metadata: run_metadata: 38 rows where devstage_curation_coarse = "Adult" and tissue

38 rows where devstage_curation_coarse = "Adult" 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.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
7950	7950	ERR015567	ERX005930	ERS000089	ERP000263	PRJEB2208	Zebrafish gene three prime end pull down for genome annotation	E-MTAB-308	Transcriptome Analysis			RNA extracted from male adult zebrafish head		SAMEA708835	SC	ENA FIRST PUBLIC:2010 02 26T10:44:13Z\|ENA LAST UPDATE:2018 03 08T15:51:30Z\|External Id:SAMEA708835\|INSDC center name:SC\|INSDC first public:2010 02 26T10:44:13Z\|INSDC last update:2018 03 08T15:51:30Z\|INSDC status:public\|Submitter Id:ZF male head sample1\|common name:zebrafish\|sample name:ZF male head sample1\|scientific name:Danio rerio\|sex:male\|strain:Tuebingen									Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation	E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish male head dpf three prime pull down paired end 250 to 300 bp insert	Zebrafish adult male head mRNA three prime end	Zebrafish gene three prime end pull down for genome annotation	20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl. RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin magnetic beads. post washing by pull down on a magnet the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB. post further washing the double strand cDNA was released from the beads with BpmI NEB. The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp.	Experimental Factor: DEVELOPMENTAL STAGE:adult\|Experimental Factor: ORGANISM PART:head\|Experimental Factor: SEX:male	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina Genome Analyzer II		ERP000263	Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation	ENA FIRST PUBLIC:2010 08 19\|ENA LAST UPDATE:2018 11 16	3444_7.srf	srf	1384012896.0	9105348.0	E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish male head dpf three prime pull down paired end 250 to 300 bp insert	0:76 1:76	A:369912216;C:306963547;G:292249178;T:392053840;N:22834115	76	76	369912216	306963547	292249178	392053840	22834115	ERX005930	ERS000089	ERA010603	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.95932	0.96084	0.20719	0.21321	0.73959	0.74763	0.47227	0.48033	76	76	B	B	biological fallback assumption	illumina	early_illumina	3prime	other	unknown	bulk	unknown	unknown	United Kingdom	2010-02-26	Adult	Adult	Head	Nervous System
8059	8059	ERR022480	ERX008923	ERS000088	ERP000400	PRJEB2333	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E-MTAB-434	Other				ZF female head sample1	SAMEA708836	Wellcome Sanger Institute	Alias:ZF female head sample1\|Description:RNA extracted from female adult zebrafish head\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2010 02 26T10:44:13Z\|INSDC last update:2018 03 08T15:24:37Z\|INSDC status:public\|SRA accession:ERS000088\|Sample Name:ERS000088\|Sex:female\|Strain:Tuebingen\|Title:Danio rerio									Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E MTAB 434:sequencing of Zebrafish adult female head	RNA from Zebrafish adult female head	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.	Experimental Factor: DEVELPOMENTAL STAGE:adult\|Experimental Factor: ORGANISM PART:head	FL-cDNA	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer II		ERP000400	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	ENA FIRST PUBLIC:2011 03 10\|ENA LAST UPDATE:2018 11 16	2719_5.srf	srf	1622590272.0	15023984.0	E MTAB 434:2719 5.srf	0:54 1:54	A:426435544;C:373743071;G:387589492;T:432086510;N:2735655	54	54	426435544	373743071	387589492	432086510	2735655	ERX008923	ERS000088	ERA015179	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.94624	0.94338	0.17949	0.17965	0.66454	0.66872	0.51097	0.51377	54	54	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2010-02-26	Adult	Adult	Head	Nervous System
8060	8060	ERR022481	ERX008923	ERS000088	ERP000400	PRJEB2333	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E-MTAB-434	Other				ZF female head sample1	SAMEA708836	Wellcome Sanger Institute	Alias:ZF female head sample1\|Description:RNA extracted from female adult zebrafish head\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2010 02 26T10:44:13Z\|INSDC last update:2018 03 08T15:24:37Z\|INSDC status:public\|SRA accession:ERS000088\|Sample Name:ERS000088\|Sex:female\|Strain:Tuebingen\|Title:Danio rerio									Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	E MTAB 434:sequencing of Zebrafish adult female head	RNA from Zebrafish adult female head	Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.	Experimental Factor: DEVELPOMENTAL STAGE:adult\|Experimental Factor: ORGANISM PART:head	FL-cDNA	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina Genome Analyzer II		ERP000400	Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer	ENA FIRST PUBLIC:2011 03 10\|ENA LAST UPDATE:2018 11 16	2719_6.srf	srf	1693460736.0	15680192.0	E MTAB 434:2719 6.srf	0:54 1:54	A:445666325;C:389360280;G:403789644;T:451529226;N:3115261	54	54	445666325	389360280	403789644	451529226	3115261	ERX008923	ERS000088	ERA015179	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.94579	0.94429	0.17895	0.17923	0.66864	0.67164	0.51788	0.51083	54	54	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2010-02-26	Adult	Adult	Head	Nervous System
33619	33619	SRR30310487	SRX25770932	SRS22407035	SRP527479	PRJNA1150074	Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling	GSE275235	Transcriptome Analysis	SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …	pubmed:40208862		DM biol rep 3	GSM8473259		source name:heads\|tissue:heads\|genotype:5a / ;5b / \|treatment:untreated\|geo loc name:missing\|collection date:missing	DM biol rep 3	Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample	heads	untreated	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle	Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning.	tissue:heads\|genotype:5a / ;5b / \|treatment:untreated	GSM8473259	GSM8473259: DM biol rep 3; Danio rerio; RNA Seq	GSM8473259 r1	GSM8473259	1	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP527479			Li47814-DM3_S6_R2_001.fastq.gz Li47814-DM3_S6_R1_001.fastq.gz	fastq fastq	4759652497.0	39356384.0	GSM8473259 r1	0:60.49 1:60.44	A:1221224093;C:1133209753;G:1144876807;T:1252303477;N:8038367	60	60	1221224093	1133209753	1144876807	1252303477	8038367	SRX25770932	SRS22407035	SRA1951631	Kurrasch Lab, Department of Medical Genetics, University of Calgary	Kurrasch Lab, Department of Medical Genetics, University of Calgary	2	0.94992	0.95405	0.07666	0.07486	0.64969	0.648	0.47911	0.48137	61	61	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Canada	2024-08-20	Adult	Adult	Head	Nervous System
33620	33620	SRR30310488	SRX25770931	SRS22407034	SRP527479	PRJNA1150074	Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling	GSE275235	Transcriptome Analysis	SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …	pubmed:40208862		DM biol rep 2	GSM8473258		source name:heads\|tissue:heads\|genotype:5a / ;5b / \|treatment:untreated\|geo loc name:missing\|collection date:missing	DM biol rep 2	Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample	heads	untreated	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle	Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning.	tissue:heads\|genotype:5a / ;5b / \|treatment:untreated	GSM8473258	GSM8473258: DM biol rep 2; Danio rerio; RNA Seq	GSM8473258 r1	GSM8473258	1	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP527479			Li47813-DM2_S5_R2_001.fastq.gz Li47813-DM2_S5_R1_001.fastq.gz	fastq fastq	5030260806.0	41607672.0	GSM8473258 r1	0:60.47 1:60.43	A:1291665135;C:1198581962;G:1206075180;T:1323425262;N:10513267	60	60	1291665135	1198581962	1206075180	1323425262	10513267	SRX25770931	SRS22407034	SRA1951631	Kurrasch Lab, Department of Medical Genetics, University of Calgary	Kurrasch Lab, Department of Medical Genetics, University of Calgary	2	0.94958	0.95221	0.08402	0.0824	0.64628	0.64553	0.47628	0.47968	61	60	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Canada	2024-08-20	Adult	Adult	Head	Nervous System
33621	33621	SRR30310489	SRX25770930	SRS22407033	SRP527479	PRJNA1150074	Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling	GSE275235	Transcriptome Analysis	SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …	pubmed:40208862		DM biol rep 1	GSM8473257		source name:heads\|tissue:heads\|genotype:5a / ;5b / \|treatment:untreated\|geo loc name:missing\|collection date:missing	DM biol rep 1	Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample	heads	untreated	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle	Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning.	tissue:heads\|genotype:5a / ;5b / \|treatment:untreated	GSM8473257	GSM8473257: DM biol rep 1; Danio rerio; RNA Seq	GSM8473257 r1	GSM8473257	1	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP527479			Li47812-DM1_S4_R2_001.fastq.gz Li47812-DM1_S4_R1_001.fastq.gz	fastq fastq	5442095245.0	45006091.0	GSM8473257 r1	0:60.48 1:60.44	A:1406768036;C:1288396960;G:1297715980;T:1439122995;N:10091274	60	60	1406768036	1288396960	1297715980	1439122995	10091274	SRX25770930	SRS22407033	SRA1951631	Kurrasch Lab, Department of Medical Genetics, University of Calgary	Kurrasch Lab, Department of Medical Genetics, University of Calgary	2	0.94722	0.95046	0.09788	0.09612	0.63984	0.6411	0.46913	0.4759	61	61	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Canada	2024-08-20	Adult	Adult	Head	Nervous System
33622	33622	SRR30310490	SRX25770929	SRS22407032	SRP527479	PRJNA1150074	Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling	GSE275235	Transcriptome Analysis	SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …	pubmed:40208862		5b biol rep 3	GSM8473256		source name:heads\|tissue:heads\|genotype:5b / \|treatment:untreated\|geo loc name:missing\|collection date:missing	5b biol rep 3	Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample	heads	untreated	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle	Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning.	tissue:heads\|genotype:5b / \|treatment:untreated	GSM8473256	GSM8473256: 5b biol rep 3; Danio rerio; RNA Seq	GSM8473256 r1	GSM8473256	1	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP527479			Li47820-5b3_S12_R2_001.fastq.gz Li47820-5b3_S12_R1_001.fastq.gz	fastq fastq	5532330845.0	45739498.0	GSM8473256 r1	0:60.50 1:60.46	A:1435251569;C:1304605813;G:1312598084;T:1471267089;N:8608290	60	60	1435251569	1304605813	1312598084	1471267089	8608290	SRX25770929	SRS22407032	SRA1951631	Kurrasch Lab, Department of Medical Genetics, University of Calgary	Kurrasch Lab, Department of Medical Genetics, University of Calgary	2	0.94396	0.94717	0.11216	0.11051	0.64717	0.64768	0.47525	0.47841	60	61	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Canada	2024-08-20	Adult	Adult	Head	Nervous System
33623	33623	SRR30310491	SRX25770928	SRS22407031	SRP527479	PRJNA1150074	Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling	GSE275235	Transcriptome Analysis	SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …	pubmed:40208862		5b biol rep 2	GSM8473255		source name:heads\|tissue:heads\|genotype:5b / \|treatment:untreated\|geo loc name:missing\|collection date:missing	5b biol rep 2	Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample	heads	untreated	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle	Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning.	tissue:heads\|genotype:5b / \|treatment:untreated	GSM8473255	GSM8473255: 5b biol rep 2; Danio rerio; RNA Seq	GSM8473255 r1	GSM8473255	1	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP527479			Li47819-5b2_S11_R2_001.fastq.gz Li47819-5b2_S11_R1_001.fastq.gz	fastq fastq	5530076725.0	45717614.0	GSM8473255 r1	0:60.50 1:60.46	A:1432780615;C:1306496067;G:1314858379;T:1467817877;N:8123787	60	60	1432780615	1306496067	1314858379	1467817877	8123787	SRX25770928	SRS22407031	SRA1951631	Kurrasch Lab, Department of Medical Genetics, University of Calgary	Kurrasch Lab, Department of Medical Genetics, University of Calgary	2	0.94205	0.94641	0.11508	0.11379	0.64788	0.64672	0.47602	0.47695	61	59	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Canada	2024-08-20	Adult	Adult	Head	Nervous System
33624	33624	SRR30310492	SRX25770927	SRS22407030	SRP527479	PRJNA1150074	Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling	GSE275235	Transcriptome Analysis	SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …	pubmed:40208862		5b biol rep 1	GSM8473254		source name:heads\|tissue:heads\|genotype:5b / \|treatment:untreated\|geo loc name:missing\|collection date:missing	5b biol rep 1	Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample	heads	untreated	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle	Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning.	tissue:heads\|genotype:5b / \|treatment:untreated	GSM8473254	GSM8473254: 5b biol rep 1; Danio rerio; RNA Seq	GSM8473254 r1	GSM8473254	1	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP527479			Li47818-5b1_S10_R2_001.fastq.gz Li47818-5b1_S10_R1_001.fastq.gz	fastq fastq	4784996431.0	39556747.0	GSM8473254 r1	0:60.50 1:60.46	A:1241886071;C:1129207908;G:1136918789;T:1270031996;N:6951667	60	60	1241886071	1129207908	1136918789	1270031996	6951667	SRX25770927	SRS22407030	SRA1951631	Kurrasch Lab, Department of Medical Genetics, University of Calgary	Kurrasch Lab, Department of Medical Genetics, University of Calgary	2	0.94373	0.94771	0.11067	0.10905	0.64729	0.64583	0.47752	0.47625	59	60	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Canada	2024-08-20	Adult	Adult	Head	Nervous System
33625	33625	SRR30310493	SRX25770926	SRS22407029	SRP527479	PRJNA1150074	Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling	GSE275235	Transcriptome Analysis	SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …	pubmed:40208862		5a biol rep 3	GSM8473253		source name:heads\|tissue:heads\|genotype:5a / \|treatment:untreated\|geo loc name:missing\|collection date:missing	5a biol rep 3	Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample	heads	untreated	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle	Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning.	tissue:heads\|genotype:5a / \|treatment:untreated	GSM8473253	GSM8473253: 5a biol rep 3; Danio rerio; RNA Seq	GSM8473253 r1	GSM8473253	1	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP527479			Li47817-5a3_S9_R2_001.fastq.gz Li47817-5a3_S9_R1_001.fastq.gz	fastq fastq	5455669007.0	45101219.0	GSM8473253 r1	0:60.51 1:60.46	A:1408981430;C:1292361893;G:1307301180;T:1439131814;N:7892690	60	60	1408981430	1292361893	1307301180	1439131814	7892690	SRX25770926	SRS22407029	SRA1951631	Kurrasch Lab, Department of Medical Genetics, University of Calgary	Kurrasch Lab, Department of Medical Genetics, University of Calgary	2	0.95182	0.95421	0.081	0.07901	0.6524	0.65115	0.48336	0.48307	61	59	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Canada	2024-08-20	Adult	Adult	Head	Nervous System
33626	33626	SRR30310494	SRX25770925	SRS22407028	SRP527479	PRJNA1150074	Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling	GSE275235	Transcriptome Analysis	SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …	pubmed:40208862		5a biol rep 2	GSM8473252		source name:heads\|tissue:heads\|genotype:5a / \|treatment:untreated\|geo loc name:missing\|collection date:missing	5a biol rep 2	Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample	heads	untreated	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle	Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning.	tissue:heads\|genotype:5a / \|treatment:untreated	GSM8473252	GSM8473252: 5a biol rep 2; Danio rerio; RNA Seq	GSM8473252 r1	GSM8473252	1	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP527479			Li47816-5a2_S8_R2_001.fastq.gz Li47816-5a2_S8_R1_001.fastq.gz	fastq fastq	5585703633.0	46182982.0	GSM8473252 r1	0:60.50 1:60.45	A:1439568272;C:1324867892;G:1340137608;T:1471972622;N:9157239	60	60	1439568272	1324867892	1340137608	1471972622	9157239	SRX25770925	SRS22407028	SRA1951631	Kurrasch Lab, Department of Medical Genetics, University of Calgary	Kurrasch Lab, Department of Medical Genetics, University of Calgary	2	0.95103	0.95419	0.0813	0.07916	0.6565	0.65563	0.47441	0.47598	61	61	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Canada	2024-08-20	Adult	Adult	Head	Nervous System
33627	33627	SRR30310495	SRX25770924	SRS22407027	SRP527479	PRJNA1150074	Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling	GSE275235	Transcriptome Analysis	SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …	pubmed:40208862		5a biol rep 1	GSM8473251		source name:heads\|tissue:heads\|genotype:5a / \|treatment:untreated\|geo loc name:missing\|collection date:missing	5a biol rep 1	Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample	heads	untreated	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle	Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning.	tissue:heads\|genotype:5a / \|treatment:untreated	GSM8473251	GSM8473251: 5a biol rep 1; Danio rerio; RNA Seq	GSM8473251 r1	GSM8473251	1	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP527479			Li47815-5a1_S7_R2_001.fastq.gz Li47815-5a1_S7_R1_001.fastq.gz	fastq fastq	5421245773.0	44832660.0	GSM8473251 r1	0:60.48 1:60.44	A:1406624107;C:1276257498;G:1288190603;T:1440236606;N:9936959	60	60	1406624107	1276257498	1288190603	1440236606	9936959	SRX25770924	SRS22407027	SRA1951631	Kurrasch Lab, Department of Medical Genetics, University of Calgary	Kurrasch Lab, Department of Medical Genetics, University of Calgary	2	0.9497	0.95318	0.08896	0.08766	0.64983	0.65009	0.46836	0.46856	60	61	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Canada	2024-08-20	Adult	Adult	Head	Nervous System
33628	33628	SRR30310496	SRX25770923	SRS22407026	SRP527479	PRJNA1150074	Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling	GSE275235	Transcriptome Analysis	SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …	pubmed:40208862		WT biol rep 3	GSM8473250		source name:heads\|tissue:heads\|genotype:WT\|treatment:untreated\|geo loc name:missing\|collection date:missing	WT biol rep 3	Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample	heads	untreated	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle	Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning.	tissue:heads\|genotype:WT\|treatment:untreated	GSM8473250	GSM8473250: WT biol rep 3; Danio rerio; RNA Seq	GSM8473250 r1	GSM8473250	1	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP527479			Li47811-WT3_S3_R2_001.fastq.gz Li47811-WT3_S3_R1_001.fastq.gz	fastq fastq	5445129556.0	45027951.0	GSM8473250 r1	0:60.48 1:60.45	A:1410861744;C:1282813821;G:1294884711;T:1446863056;N:9706224	60	60	1410861744	1282813821	1294884711	1446863056	9706224	SRX25770923	SRS22407026	SRA1951631	Kurrasch Lab, Department of Medical Genetics, University of Calgary	Kurrasch Lab, Department of Medical Genetics, University of Calgary	2	0.94943	0.95269	0.11544	0.11414	0.64644	0.64699	0.46439	0.47415	61	61	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Canada	2024-08-20	Adult	Adult	Head	Nervous System
33629	33629	SRR30310497	SRX25770922	SRS22407025	SRP527479	PRJNA1150074	Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling	GSE275235	Transcriptome Analysis	SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …	pubmed:40208862		WT biol rep 2	GSM8473249		source name:heads\|tissue:heads\|genotype:WT\|treatment:untreated\|geo loc name:missing\|collection date:missing	WT biol rep 2	Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample	heads	untreated	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle	Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning.	tissue:heads\|genotype:WT\|treatment:untreated	GSM8473249	GSM8473249: WT biol rep 2; Danio rerio; RNA Seq	GSM8473249 r1	GSM8473249	1	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP527479			Li47810-WT2_S2_R2_001.fastq.gz Li47810-WT2_S2_R1_001.fastq.gz	fastq fastq	4788359140.0	39599012.0	GSM8473249 r1	0:60.48 1:60.44	A:1237189996;C:1129331953;G:1143753687;T:1268980159;N:9103345	60	60	1237189996	1129331953	1143753687	1268980159	9103345	SRX25770922	SRS22407025	SRA1951631	Kurrasch Lab, Department of Medical Genetics, University of Calgary	Kurrasch Lab, Department of Medical Genetics, University of Calgary	2	0.94746	0.95043	0.1121	0.11092	0.64411	0.64342	0.46922	0.47301	59	61	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Canada	2024-08-20	Adult	Adult	Head	Nervous System
33630	33630	SRR30310498	SRX25770921	SRS22407024	SRP527479	PRJNA1150074	Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling	GSE275235	Transcriptome Analysis	SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …	pubmed:40208862		WT biol rep 1	GSM8473248		source name:heads\|tissue:heads\|genotype:WT\|treatment:untreated\|geo loc name:missing\|collection date:missing	WT biol rep 1	Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample	heads	untreated	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle	Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning.	tissue:heads\|genotype:WT\|treatment:untreated	GSM8473248	GSM8473248: WT biol rep 1; Danio rerio; RNA Seq	GSM8473248 r1	GSM8473248	1	Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP527479			Li47809-WT1_S1_R2_001.fastq.gz Li47809-WT1_S1_R1_001.fastq.gz	fastq fastq	5047587318.0	41741097.0	GSM8473248 r1	0:60.48 1:60.44	A:1311031310;C:1185882586;G:1198272234;T:1343072853;N:9328335	60	60	1311031310	1185882586	1198272234	1343072853	9328335	SRX25770921	SRS22407024	SRA1951631	Kurrasch Lab, Department of Medical Genetics, University of Calgary	Kurrasch Lab, Department of Medical Genetics, University of Calgary	2	0.94688	0.95005	0.12622	0.12476	0.6463	0.64528	0.47305	0.47428	61	61	B	B	biological fallback assumption	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Canada	2024-08-20	Adult	Adult	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
40494	40494	SRR3204724	SRX1614066	SRS1323928	SRP070923	PRJNA313387	Transcriptomic of ß diketone antibiotics on zebrafish post a 3 month DKAs exposure.	PRJNA313387	Other	RNA libraries were constructed from control 6.25 and 12.5 mg/L treatment groups respectively. post DKAs exposure to 3 mpf zebrafish the whole transcriptome was determined.		12.5 mg/L with equal weight concentrations and volumes for each of the six DKA species ofloxacin ciprofloxacin enrofloxacin doxycycline chlortetracycline and oxytetracycline was exposure to zebrafish from embryo to 90 dpf dpf	12.5mg/L DKAs	T21		strain:AB strain\|isolate:Oregon State University\|breed:Danio rerio\|cultivar:not applicable\|ecotype:Wild type\|age:3 mpf\|dev stage:3 mpf\|sex:pooled male and female\|tissue:we performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems.\|treatment:12.5 mg/L DKAs exposure\|BioSampleModel:Model organism or animal									12.5mg/L DKAs	T21	1	Zebrafish in 12.5 mg/L β diketone antibiotics treatment groupwith equal weight concentrations and volumes for ofloxacin ciprofloxacin enrofloxacin doxycycline chlortetracycline and oxytetracycline with purity of 99% except for 95% for chlortetracycline were randomly selected post DKAs exposure at 90 dpf and rinsed with phosphorous buffer solution. We performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems. The retained tissues were used to extract total RNA using Trizol Invitrogen Carlsbad CA USA according to the manufacturer's procedures. The quantity and purity of total RNA were analyzed by employing a Bioanalyzer 2100 and RNA 6000 Nano LabChipKit Agilent Santa Clara CA USA with RIN number >7.0. Poly A mRNA was isolated by poly T oligo attached magnetic beads Invitrogen. The purified mRNA was fragmented into small pieces by divalent cations under elevated temperature. Then the final cDNA library was produced by the reverse transcription of the cleaved RNA fragments on the basis of the mRNA Seq sample preparation kit Illumina San Diego USA and the average 300±50 bp insert size was used for the paired end libraries. Finally the paired end sequencing was performed on an Illumina Hiseq2000/2500. Prior to assembly the low quality reads 1 reads containing sequencing adaptors; 2 reads containing sequencing primer; 3 nucleotide with q scores lower than 20 were removed. Next the cleaned and paired end reads were produced.			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070923			T21_Clean_Data1.fq.gz T21_Clean_Data2.fq.gz	fastq fastq	10502615500.0	42010462.0	T21	0:125 1:125	A:2848309151;C:2371408734;G:2356749579;T:2925931092;N:216944	125	125	2848309151	2371408734	2356749579	2925931092	216944	SRX1614066	SRS1323928	SRA359545	School of Life Sciences	School of Life Sciences	2	0.87768	0.88612	0.29688	0.29743	0.68738	0.68363	0.52932	0.52507	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	bulk	unknown	unknown	Unknown	2016-03-16	Adult	Adult	Head	Nervous System
40495	40495	SRR3203073	SRX1612569	SRS1321766	SRP070923	PRJNA313387	Transcriptomic of ß diketone antibiotics on zebrafish post a 3 month DKAs exposure.	PRJNA313387	Other	RNA libraries were constructed from control 6.25 and 12.5 mg/L treatment groups respectively. post DKAs exposure to 3 mpf zebrafish the whole transcriptome was determined.		6.25 mg/L with equal weight concentrations and volumes for each of the six DKA species ofloxacin ciprofloxacin enrofloxacin doxycycline chlortetracycline and oxytetracycline was exposure to zebrafish from embryo to 90 dpf dpf	6.25mg/L DKAs	T11		strain:AB strain\|isolate:Oregon State University\|breed:Danio rerio\|cultivar:not applicable\|ecotype:Wild type\|age:3 mpf\|dev stage:3 mpf\|sex:pooled male and female\|tissue:we performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems.\|treatment:6.25 mg/L DKAs exposure\|BioSampleModel:Model organism or animal									6.25 mg/L DKAs	T11	1	Zebrafish in 6.25 mg/L β diketone antibiotics treatment groupwith equal weight concentrations and volumes for ofloxacin ciprofloxacin enrofloxacin doxycycline chlortetracycline and oxytetracycline with purity of 99% except for 95% for chlortetracycline were randomly selected post DKAs exposure at 90 dpf and rinsed with phosphorous buffer solution. We performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems. The retained tissues were used to extract total RNA using Trizol Invitrogen Carlsbad CA USA according to the manufacturer's procedures. The quantity and purity of total RNA were analyzed by employing a Bioanalyzer 2100 and RNA 6000 Nano LabChipKit Agilent Santa Clara CA USA with RIN number >7.0. Poly A mRNA was isolated by poly T oligo attached magnetic beads Invitrogen. The purified mRNA was fragmented into small pieces by divalent cations under elevated temperature. Then the final cDNA library was produced by the reverse transcription of the cleaved RNA fragments on the basis of the mRNA Seq sample preparation kit Illumina San Diego USA and the average 300±50 bp insert size was used for the paired end libraries. Finally the paired end sequencing was performed on an Illumina Hiseq2000/2500. Prior to assembly the low quality reads 1 reads containing sequencing adaptors; 2 reads containing sequencing primer; 3 nucleotide with q scores lower than 20 were removed. Next the cleaned and paired end reads were produced.			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070923			T11_Clean_Data1.fq.gz T11_Clean_Data2.fq.gz	fastq fastq	8178356500.0	32713426.0	T11	0:125 1:125	A:2135090304;C:1929011381;G:1912585084;T:2201518295;N:151436	125	125	2135090304	1929011381	1912585084	2201518295	151436	SRX1612569	SRS1321766	SRA359545	School of Life Sciences	School of Life Sciences	2	0.84003	0.84827	0.32283	0.32402	0.71031	0.70502	0.58398	0.58631	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	bulk	unknown	unknown	Unknown	2016-03-15	Adult	Adult	Head	Nervous System
40496	40496	SRR3195594	SRX1604653	SRS1314385	SRP070923	PRJNA313387	Transcriptomic of ß diketone antibiotics on zebrafish post a 3 month DKAs exposure.	PRJNA313387	Other	RNA libraries were constructed from control 6.25 and 12.5 mg/L treatment groups respectively. post DKAs exposure to 3 mpf zebrafish the whole transcriptome was determined.				zebrafish		strain:AB strain\|isolate:Oregon State University\|breed:Danio rerio\|cultivar:not applicable\|ecotype:Wild type\|age:3 mpf\|dev stage:3 mpf\|sex:pooled male and female\|tissue:we performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems.\|BioSampleModel:Model organism or animal									control	CON 01	1	Zebrafish in control group were randomly selected post DKAs exposure at 90 dpf and rinsed with phosphorous buffer solution. We performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems. The retained tissues were used to extract total RNA according to the manufacturer's procedures. The quantity and purity of total RNA were analyzed by employing a Bioanalyzer 2100 and RNA 6000 Nano LabChipKit Agilent Santa Clara CA USA with RIN number >7.0. Poly A mRNA was isolated by poly T oligo attached magnetic beads Invitrogen. The purified mRNA was fragmented into small pieces by divalent cations under elevated temperature. Then the final cDNA library was produced by the reverse transcription of the cleaved RNA fragments on the basis of the mRNA Seq sample preparation kit Illumina San Diego USA and the average 300±50 bp insert size was used for the paired end libraries. Finally the paired end sequencing was performed on an Illumina Hiseq2000/2500. Prior to assembly the low quality reads 1 reads containing sequencing adaptors; 2 reads containing sequencing primer; 3 nucleotide with q scores lower than 20 were removed. Next the cleaned and paired end reads were produced.			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070923			CON_01_Clean_Data2.fq.gz CON_01_Clean_Data1.fq.gz	fastq fastq	8941582750.0	35766331.0	control	0:125 1:125	A:2282842470;C:2172817074;G:2169521320;T:2316254609;N:147277	125	125	2282842470	2172817074	2169521320	2316254609	147277	SRX1604653	SRS1314385	SRA359545	School of Life Sciences	School of Life Sciences	2	0.62865	0.62758	0.22408	0.21961	0.7525	0.75024	0.5332	0.519	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	bulk	unknown	unknown	Unknown	2016-03-15	Adult	Adult	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
52285	52285	SRR9077089	SRX5852368	SRS4776361	SRP198708	PRJNA543385	mRNA sequence of zebrafish head and body	PRJNA543385	Other	RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing			head1 mock	s1		breed:zebrafish\|dev stage:adult\|sex:NA\|tissue:head1\|BioSampleModel:Model organism or animal									head1 mock	WC TC 041	WC TC 041	TRUEseq standardised protocol			RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP198708			WC_TC_041_S8.R1.fastq.gz WC_TC_041_S8.R2.fastq.gz	fastq fastq	5480620528.0	36056714.0	WC TC 041 S8.R1.fastq.gz	0:101 1:51	A:1456079218;C:1286879398;G:1250199115;T:1487095432;N:367365	101	51	1456079218	1286879398	1250199115	1487095432	367365	SRX5852368	SRS4776361	SRA887738	Southern University of Science and Technology\|Department of Biology	Southern University of Science and Technology	2	0.96102	0.95396	0.09057	0.09452	0.70285	0.70573	0.474	0.47396	101	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	China	2019-10-08	Adult	Adult	Head	Nervous System
52286	52286	SRR9077090	SRX5852367	SRS4776360	SRP198708	PRJNA543385	mRNA sequence of zebrafish head and body	PRJNA543385	Other	RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing			head1 control	s2		breed:zebrafish\|dev stage:adult\|sex:NA\|tissue:head2\|BioSampleModel:Model organism or animal									head1 control	WC TC 042	WC TC 042	TRUEseq standardised protocol			RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP198708			WC_TC_042_S9.R1.fastq.gz WC_TC_042_S9.R2.fastq.gz	fastq fastq	5011160472.0	32968161.0	WC TC 042 S9.R1.fastq.gz	0:101 1:51	A:1328768028;C:1179737412;G:1141948263;T:1360371072;N:335697	101	51	1328768028	1179737412	1141948263	1360371072	335697	SRX5852367	SRS4776360	SRA887738	Southern University of Science and Technology\|Department of Biology	Southern University of Science and Technology	2	0.96134	0.95488	0.09183	0.09597	0.70203	0.70398	0.4719	0.46265	101	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	China	2019-10-08	Adult	Adult	Head	Nervous System
52287	52287	SRR9077091	SRX5852366	SRS4776359	SRP198708	PRJNA543385	mRNA sequence of zebrafish head and body	PRJNA543385	Other	RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing			head1 kd	s3		breed:zebrafish\|dev stage:adult\|sex:NA\|tissue:head3\|BioSampleModel:Model organism or animal									head1 kd	WC TC 043	WC TC 043	TRUEseq standardised protocol			RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP198708			WC_TC_043_S10.R1.fastq.gz WC_TC_043_S10.R2.fastq.gz	fastq fastq	5709609744.0	37563222.0	WC TC 043 S10.R1.fastq.gz	0:101 1:51	A:1517831332;C:1339538042;G:1299421324;T:1552434811;N:384235	101	51	1517831332	1339538042	1299421324	1552434811	384235	SRX5852366	SRS4776359	SRA887738	Southern University of Science and Technology\|Department of Biology	Southern University of Science and Technology	2	0.95768	0.95177	0.10352	0.10892	0.69209	0.69556	0.4693	0.47272	101	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	China	2019-10-08	Adult	Adult	Head	Nervous System
52288	52288	SRR9077092	SRX5852365	SRS4776358	SRP198708	PRJNA543385	mRNA sequence of zebrafish head and body	PRJNA543385	Other	RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing			head1 kd+wt	s4		breed:zebrafish\|dev stage:adult\|sex:NA\|tissue:head4\|BioSampleModel:Model organism or animal									head1 kd+wt	WC TC 044	WC TC 044	TRUEseq standardised protocol			RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP198708			WC_TC_044_S11.R2.fastq.gz WC_TC_044_S11.R1.fastq.gz	fastq fastq	4776327920.0	31423210.0	WC TC 044 S11.R1.fastq.gz	0:101 1:51	A:1272079335;C:1117051709;G:1087240750;T:1299640784;N:315342	101	51	1272079335	1117051709	1087240750	1299640784	315342	SRX5852365	SRS4776358	SRA887738	Southern University of Science and Technology\|Department of Biology	Southern University of Science and Technology	2	0.9572	0.95024	0.10519	0.11173	0.69412	0.69621	0.47948	0.46528	101	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	China	2019-05-17	Adult	Adult	Head	Nervous System
52292	52292	SRR9077096	SRX5852361	SRS4776354	SRP198708	PRJNA543385	mRNA sequence of zebrafish head and body	PRJNA543385	Other	RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing			head1 kd+mt	s5		breed:zebrafish\|dev stage:adult\|sex:NA\|tissue:head5\|BioSampleModel:Model organism or animal									head1 kd+mt	WC TC 045	WC TC 045	TRUEseq standardised protocol			RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP198708			WC_TC_045_S12.R1.fastq.gz WC_TC_045_S12.R2.fastq.gz	fastq fastq	4914615696.0	32332998.0	WC TC 045 S12.R1.fastq.gz	0:101 1:51	A:1304784949;C:1154087581;G:1119502459;T:1335912697;N:328010	101	51	1304784949	1154087581	1119502459	1335912697	328010	SRX5852361	SRS4776354	SRA887738	Southern University of Science and Technology\|Department of Biology	Southern University of Science and Technology	2	0.95742	0.95094	0.10146	0.1069	0.69686	0.69978	0.47629	0.469	101	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	China	2019-10-08	Adult	Adult	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");;