S10L003-1.fastq.gz	fastq	727263626.0	9629858.0	E MTAB 11505:sv2aHO4S10L003	0:75.52 1:0	A:181201278;C:172619520;G:170780953;T:202550397;N:111478	75	0	181201278	172619520	170780953	202550397	111478	ERX8620331	ERS10857219	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.94768	0.12827	0.66596	0.47332	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10430	10430	ERR9077185	ERX8620331	ERS10857219	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHO4S10	SAMEA13254176	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254176\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHO4S10\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a / \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHO4S10\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHO4S10 s	Sv2aHO4S10 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a /	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHO4S10L004-1.fastq.gz	fastq	736595278.0	9753337.0	E MTAB 11505:sv2aHO4S10L004	0:75.52 1:0	A:183510872;C:174806534;G:173027794;T:205140640;N:109438	75	0	183510872	174806534	173027794	205140640	109438	ERX8620331	ERS10857219	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.94925	0.12904	0.66417	0.47297	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10431	10431	ERR9077178	ERX8620330	ERS10857218	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHO3S6	SAMEA13254175	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254175\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHO3S6\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a / \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHO3S6\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHO3S6 s	Sv2aHO3S6 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a /	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHO3S6L001-1.fastq.gz	fastq	710756305.0	9410862.0	E MTAB 11505:sv2aHO3S6L001	0:75.53 1:0	A:175585613;C:170261120;G:166658917;T:198106388;N:144267	75	0	175585613	170261120	166658917	198106388	144267	ERX8620330	ERS10857218	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.94827	0.14002	0.66785	0.474	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10432	10432	ERR9077179	ERX8620330	ERS10857218	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHO3S6	SAMEA13254175	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254175\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHO3S6\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a / \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHO3S6\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHO3S6 s	Sv2aHO3S6 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a /	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHO3S6L002-1.fastq.gz	fastq	715330324.0	9471415.0	E MTAB 11505:sv2aHO3S6L002	0:75.53 1:0	A:176679775;C:171311031;G:167903237;T:199299483;N:136798	75	0	176679775	171311031	167903237	199299483	136798	ERX8620330	ERS10857218	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.9469	0.13915	0.67004	0.47654	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10433	10433	ERR9077180	ERX8620330	ERS10857218	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHO3S6	SAMEA13254175	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254175\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHO3S6\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a / \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHO3S6\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHO3S6 s	Sv2aHO3S6 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a /	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHO3S6L003-1.fastq.gz	fastq	722810562.0	9570364.0	E MTAB 11505:sv2aHO3S6L003	0:75.53 1:0	A:178442845;C:173192786;G:169595085;T:201465522;N:114324	75	0	178442845	173192786	169595085	201465522	114324	ERX8620330	ERS10857218	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.94918	0.13979	0.66902	0.47572	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10434	10434	ERR9077181	ERX8620330	ERS10857218	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHO3S6	SAMEA13254175	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254175\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHO3S6\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a / \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHO3S6\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHO3S6 s	Sv2aHO3S6 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a /	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHO3S6L004-1.fastq.gz	fastq	732990507.0	9705054.0	E MTAB 11505:sv2aHO3S6L004	0:75.53 1:0	A:180951130;C:175567778;G:172037542;T:204323488;N:110569	75	0	180951130	175567778	172037542	204323488	110569	ERX8620330	ERS10857218	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.94812	0.13893	0.67085	0.47502	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10435	10435	ERR9077174	ERX8620329	ERS10857217	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET7S9	SAMEA13254174	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254174\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET7S9\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET7S9\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET7S9 s	Sv2aHET7S9 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET7S9L001-1.fastq.gz	fastq	773209432.0	10238087.0	E MTAB 11505:sv2aHET7S9L001	0:75.52 1:0	A:191962953;C:184699376;G:180774008;T:215620759;N:152336	75	0	191962953	184699376	180774008	215620759	152336	ERX8620329	ERS10857217	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95047	0.12485	0.65705	0.4775	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10436	10436	ERR9077175	ERX8620329	ERS10857217	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET7S9	SAMEA13254174	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254174\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET7S9\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET7S9\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET7S9 s	Sv2aHET7S9 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET7S9L002-1.fastq.gz	fastq	773106152.0	10236677.0	E MTAB 11505:sv2aHET7S9L002	0:75.52 1:0	A:191812833;C:184676419;G:180997547;T:215473732;N:145621	75	0	191812833	184676419	180997547	215473732	145621	ERX8620329	ERS10857217	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95016	0.12464	0.65482	0.47419	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10437	10437	ERR9077176	ERX8620329	ERS10857217	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET7S9	SAMEA13254174	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254174\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET7S9\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET7S9\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET7S9 s	Sv2aHET7S9 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET7S9L003-1.fastq.gz	fastq	783061051.0	10368445.0	E MTAB 11505:sv2aHET7S9L003	0:75.52 1:0	A:194289152;C:187108364;G:183177036;T:218370500;N:115999	75	0	194289152	187108364	183177036	218370500	115999	ERX8620329	ERS10857217	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95172	0.12488	0.65445	0.48157	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10438	10438	ERR9077177	ERX8620329	ERS10857217	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET7S9	SAMEA13254174	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254174\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET7S9\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET7S9\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET7S9 s	Sv2aHET7S9 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET7S9L004-1.fastq.gz	fastq	790150025.0	10462214.0	E MTAB 11505:sv2aHET7S9L004	0:75.52 1:0	A:196056500;C:188746833;G:184927588;T:220305922;N:113182	75	0	196056500	188746833	184927588	220305922	113182	ERX8620329	ERS10857217	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95285	0.12478	0.65551	0.4763	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10439	10439	ERR9077170	ERX8620328	ERS10857216	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET4S5	SAMEA13254173	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254173\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET4S5\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET4S5\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET4S5 s	Sv2aHET4S5 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET4S5L001-1.fastq.gz	fastq	685650097.0	9076481.0	E MTAB 11505:sv2aHET4S5L001	0:75.54 1:0	A:161812875;C:167870520;G:166985310;T:188850530;N:130862	75	0	161812875	167870520	166985310	188850530	130862	ERX8620328	ERS10857216	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95733	0.09974	0.65691	0.47392	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10440	10440	ERR9077171	ERX8620328	ERS10857216	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET4S5	SAMEA13254173	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254173\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET4S5\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET4S5\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET4S5 s	Sv2aHET4S5 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET4S5L002-1.fastq.gz	fastq	684402241.0	9059974.0	E MTAB 11505:sv2aHET4S5L002	0:75.54 1:0	A:161493428;C:167520248;G:166882054;T:188383816;N:122695	75	0	161493428	167520248	166882054	188383816	122695	ERX8620328	ERS10857216	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95537	0.09915	0.65719	0.48261	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10441	10441	ERR9077172	ERX8620328	ERS10857216	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET4S5	SAMEA13254173	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254173\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET4S5\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET4S5\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET4S5 s	Sv2aHET4S5 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET4S5L003-1.fastq.gz	fastq	694099126.0	9188245.0	E MTAB 11505:sv2aHET4S5L003	0:75.54 1:0	A:163727378;C:169989210;G:169143224;T:191137588;N:101726	75	0	163727378	169989210	169143224	191137588	101726	ERX8620328	ERS10857216	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95629	0.09861	0.65705	0.47187	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10442	10442	ERR9077173	ERX8620328	ERS10857216	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET4S5	SAMEA13254173	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254173\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET4S5\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET4S5\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET4S5 s	Sv2aHET4S5 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET4S5L004-1.fastq.gz	fastq	698753836.0	9249820.0	E MTAB 11505:sv2aHET4S5L004	0:75.54 1:0	A:164809473;C:171057633;G:170349692;T:192441413;N:95625	75	0	164809473	171057633	170349692	192441413	95625	ERX8620328	ERS10857216	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95613	0.09885	0.65798	0.47227	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10443	10443	ERR9077166	ERX8620327	ERS10857215	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET3S4	SAMEA13254172	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254172\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET3S4\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET3S4\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET3S4 s	Sv2aHET3S4 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET3S4L001-1.fastq.gz	fastq	691298605.0	9151512.0	E MTAB 11505:sv2aHET3S4L001	0:75.54 1:0	A:164743919;C:170752099;G:164763621;T:190912044;N:126922	75	0	164743919	170752099	164763621	190912044	126922	ERX8620327	ERS10857215	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95684	0.09604	0.6603	0.47285	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10444	10444	ERR9077167	ERX8620327	ERS10857215	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET3S4	SAMEA13254172	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254172\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET3S4\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET3S4\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET3S4 s	Sv2aHET3S4 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET3S4L002-1.fastq.gz	fastq	694080975.0	9188259.0	E MTAB 11505:sv2aHET3S4L002	0:75.54 1:0	A:165336810;C:171397273;G:165632321;T:191591872;N:122699	75	0	165336810	171397273	165632321	191591872	122699	ERX8620327	ERS10857215	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95612	0.09694	0.65993	0.46918	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10445	10445	ERR9077168	ERX8620327	ERS10857215	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET3S4	SAMEA13254172	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254172\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET3S4\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET3S4\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET3S4 s	Sv2aHET3S4 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET3S4L003-1.fastq.gz	fastq	703689889.0	9315387.0	E MTAB 11505:sv2aHET3S4L003	0:75.54 1:0	A:167575230;C:173881977;G:167845574;T:194289403;N:97705	75	0	167575230	173881977	167845574	194289403	97705	ERX8620327	ERS10857215	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.9577	0.09608	0.66042	0.47022	74	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10446	10446	ERR9077169	ERX8620327	ERS10857215	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET3S4	SAMEA13254172	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254172\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET3S4\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET3S4\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET3S4 s	Sv2aHET3S4 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET3S4L004-1.fastq.gz	fastq	712116538.0	9426961.0	E MTAB 11505:sv2aHET3S4L004	0:75.54 1:0	A:169598596;C:175885948;G:169866534;T:196669400;N:96060	75	0	169598596	175885948	169866534	196669400	96060	ERX8620327	ERS10857215	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95734	0.09716	0.66054	0.47257	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10447	10447	ERR9077162	ERX8620326	ERS10857214	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET2S3	SAMEA13254171	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254171\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET2S3\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET2S3\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET2S3 s	Sv2aHET2S3 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET2S3L001-1.fastq.gz	fastq	733440522.0	9709422.0	E MTAB 11505:sv2aHET2S3L001	0:75.54 1:0	A:173670000;C:181175353;G:175392793;T:203059256;N:143120	75	0	173670000	181175353	175392793	203059256	143120	ERX8620326	ERS10857214	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95885	0.08758	0.65393	0.47249	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10448	10448	ERR9077163	ERX8620326	ERS10857214	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET2S3	SAMEA13254171	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254171\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET2S3\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET2S3\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET2S3 s	Sv2aHET2S3 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET2S3L002-1.fastq.gz	fastq	732121929.0	9691967.0	E MTAB 11505:sv2aHET2S3L002	0:75.54 1:0	A:173332091;C:180805738;G:175271736;T:202574727;N:137637	75	0	173332091	180805738	175271736	202574727	137637	ERX8620326	ERS10857214	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95775	0.08879	0.6564	0.4718	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10449	10449	ERR9077164	ERX8620326	ERS10857214	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET2S3	SAMEA13254171	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254171\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET2S3\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET2S3\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET2S3 s	Sv2aHET2S3 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET2S3L003-1.fastq.gz	fastq	743488189.0	9842286.0	E MTAB 11505:sv2aHET2S3L003	0:75.54 1:0	A:175979238;C:183726319;G:177933958;T:205735955;N:112719	75	0	175979238	183726319	177933958	205735955	112719	ERX8620326	ERS10857214	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.9593	0.08716	0.65437	0.46976	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
10450	10450	ERR9077165	ERX8620326	ERS10857214	ERP135966	PRJEB51339	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E-MTAB-11505	Transcriptome Analysis	Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21		Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Sv2aHET2S3	SAMEA13254171	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg	ENA first public:2022 04 21\|ENA last update:2022 04 21\|External Id:SAMEA13254171\|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg\|INSDC first public:2022 04 21T00:32:07Z\|INSDC last update:2022 04 21T00:32:07Z\|INSDC status:public\|Submitter Id:E MTAB 11505:Sv2aHET2S3\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:sv2a+/ \|individual:pool of 10 heads\|organism part:head\|sample name:E MTAB 11505:Sv2aHET2S3\|sex:not available\|strain:AB								NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	E MTAB 11505:Sv2aHET2S3 s	Sv2aHET2S3 s	RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.	Experimental Factor: genotype:sv2a+/	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 500		ERP135966	NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae	ENA FIRST PUBLIC:2022 04 21\|ENA LAST UPDATE:2022 04 21	sv2aHET2S3L004-1.fastq.gz	fastq	747723481.0	9898304.0	E MTAB 11505:sv2aHET2S3L004	0:75.54 1:0	A:176935451;C:184684782;G:179046040;T:206946124;N:111084	75	0	176935451	184684782	179046040	206946124	111084	ERX8620326	ERS10857214	ERA9644804	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg\|European Nucleotide Archive	1	0.95934	0.08676	0.65533	0.47523	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	Belgium	2022-04-21	Larval	Larval	Head	Nervous System
32037	32037	SRR28992909	SRX24520261	SRS21267950	SRP506997	PRJNA1110229	Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability	PRJNA1110229	Other	Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.					Kcnd2 Wt1		strain:Casper\|age:5dpf\|collection date:2022 12 09\|geo loc name:USA: Boston MA\|sex:not applicable\|tissue:Head\|genotype:Kcnd2 Wt1\|BioSampleModel:Model organism or animal								RNA Seq of Danio Rerio: pools of isolated larval head	Kcnd2 Wt1	Kcnd2 Wt1	Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP506997			Kcnd2_Wt1.fq.gz	fastq	3386455050.0	22576367.0	Kcnd2 Wt1.fq.gz	0:150	A:967137430;C:730108913;G:738646978;T:950549427;N:12302	150		967137430	730108913	738646978	950549427	12302	SRX24520261	SRS21267950	SRA1863814	Boston Childrens Hospital\|Neurobiology	Boston Childrens Hospital							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2024-05-10	Larval	Larval	Head	Nervous System
32038	32038	SRR28992910	SRX24520260	SRS21267949	SRP506997	PRJNA1110229	Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability	PRJNA1110229	Other	Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.					Arfgef1 Hom3		strain:Casper\|age:5dpf\|collection date:2022 12 09\|geo loc name:USA: Boston MA\|sex:not applicable\|tissue:Head\|genotype:Arfgef1 Hom3\|BioSampleModel:Model organism or animal								RNA Seq of Danio Rerio: pools of isolated larval head	Arfgef1 Hom3	Arfgef1 Hom3	Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP506997			Arfgef1_Hom3.fq.gz	fastq	3647365500.0	24315770.0	Arfgef1 Hom3.fq.gz	0:150	A:923919033;C:903440333;G:911845870;T:908147370;N:12894	150		923919033	903440333	911845870	908147370	12894	SRX24520260	SRS21267949	SRA1863814	Boston Childrens Hospital\|Neurobiology	Boston Childrens Hospital							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2024-05-10	Larval	Larval	Head	Nervous System
32039	32039	SRR28992915	SRX24520258	SRS21267947	SRP506997	PRJNA1110229	Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability	PRJNA1110229	Other	Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.					Arfgef1 Hom1		strain:Casper\|age:5dpf\|collection date:2022 12 09\|geo loc name:USA: Boston MA\|sex:not applicable\|tissue:Head\|genotype:Arfgef1 Hom1\|BioSampleModel:Model organism or animal								RNA Seq of Danio Rerio: pools of isolated larval head	Arfgef1 Hom1	Arfgef1 Hom1	Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP506997			Arfgef1_Hom1.fq.gz	fastq	3388869300.0	22592462.0	Arfgef1 Hom1.fq.gz	0:150	A:869162615;C:827706442;G:835453288;T:856534517;N:12438	150		869162615	827706442	835453288	856534517	12438	SRX24520258	SRS21267947	SRA1863814	Boston Childrens Hospital\|Neurobiology	Boston Childrens Hospital							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2024-05-10	Larval	Larval	Head	Nervous System
32040	32040	SRR28992912	SRX24520257	SRS21267946	SRP506997	PRJNA1110229	Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability	PRJNA1110229	Other	Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.					Arfgef1 Het3		strain:Casper\|age:5dpf\|collection date:2022 12 09\|geo loc name:USA: Boston MA\|sex:not applicable\|tissue:Head\|genotype:Arfgef1 Het3\|BioSampleModel:Model organism or animal								RNA Seq of Danio Rerio: pools of isolated larval head	Arfgef1 Het3	Arfgef1 Het3	Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP506997			Arfgef1_Het3.fq.gz	fastq	3369996750.0	22466645.0	Arfgef1 Het3.fq.gz	0:150	A:861941573;C:824864964;G:833793356;T:849388791;N:8066	150		861941573	824864964	833793356	849388791	8066	SRX24520257	SRS21267946	SRA1863814	Boston Childrens Hospital\|Neurobiology	Boston Childrens Hospital							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2024-05-10	Larval	Larval	Head	Nervous System
32041	32041	SRR28992913	SRX24520256	SRS21267945	SRP506997	PRJNA1110229	Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability	PRJNA1110229	Other	Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.					Arfgef1 Het2		strain:Casper\|age:5dpf\|collection date:2022 12 09\|geo loc name:USA: Boston MA\|sex:not applicable\|tissue:Head\|genotype:Arfgef1 Het2\|BioSampleModel:Model organism or animal								RNA Seq of Danio Rerio: pools of isolated larval head	Arfgef1 Het2	Arfgef1 Het2	Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP506997			Arfgef1_Het2.fq.gz	fastq	4755406500.0	31702710.0	Arfgef1 Het2.fq.gz	0:150	A:1254995507;C:1127923454;G:1138127034;T:1234180808;N:179697	150		1254995507	1127923454	1138127034	1234180808	179697	SRX24520256	SRS21267945	SRA1863814	Boston Childrens Hospital\|Neurobiology	Boston Childrens Hospital							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2024-05-10	Larval	Larval	Head	Nervous System
32042	32042	SRR28992916	SRX24520254	SRS21267943	SRP506997	PRJNA1110229	Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability	PRJNA1110229	Other	Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.					Wnt8b Hom3		strain:Casper\|age:5dpf\|collection date:2022 12 09\|geo loc name:USA: Boston MA\|sex:not applicable\|tissue:Head\|genotype:Wnt8b Hom3\|BioSampleModel:Model organism or animal								RNA Seq of Danio Rerio: pools of isolated larval head	Wnt8b Hom3	Wnt8b Hom3	Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP506997			Wnt8b_Hom3.fq.gz	fastq	5283928950.0	35226193.0	Wnt8b Hom3.fq.gz	0:150	A:1389228037;C:1262004726;G:1265392219;T:1367105548;N:198420	150		1389228037	1262004726	1265392219	1367105548	198420	SRX24520254	SRS21267943	SRA1863814	Boston Childrens Hospital\|Neurobiology	Boston Childrens Hospital							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2024-05-10	Larval	Larval	Head	Nervous System
32043	32043	SRR28992919	SRX24520251	SRS21267940	SRP506997	PRJNA1110229	Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability	PRJNA1110229	Other	Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.					Wnt8b Het3		strain:Casper\|age:5dpf\|collection date:2022 12 09\|geo loc name:USA: Boston MA\|sex:not applicable\|tissue:Head\|genotype:Wnt8b Het3\|BioSampleModel:Model organism or animal								RNA Seq of Danio Rerio: pools of isolated larval head	Wnt8b Het3	Wnt8b Het3	Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP506997			Wnt8b_Het3.fq.gz	fastq	4357330950.0	29048873.0	Wnt8b Het3.fq.gz	0:150	A:1179652667;C:1002955689;G:1008147493;T:1166494534;N:80567	150		1179652667	1002955689	1008147493	1166494534	80567	SRX24520251	SRS21267940	SRA1863814	Boston Childrens Hospital\|Neurobiology	Boston Childrens Hospital							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2024-05-10	Larval	Larval	Head	Nervous System
36479	36479	SRR527834	SRX171221	SRS352107	SRP014596	PRJNA171539	Transcriptomic analysis of zebrafish during development and homeostasis	GSE39703	Transcriptome Analysis	Sequencing libraries were generated from total RNA samples following the mRNAseq protocol for the generation of single end 16 hpf 36 hpf 5 day larvae adult head and adult tail or paired end 24 hpf libraries Illumina. Single end reads of 36 nucleotides and paired end reads 2 x 76 nucleotides were obtained with a GAIIx Illumina. Gene expression at the different stages/tissu was assessed by cufflinks and HTseq. Overall design: RNAseq on 5 differents samples: 24hpf embryos pool of 16 hour to 36 hour embryos 5 dpf larvea adult head and adult tail		pubmed:23684812		head	GSM977959		tissue:entire adult head\|genotype:Wild type\|strain:AB\|Stage:adult head	head	Basecalls performed using CASAVA version 1.4 Reads aligned to zebrafish genome Zv9 Ensembl with Tophat v 1.4.1 and Bowtie v 0.12.7 options: butterfly search coverage search microexon search min anchor length 5 G GTF Determination of raw reads aligned to ZV9 with HTSeq v0.5.3p3 and gtf file ensembl zv9 release 60 Determination of RPKM/FPKM with cufflinks v 1.3.0 with the options u b M rRNA/Mtgenes mask G gtf Genome build: Zv9 v 60 Supplementary files format and content: .count file are the output of Htseq reads quantification. .fpkm files are the output of cufflinks quantification	entire adult head		Extraction of total RNA with Trizol following manufacturer's instruction. Generation of mRNA libraries with Trueseq RNA kit following Illumina's instructions	genotype:Wild type\|strain:AB\|Stage:adult head	GSM977959	GSM977959: head; Danio rerio; RNA Seq	GSM977959 1	GSM977959: head	1		GEO Accession:GSM977959	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014596					516054600.0	14334850.0	GSM977959 r1	0:36	A:144148482;C:115800670;G:121205261;T:134746787;N:153400	36		144148482	115800670	121205261	134746787	153400	SRX171221	SRS352107	SRA056408	GEO	ITG	1	0.89668	0.12577	0.66803	0.45871	36	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2012-07-27	Adult	Adult	Head	Nervous System
39887	39887	SRR2239197	SRX1181673	SRS1053962	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		mutant 5 hr treatment replicate 3	GSM1868446		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:metronidazole\|time:5 hr\|tissue:head	mutant 5 hr treatment replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868446	GSM1868446: mutant 5 hr treatment replicate 3; Danio rerio; RNA Seq	GSM1868446		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868446	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1349_s_3_withindex_sequence.txt_AGGCGAA.fq.gz	fastq	1486758800.0	29735176.0	GSM1868446 r1	0:50	A:407157206;C:348516474;G:333581236;T:397373823;N:130061	50		407157206	348516474	333581236	397373823	130061	SRX1181673	SRS1053962	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89356	0.24716	0.66348	0.55072	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39888	39888	SRR2239196	SRX1181672	SRS1053963	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		mutant 5 hr treatment replicate 2	GSM1868445		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:metronidazole\|time:5 hr\|tissue:head	mutant 5 hr treatment replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868445	GSM1868445: mutant 5 hr treatment replicate 2; Danio rerio; RNA Seq	GSM1868445		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868445	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1349_s_3_withindex_sequence.txt_AATTCAT.fq.gz	fastq	1324305100.0	26486102.0	GSM1868445 r1	0:50	A:346866338;C:322967018;G:303987755;T:350367920;N:116069	50		346866338	322967018	303987755	350367920	116069	SRX1181672	SRS1053963	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.86992	0.2794	0.67087	0.45	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39889	39889	SRR2239195	SRX1181671	SRS1053965	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		mutant 5 hr treatment replicate 1	GSM1868444		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:metronidazole\|time:5 hr\|tissue:head	mutant 5 hr treatment replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868444	GSM1868444: mutant 5 hr treatment replicate 1; Danio rerio; RNA Seq	GSM1868444		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868444	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1349_s_3_withindex_sequence.txt_CTGCAAT.fq.gz	fastq	1996223000.0	39924460.0	GSM1868444 r1	0:50	A:548376523;C:462971670;G:439194387;T:545504649;N:175771	50		548376523	462971670	439194387	545504649	175771	SRX1181671	SRS1053965	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.90072	0.27661	0.66809	0.54999	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39890	39890	SRR2239194	SRX1181670	SRS1053966	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		mutant control replicate 3	GSM1868443		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:control\|tissue:head	mutant control replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:control\|tissue:head	GSM1868443	GSM1868443: mutant control replicate 3; Danio rerio; RNA Seq	GSM1868443		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868443	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1349_s_3_withindex_sequence.txt_GTAAAAA.fq.gz	fastq	1689695100.0	33793902.0	GSM1868443 r1	0:50	A:469281850;C:387188418;G:368970934;T:464103273;N:150625	50		469281850	387188418	368970934	464103273	150625	SRX1181670	SRS1053966	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.88353	0.30543	0.66785	0.53952	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39891	39891	SRR2239193	SRX1181669	SRS1053964	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		mutant control replicate 2	GSM1868442		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:control\|tissue:head	mutant control replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:control\|tissue:head	GSM1868442	GSM1868442: mutant control replicate 2; Danio rerio; RNA Seq	GSM1868442		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868442	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1349_s_3_withindex_sequence.txt_TGGCATA.fq.gz	fastq	1744754500.0	34895090.0	GSM1868442 r1	0:50	A:475432211;C:407457752;G:387941759;T:473768506;N:154272	50		475432211	407457752	387941759	473768506	154272	SRX1181669	SRS1053964	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.8967	0.27571	0.66342	0.5413	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39892	39892	SRR2239192	SRX1181668	SRS1053967	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		mutant control replicate 1	GSM1868441		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:control\|tissue:head	mutant control replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:foxd3 / \|agent:control\|tissue:head	GSM1868441	GSM1868441: mutant control replicate 1; Danio rerio; RNA Seq	GSM1868441		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868441	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1349_s_3_withindex_sequence.txt_GGAGTCC.fq.gz	fastq	1300091300.0	26001826.0	GSM1868441 r1	0:50	A:356312292;C:301731841;G:287159447;T:354773803;N:113917	50		356312292	301731841	287159447	354773803	113917	SRX1181668	SRS1053967	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89407	0.27485	0.66263	0.54402	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39893	39893	SRR2239190	SRX1181667	SRS1053968	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 5 hr treatment replicate 3	GSM1868440		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	wild type 5 hr treatment replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868440	GSM1868440: wild type 5 hr treatment replicate 3; Danio rerio; RNA Seq	GSM1868440		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868440	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_GGTCCTC.fq.gz	fastq	788127550.0	15762551.0	GSM1868440 r1	0:50	A:219123307;C:174342061;G:168810140;T:225814483;N:37559	50		219123307	174342061	168810140	225814483	37559	SRX1181667	SRS1053968	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89391	0.27826	0.67034	0.55775	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39894	39894	SRR2239191	SRX1181667	SRS1053968	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 5 hr treatment replicate 3	GSM1868440		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	wild type 5 hr treatment replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868440	GSM1868440: wild type 5 hr treatment replicate 3; Danio rerio; RNA Seq	GSM1868440		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868440	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_GGTCCTC.fq.gz	fastq	779058950.0	15581179.0	GSM1868440 r2	0:50	A:216843690;C:172197112;G:166801096;T:223172377;N:44675	50		216843690	172197112	166801096	223172377	44675	SRX1181667	SRS1053968	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89268	0.27974	0.67067	0.55617	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39895	39895	SRR2239188	SRX1181666	SRS1053969	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 5 hr treatment replicate 2	GSM1868439		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	wild type 5 hr treatment replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868439	GSM1868439: wild type 5 hr treatment replicate 2; Danio rerio; RNA Seq	GSM1868439		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868439	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_GCTTAGA.fq.gz	fastq	884810450.0	17696209.0	GSM1868439 r1	0:50	A:244801024;C:196884736;G:189692109;T:253390454;N:42127	50		244801024	196884736	189692109	253390454	42127	SRX1181666	SRS1053969	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89625	0.26571	0.66247	0.52896	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39896	39896	SRR2239189	SRX1181666	SRS1053969	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 5 hr treatment replicate 2	GSM1868439		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	wild type 5 hr treatment replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868439	GSM1868439: wild type 5 hr treatment replicate 2; Danio rerio; RNA Seq	GSM1868439		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868439	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_GCTTAGA.fq.gz	fastq	875476350.0	17509527.0	GSM1868439 r2	0:50	A:242411986;C:194719083;G:187698234;T:250595738;N:51309	50		242411986	194719083	187698234	250595738	51309	SRX1181666	SRS1053969	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89632	0.26574	0.66332	0.53633	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39897	39897	SRR2239186	SRX1181665	SRS1053970	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 5 hr treatment replicate 1	GSM1868438		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	wild type 5 hr treatment replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868438	GSM1868438: wild type 5 hr treatment replicate 1; Danio rerio; RNA Seq	GSM1868438		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868438	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_GTCGATA.fq.gz	fastq	981479900.0	19629598.0	GSM1868438 r1	0:50	A:272447863;C:217586061;G:210457740;T:280941539;N:46697	50		272447863	217586061	210457740	280941539	46697	SRX1181665	SRS1053970	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89259	0.28519	0.66413	0.54434	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39898	39898	SRR2239187	SRX1181665	SRS1053970	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 5 hr treatment replicate 1	GSM1868438		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	wild type 5 hr treatment replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:5 hr\|tissue:head	GSM1868438	GSM1868438: wild type 5 hr treatment replicate 1; Danio rerio; RNA Seq	GSM1868438		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868438	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_GTCGATA.fq.gz	fastq	970627300.0	19412546.0	GSM1868438 r2	0:50	A:269587370;C:215107358;G:208077535;T:277799059;N:55978	50		269587370	215107358	208077535	277799059	55978	SRX1181665	SRS1053970	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.8924	0.2863	0.66486	0.54277	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39899	39899	SRR2239184	SRX1181664	SRS1053971	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 2 hr treatment replicate 3	GSM1868437		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	wild type 2 hr treatment replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	GSM1868437	GSM1868437: wild type 2 hr treatment replicate 3; Danio rerio; RNA Seq	GSM1868437		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868437	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_AGATACT.fq.gz	fastq	1034107450.0	20682149.0	GSM1868437 r1	0:50	A:263807622;C:250451504;G:242163638;T:277636652;N:48034	50		263807622	250451504	242163638	277636652	48034	SRX1181664	SRS1053971	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.90878	0.23218	0.65916	0.49411	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39900	39900	SRR2239185	SRX1181664	SRS1053971	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 2 hr treatment replicate 3	GSM1868437		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	wild type 2 hr treatment replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	GSM1868437	GSM1868437: wild type 2 hr treatment replicate 3; Danio rerio; RNA Seq	GSM1868437		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868437	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_AGATACT.fq.gz	fastq	1021705150.0	20434103.0	GSM1868437 r2	0:50	A:260838269;C:247381617;G:239188036;T:274238961;N:58267	50		260838269	247381617	239188036	274238961	58267	SRX1181664	SRS1053971	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.91116	0.23255	0.65918	0.49596	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39901	39901	SRR2239182	SRX1181663	SRS1053972	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 2 hr treatment replicate 2	GSM1868436		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	wild type 2 hr treatment replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	GSM1868436	GSM1868436: wild type 2 hr treatment replicate 2; Danio rerio; RNA Seq	GSM1868436		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868436	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_GGGTCAA.fq.gz	fastq	756008650.0	15120173.0	GSM1868436 r1	0:50	A:209261412;C:168123618;G:163450516;T:215134424;N:38680	50		209261412	168123618	163450516	215134424	38680	SRX1181663	SRS1053972	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.8978	0.26699	0.66172	0.53653	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39902	39902	SRR2239183	SRX1181663	SRS1053972	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 2 hr treatment replicate 2	GSM1868436		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	wild type 2 hr treatment replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	GSM1868436	GSM1868436: wild type 2 hr treatment replicate 2; Danio rerio; RNA Seq	GSM1868436		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868436	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_GGGTCAA.fq.gz	fastq	747959000.0	14959180.0	GSM1868436 r2	0:50	A:207110574;C:166254650;G:161670187;T:212878047;N:45542	50		207110574	166254650	161670187	212878047	45542	SRX1181663	SRS1053972	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89508	0.26657	0.66373	0.53734	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39903	39903	SRR2239180	SRX1181662	SRS1053973	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 2 hr treatment replicate 1	GSM1868435		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	wild type 2 hr treatment replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	GSM1868435	GSM1868435: wild type 2 hr treatment replicate 1; Danio rerio; RNA Seq	GSM1868435		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868435	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_CAATATC.fq.gz	fastq	843938700.0	16878774.0	GSM1868435 r1	0:50	A:235353785;C:185755129;G:180220044;T:242567413;N:42329	50		235353785	185755129	180220044	242567413	42329	SRX1181662	SRS1053973	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.8819	0.31587	0.6719	0.53852	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39904	39904	SRR2239181	SRX1181662	SRS1053973	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type 2 hr treatment replicate 1	GSM1868435		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	wild type 2 hr treatment replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:metronidazole\|time:2 hr\|tissue:head	GSM1868435	GSM1868435: wild type 2 hr treatment replicate 1; Danio rerio; RNA Seq	GSM1868435		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868435	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_CAATATC.fq.gz	fastq	837375500.0	16747510.0	GSM1868435 r2	0:50	A:233691274;C:184249473;G:178762050;T:240622009;N:50694	50		233691274	184249473	178762050	240622009	50694	SRX1181662	SRS1053973	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.88228	0.31306	0.67042	0.53933	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39905	39905	SRR2239178	SRX1181661	SRS1053976	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type control replicate 3	GSM1868434		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	wild type control replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	GSM1868434	GSM1868434: wild type control replicate 3; Danio rerio; RNA Seq	GSM1868434		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868434	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_ACCCACT.fq.gz	fastq	946427500.0	18928550.0	GSM1868434 r1	0:50	A:260851494;C:211313068;G:205344403;T:268874280;N:44255	50		260851494	211313068	205344403	268874280	44255	SRX1181661	SRS1053976	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89626	0.27082	0.66058	0.53343	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39906	39906	SRR2239179	SRX1181661	SRS1053976	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type control replicate 3	GSM1868434		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	wild type control replicate 3	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	GSM1868434	GSM1868434: wild type control replicate 3; Danio rerio; RNA Seq	GSM1868434		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868434	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_ACCCACT.fq.gz	fastq	935318450.0	18706369.0	GSM1868434 r2	0:50	A:258004973;C:208706255;G:202911059;T:265642847;N:53316	50		258004973	208706255	202911059	265642847	53316	SRX1181661	SRS1053976	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89576	0.27216	0.663	0.53587	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39907	39907	SRR2239176	SRX1181660	SRS1053974	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type control replicate 2	GSM1868433		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	wild type control replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	GSM1868433	GSM1868433: wild type control replicate 2; Danio rerio; RNA Seq	GSM1868433		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868433	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_TCAACTG.fq.gz	fastq	914021500.0	18280430.0	GSM1868433 r1	0:50	A:252009242;C:204125475;G:197760562;T:260083313;N:42908	50		252009242	204125475	197760562	260083313	42908	SRX1181660	SRS1053974	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89646	0.26998	0.65979	0.53202	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39908	39908	SRR2239177	SRX1181660	SRS1053974	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type control replicate 2	GSM1868433		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	wild type control replicate 2	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	GSM1868433	GSM1868433: wild type control replicate 2; Danio rerio; RNA Seq	GSM1868433		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868433	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_TCAACTG.fq.gz	fastq	904836300.0	18096726.0	GSM1868433 r2	0:50	A:249726925;C:201939252;G:195727802;T:257389594;N:52727	50		249726925	201939252	195727802	257389594	52727	SRX1181660	SRS1053974	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89504	0.27105	0.6607	0.5314	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39909	39909	SRR2239174	SRX1181659	SRS1053975	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type control replicate 1	GSM1868432		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	wild type control replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	GSM1868432	GSM1868432: wild type control replicate 1; Danio rerio; RNA Seq	GSM1868432		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868432	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_6_withindex_sequence.txt_TTTAACT.fq.gz	fastq	919147800.0	18382956.0	GSM1868432 r1	0:50	A:255238211;C:203629686;G:197780664;T:262454873;N:44366	50		255238211	203629686	197780664	262454873	44366	SRX1181659	SRS1053975	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89498	0.2793	0.6636	0.54563	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
39910	39910	SRR2239175	SRX1181659	SRS1053975	SRP063290	PRJNA294660	Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish	GSE72682	Transcriptome Analysis	Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.		pubmed:26863206		wild type control replicate 1	GSM1868432		source name:head\|age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	wild type control replicate 1	Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs	head	For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	age:4 dpf\|developmental stage:larvae\|genotype/variation:AB wild type\|agent:control\|tissue:head	GSM1868432	GSM1868432: wild type control replicate 1; Danio rerio; RNA Seq	GSM1868432		1	Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.	GEO Accession:GSM1868432	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP063290			run_1266_s_7_withindex_sequence.txt_TTTAACT.fq.gz	fastq	908786950.0	18175739.0	GSM1868432 r2	0:50	A:252518589;C:201251252;G:195514386;T:259449857;N:52866	50		252518589	201251252	195514386	259449857	52866	SRX1181659	SRS1053975	SRA294351	GEO	Voigt, Pharmacology and Physiology, Saint Louis University	1	0.89351	0.27857	0.66492	0.54418	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	ribozero	bulk	unknown	unknown	United States	2015-09-03	Larval	Larval	Head	Nervous System
41655	41655	SRR5115728	SRX2431099	SRS1866976	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		18 hpi rep5	GSM2430667		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	18 hpi rep5	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	GSM2430667	GSM2430667: 18 hpi rep5; Danio rerio; RNA Seq	GSM2430667		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430667	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			18hpi_54366.fastq.gz	fastq	3043532908.0	58529479.0	GSM2430667 r1	0:52	A:729034781;C:769509924;G:743085356;T:801831768;N:71079	52		729034781	769509924	743085356	801831768	71079	SRX2431099	SRS1866976	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.73906	0.22225	0.74061	0.49988	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41656	41656	SRR5115727	SRX2431098	SRS1866975	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		18 hpi rep4	GSM2430666		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	18 hpi rep4	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	GSM2430666	GSM2430666: 18 hpi rep4; Danio rerio; RNA Seq	GSM2430666		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430666	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			18hpi_48592.fastq.gz	fastq	2622132240.0	50425620.0	GSM2430666 r1	0:52	A:566371236;C:777180578;G:659521124;T:618999154;N:60148	52		566371236	777180578	659521124	618999154	60148	SRX2431098	SRS1866975	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.92057	0.28475	0.86833	0.72823	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41657	41657	SRR5115726	SRX2431097	SRS1866974	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		18 hpi rep3	GSM2430665		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	18 hpi rep3	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	GSM2430665	GSM2430665: 18 hpi rep3; Danio rerio; RNA Seq	GSM2430665		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430665	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			18hpi_48591.fastq.gz	fastq	2478119176.0	47656138.0	GSM2430665 r1	0:52	A:493736890;C:768557459;G:661870968;T:553896608;N:57251	52		493736890	768557459	661870968	553896608	57251	SRX2431097	SRS1866974	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.96537	0.26164	0.87892	0.7204	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41658	41658	SRR5115725	SRX2431096	SRS1866973	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		18 hpi rep2	GSM2430664		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	18 hpi rep2	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	GSM2430664	GSM2430664: 18 hpi rep2; Danio rerio; RNA Seq	GSM2430664		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430664	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			18hpi_48590.fastq.gz	fastq	2414695452.0	46436451.0	GSM2430664 r1	0:52	A:475090050;C:755838280;G:657771658;T:525939134;N:56330	52		475090050	755838280	657771658	525939134	56330	SRX2431096	SRS1866973	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.9654	0.26982	0.89676	0.72161	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41659	41659	SRR5115724	SRX2431095	SRS1866972	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		18 hpi rep1	GSM2430663		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	18 hpi rep1	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:18	GSM2430663	GSM2430663: 18 hpi rep1; Danio rerio; RNA Seq	GSM2430663		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430663	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			18hpi_48589.fastq.gz	fastq	2275983060.0	43768905.0	GSM2430663 r1	0:52	A:466133336;C:694614756;G:598071579;T:517110546;N:52843	52		466133336	694614756	598071579	517110546	52843	SRX2431095	SRS1866972	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.94909	0.2695	0.86809	0.70019	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41660	41660	SRR5115723	SRX2431094	SRS1866971	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		9 hpi rep5	GSM2430662		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	9 hpi rep5	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	GSM2430662	GSM2430662: 9 hpi rep5; Danio rerio; RNA Seq	GSM2430662		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430662	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			9hpi_54368.fastq.gz	fastq	2831111348.0	54444449.0	GSM2430662 r1	0:52	A:674270099;C:713818041;G:694997603;T:747958840;N:66765	52		674270099	713818041	694997603	747958840	66765	SRX2431094	SRS1866971	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.81449	0.24117	0.74091	0.53961	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41661	41661	SRR5115722	SRX2431093	SRS1866970	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		9 hpi rep4	GSM2430661		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	9 hpi rep4	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	GSM2430661	GSM2430661: 9 hpi rep4; Danio rerio; RNA Seq	GSM2430661		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430661	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			9hpi_48586.fastq.gz	fastq	3247890880.0	62459440.0	GSM2430661 r1	0:52	A:737775958;C:866361850;G:806031275;T:837644754;N:77043	52		737775958	866361850	806031275	837644754	77043	SRX2431093	SRS1866970	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.88824	0.26531	0.77619	0.64707	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41662	41662	SRR5115721	SRX2431092	SRS1866969	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		9 hpi rep3	GSM2430660		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	9 hpi rep3	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	GSM2430660	GSM2430660: 9 hpi rep3; Danio rerio; RNA Seq	GSM2430660		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430660	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			9hpi_48585.fastq.gz	fastq	2383588948.0	45838249.0	GSM2430660 r1	0:52	A:471509922;C:736118462;G:639172021;T:536732824;N:55719	52		471509922	736118462	639172021	536732824	55719	SRX2431092	SRS1866969	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.96831	0.25406	0.88327	0.69186	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41663	41663	SRR5115720	SRX2431091	SRS1866968	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		9 hpi rep2	GSM2430659		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	9 hpi rep2	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	GSM2430659	GSM2430659: 9 hpi rep2; Danio rerio; RNA Seq	GSM2430659		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430659	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			9hpi_48584.fastq.gz	fastq	2858494184.0	54971042.0	GSM2430659 r1	0:52	A:601123087;C:841668883;G:744364922;T:671270980;N:66312	52		601123087	841668883	744364922	671270980	66312	SRX2431091	SRS1866968	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.93531	0.28407	0.86277	0.73297	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41664	41664	SRR5115719	SRX2431090	SRS1866967	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		9 hpi rep1	GSM2430658		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	9 hpi rep1	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:9	GSM2430658	GSM2430658: 9 hpi rep1; Danio rerio; RNA Seq	GSM2430658		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430658	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			9hpi_48583.fastq.gz	fastq	2348023808.0	45154304.0	GSM2430658 r1	0:52	A:520788777;C:655035758;G:589264364;T:582879912;N:54997	52		520788777	655035758	589264364	582879912	54997	SRX2431090	SRS1866967	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.90637	0.26958	0.80649	0.68165	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41665	41665	SRR5115718	SRX2431089	SRS1866966	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		0 hpi rep4	GSM2430657		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	0 hpi rep4	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	GSM2430657	GSM2430657: 0 hpi rep4; Danio rerio; RNA Seq	GSM2430657		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430657	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			0hpi_54367.fastq.gz	fastq	3737365060.0	71872405.0	GSM2430657 r1	0:52	A:898855616;C:929504130;G:883445728;T:1025471492;N:88094	52		898855616	929504130	883445728	1025471492	88094	SRX2431089	SRS1866966	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.80824	0.21971	0.75511	0.45635	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41666	41666	SRR5115717	SRX2431088	SRS1866965	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		0 hpi rep3	GSM2430656		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	0 hpi rep3	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	GSM2430656	GSM2430656: 0 hpi rep3; Danio rerio; RNA Seq	GSM2430656		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430656	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			0hpi_54365.fastq.gz	fastq	2479423440.0	47681220.0	GSM2430656 r1	0:52	A:585035619;C:641794408;G:600148220;T:652388942;N:56251	52		585035619	641794408	600148220	652388942	56251	SRX2431088	SRS1866965	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.7459	0.20704	0.76674	0.44617	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41667	41667	SRR5115716	SRX2431087	SRS1866964	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		0 hpi rep2	GSM2430655		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	0 hpi rep2	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	GSM2430655	GSM2430655: 0 hpi rep2; Danio rerio; RNA Seq	GSM2430655		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430655	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			0hpi_48587.fastq.gz	fastq	2251744196.0	43302773.0	GSM2430655 r1	0:52	A:446930339;C:692500195;G:602614693;T:509646110;N:52859	52		446930339	692500195	602614693	509646110	52859	SRX2431087	SRS1866964	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.96295	0.25309	0.90035	0.717	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
41668	41668	SRR5115715	SRX2431086	SRS1866963	SRP095238	PRJNA357683	Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A “Post Mitotic” Cell	GSE92489	Transcriptome Analysis	Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 µg total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic “switch like” expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a “post mitotic” myocyte into a dedifferentiated myoblast requir…		pubmed:29121865		0 hpi rep1	GSM2430654		source name:lateral rectus EOM\|genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	0 hpi rep1	We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: “ b2 very sensitive” telling the software to spend extra time searching for valid alignments and “ max intron length” of 400 kbs. Novel transcript discovery was not performed employing “ no coverage search” and “ no novel juncs” to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: “ multi read correct” to adjust expression calculations for reads that map in more than one locus as well as “ compatible hits norm” and “ upper quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files	lateral rectus EOM		Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	genotype:actin:GFP\|tissue:lateral rectus EOM\|xxx post injury:0	GSM2430654	GSM2430654: 0 hpi rep1; Danio rerio; RNA Seq	GSM2430654		1	Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2430654	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP095238			0hpi_44113.fastq.gz	fastq	2656056728.0	51078014.0	GSM2430654 r1	0:52	A:652742098;C:649243306;G:612049135;T:741907471;N:114718	52		652742098	649243306	612049135	741907471	114718	SRX2431086	SRS1866963	SRA504806	GEO	Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan	1	0.85198	0.24059	0.73357	0.48804	52	B	usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	United States	2016-12-16	Undetermined	Adult	Head	Nervous System
48776	48776	SRR7299203	SRX4201637	SRS3411871	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		WT3b	GSM3188319		source name:Wildtype head\|strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	WT3b	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	Wildtype head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188319	GSM3188319: WT3b; Danio rerio; RNA Seq	GSM3188319		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188319	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			4_WT_GTGAAA_L002_R1_001.fastq.gz	fastq	1515830415.0	29722165.0	GSM3188319 r1	0:51 1:0	A:394794389;C:366496372;G:355480667;T:399049574;N:9413	51	0	394794389	366496372	355480667	399049574	9413	SRX4201637	SRS3411871	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91648	0.0991	0.66042	0.46623	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48777	48777	SRR7299202	SRX4201636	SRS3411870	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		WT3a	GSM3188318		source name:Wildtype head\|strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	WT3a	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	Wildtype head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188318	GSM3188318: WT3a; Danio rerio; RNA Seq	GSM3188318		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188318	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			4_WT_GTGAAA_L001_R1_001.fastq.gz	fastq	1530012342.0	30000242.0	GSM3188318 r1	0:51 1:0	A:398681114;C:369811969;G:358638504;T:402843884;N:36871	51	0	398681114	369811969	358638504	402843884	36871	SRX4201636	SRS3411870	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91534	0.09956	0.65827	0.46141	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48778	48778	SRR7299201	SRX4201635	SRS3411869	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		WT2b	GSM3188317		source name:Wildtype head\|strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	WT2b	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	Wildtype head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188317	GSM3188317: WT2b; Danio rerio; RNA Seq	GSM3188317		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188317	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			3_WT_CAGATC_L002_R1_001.fastq.gz	fastq	1369591128.0	26854728.0	GSM3188317 r1	0:51 1:0	A:357550847;C:329596101;G:321156412;T:361279585;N:8183	51	0	357550847	329596101	321156412	361279585	8183	SRX4201635	SRS3411869	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91614	0.1006	0.66103	0.45858	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48779	48779	SRR7299200	SRX4201634	SRS3411868	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		WT2a	GSM3188316		source name:Wildtype head\|strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	WT2a	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	Wildtype head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188316	GSM3188316: WT2a; Danio rerio; RNA Seq	GSM3188316		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188316	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			3_WT_CAGATC_L001_R1_001.fastq.gz	fastq	1382657328.0	27110928.0	GSM3188316 r1	0:51 1:0	A:361162409;C:332612483;G:324077790;T:364769956;N:34690	51	0	361162409	332612483	324077790	364769956	34690	SRX4201634	SRS3411868	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91539	0.10075	0.65817	0.4455	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48780	48780	SRR7299199	SRX4201633	SRS3411867	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		WT1b	GSM3188315		source name:Wildtype head\|strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	WT1b	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	Wildtype head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188315	GSM3188315: WT1b; Danio rerio; RNA Seq	GSM3188315		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188315	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			1_WT_ACAGTG_L002_R1_001.fastq.gz	fastq	1524014640.0	29882640.0	GSM3188315 r1	0:51 1:0	A:396270551;C:368829474;G:359483222;T:399422211;N:9182	51	0	396270551	368829474	359483222	399422211	9182	SRX4201633	SRS3411867	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91922	0.09077	0.65447	0.45526	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48781	48781	SRR7299198	SRX4201632	SRS3411866	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		WT1a	GSM3188314		source name:Wildtype head\|strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	WT1a	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	Wildtype head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	strain/background:WIK\|genotype/variation:wildtype +/+\|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188314	GSM3188314: WT1a; Danio rerio; RNA Seq	GSM3188314		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188314	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			1_WT_ACAGTG_L001_R1_001.fastq.gz	fastq	1538497671.0	30166621.0	GSM3188314 r1	0:51 1:0	A:400221457;C:372214397;G:362764636;T:403260458;N:36723	51	0	400221457	372214397	362764636	403260458	36723	SRX4201632	SRS3411866	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91885	0.09093	0.65529	0.45611	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48782	48782	SRR7299197	SRX4201631	SRS3411865	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		Mut3b	GSM3188313		source name:rb1 homozygous mutant head\|strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	Mut3b	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	rb1 homozygous mutant head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188313	GSM3188313: Mut3b; Danio rerio; RNA Seq	GSM3188313		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188313	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			4_HOM_CTTGTA_L002_R1_001.fastq.gz	fastq	1461642252.0	28659652.0	GSM3188313 r1	0:51 1:0	A:378302770;C:355129502;G:346531981;T:381669069;N:8930	51	0	378302770	355129502	346531981	381669069	8930	SRX4201631	SRS3411865	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.92266	0.08429	0.65376	0.47318	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48783	48783	SRR7299196	SRX4201630	SRS3411864	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		Mut3a	GSM3188312		source name:rb1 homozygous mutant head\|strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	Mut3a	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	rb1 homozygous mutant head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188312	GSM3188312: Mut3a; Danio rerio; RNA Seq	GSM3188312		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188312	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			4_HOM_CTTGTA_L001_R1_001.fastq.gz	fastq	1475994978.0	28941078.0	GSM3188312 r1	0:51 1:0	A:382182767;C:358528625;G:349827681;T:385419945;N:35960	51	0	382182767	358528625	349827681	385419945	35960	SRX4201630	SRS3411864	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.92088	0.0857	0.65525	0.47511	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48784	48784	SRR7299195	SRX4201629	SRS3411863	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		Mut2b	GSM3188311		source name:rb1 homozygous mutant head\|strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	Mut2b	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	rb1 homozygous mutant head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188311	GSM3188311: Mut2b; Danio rerio; RNA Seq	GSM3188311		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188311	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			3_HOM_GCCAAT_L002_R1_001.fastq.gz	fastq	1590786798.0	31191898.0	GSM3188311 r1	0:51 1:0	A:415295793;C:382664391;G:373902522;T:418914651;N:9441	51	0	415295793	382664391	373902522	418914651	9441	SRX4201629	SRS3411863	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91457	0.10759	0.65675	0.45366	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System
48785	48785	SRR7299194	SRX4201628	SRS3411862	SRP150379	PRJNA475808	Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq	GSE115720	Transcriptome Analysis	The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries.	parent bioproject:PRJNA475805	pubmed:29914980		Mut2a	GSM3188310		source name:rb1 homozygous mutant head\|strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	Mut2a	Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics.	rb1 homozygous mutant head		Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	strain/background:WIK\|genotype/variation:rb1 / \|age:5 dpf larva\|tissue:5 pooled dissected heads	GSM3188310	GSM3188310: Mut2a; Danio rerio; RNA Seq	GSM3188310		1	Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA.	GEO Accession:GSM3188310	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP150379			3_HOM_GCCAAT_L001_R1_001.fastq.gz	fastq	1605491628.0	31480228.0	GSM3188310 r1	0:51 1:0	A:419379536;C:386061723;G:377175409;T:422836209;N:38751	51	0	419379536	386061723	377175409	422836209	38751	SRX4201628	SRS3411862	SRA720942	GEO	Maura McGrail, GDCB, Iowa State University	1	0.91489	0.10727	0.65695	0.45692	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2018-06-12	Larval	Larval	Head	Nervous System

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