metadata: run_metadata: 22 rows where devstage_curation = "Adult" and experiment.platform = "ABI

22 rows where devstage_curation = "Adult" and experiment.platform = "ABI_SOLID"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	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.study_ref	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.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
37108	37108	SRR924082	SRX316721	SRS472258	SRP026400	PRJNA210007	Genome wide identification of molecular pathways and biomarkers in response to arsenic exposure in zebrafish liver	GSE48427	Transcriptome Analysis	In the present study we employed the RNA sequencing platform to examine the molecular response of zebrafish liver to arsenic exposure and carry out detailed transcriptomic analyses for further understanding of molecular toxicity. We found that several important biological processes were perturbed by arsenic exposure including oxidation reduction translation iron ion transport cell redox and homeostasis as well as related pathways in metabolism and diseases. Furthermore as there are currently no biomarker genes available for predicting arsenic exposure we took the advantage of RNA sequencing platform to identify most suitable biomarker genes from top responsive genes to arsenic exposure. We first validated these top responsive genes by RT qPCR in zebrafish and then in Japanese medaka Oryzias latipes at individual fish level for more robustly responsive genes across different fish species. Overall design: Transcriptome profiling of arsenic treated sample and control sample were generated by deep sequencing using three prime RNA SAGE on the SOLiD system.	pubmed:24176670;pubmed:23922661	H2O treated zebrafish liver	GSM1177837	source name:liver control\|genotype/variation:wildtype\|tissue:liver\|age:3 month\|treatment:water control	H2O treated zebrafish liver	The SOLiD generated RNA Seq reads were 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maximum mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 58 Supplementary files format and content: Tab delimited text file. The mapped transcripts are listed with GI RefSeq accession and expression levels in TPM.	liver control	3 mpf wildtype zebrafish were treated for 96 hrs. Sodium arsenate treatment was conducted in 3 L tanks with around 15 adults and water was changed every day.	Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.		genotype/variation:wildtype\|tissue:liver\|age:3 month\|treatment:water control	GSM1177837	GSM1177837: H2O treated zebrafish liver; Danio rerio; RNA Seq	GSM1177837	1	Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.	GEO Accession:GSM1177837	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD 3 Plus System	SRP026400		solid0518_20101014_Gong_1_SetA_F3_0_1H2O.csfasta solid0518_20101014_Gong_1_SetA_F3_QV_0_1H2O.qual	SOLiD_native SOLiD_native	477311205.0	13637463.0	GSM1177837 r1	0:35	0:176467601;1:101093405;2:105775125;3:93265462;.:709612	35						SRX316721	SRS472258	SRA091803	GEO	National University of Singapore	1	0.02019	0.01385	0.9973	0.64062	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2013-06-28	Adult	Adult	Liver	Liver and Biliary System
37109	37109	SRR924081	SRX316720	SRS454027	SRP026400	PRJNA210007	Genome wide identification of molecular pathways and biomarkers in response to arsenic exposure in zebrafish liver	GSE48427	Transcriptome Analysis	In the present study we employed the RNA sequencing platform to examine the molecular response of zebrafish liver to arsenic exposure and carry out detailed transcriptomic analyses for further understanding of molecular toxicity. We found that several important biological processes were perturbed by arsenic exposure including oxidation reduction translation iron ion transport cell redox and homeostasis as well as related pathways in metabolism and diseases. Furthermore as there are currently no biomarker genes available for predicting arsenic exposure we took the advantage of RNA sequencing platform to identify most suitable biomarker genes from top responsive genes to arsenic exposure. We first validated these top responsive genes by RT qPCR in zebrafish and then in Japanese medaka Oryzias latipes at individual fish level for more robustly responsive genes across different fish species. Overall design: Transcriptome profiling of arsenic treated sample and control sample were generated by deep sequencing using three prime RNA SAGE on the SOLiD system.	pubmed:24176670;pubmed:23922661	Arsenic treated zebrafish liver	GSM1177836	source name:liver arsenic\|genotype/variation:wildtype\|tissue:liver\|age:3 month\|treatment:arsenate sodium	Arsenic treated zebrafish liver	The SOLiD generated RNA Seq reads were 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maximum mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 58 Supplementary files format and content: Tab delimited text file. The mapped transcripts are listed with GI RefSeq accession and expression levels in TPM.	liver arsenic	3 mpf wildtype zebrafish were treated for 96 hrs. Sodium arsenate treatment was conducted in 3 L tanks with around 15 adults and water was changed every day.	Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.		genotype/variation:wildtype\|tissue:liver\|age:3 month\|treatment:arsenate sodium	GSM1177836	GSM1177836: Arsenic treated zebrafish liver; Danio rerio; RNA Seq	GSM1177836	1	Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.	GEO Accession:GSM1177836	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD 3 Plus System	SRP026400		solid0518_20101014_Gong_1_SetA_F3_QV_2_2Arsenic.qual solid0518_20101014_Gong_1_SetA_F3_2_2Arsenic.csfasta	SOLiD_native SOLiD_native	477279215.0	13636549.0	GSM1177836 r1	0:35	0:135280436;1:121477647;2:102046207;3:117826846;.:648079	35						SRX316720	SRS454027	SRA091803	GEO	National University of Singapore	1	0.0161	0.00302	0.99334	0.51629	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2013-06-28	Adult	Adult	Liver	Liver and Biliary System
37130	37130	SRR952910	SRX335554	SRS470625	SRP028848	PRJNA215326	Transcriptomic analyses of TCDD treated zebrafish liver	GSE49915	Transcriptome Analysis	To fully understand molecular toxicity of TCDD in an in vivo animal model adult zebrafish were exposed to TCDD at xxx nM for xxx h and the livers were sampled for RNA sequencing based transcriptomic profiling. A total of 1 058 differently expressed genes were identified based on fold change>2 and TPM transcripts per million >10. Among the top 20 up regulated genes 10 novel responsive genes were identified and verified by qRT PCR analysis on independent samples. Transcriptomic analysis indicated several deregulated pathways associated with cell cycle endocrine disruptors signal transduction and immune systems. Comparative analyses of TCDD induced transcriptomic changes between fish and mammalian models revealed that proteomic pathway is consistently up regulated while calcium signaling pathway and several immune related pathways are generally down regulated. Overall design: Transcriptome profiling of treated sample TCDD and control sample DMSO were generated by deep sequencing using three prime RNA SAGE with SOLiD system	pubmed:24204792	DMSO	GSM1209643	source name:liver\|tissue:liver\|genotype:wildtype sibling\|treatment:DMSO	DMSO	The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Supplementary files format and content: The mapped transcripts were listed with GI and expression levels in TPM.	liver	3 mpf wildtype zebrafish were treated for 96 hrs. TCDD or DMSO treatment was conducted in 3 L tanks with around 15 adult and water was changed every day.	Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.		tissue:liver\|genotype:wildtype sibling\|treatment:DMSO	GSM1209643	GSM1209643: DMSO; Danio rerio; RNA Seq	GSM1209643	1	Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.	GEO Accession:GSM1209643	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	SRP028848		solid0518_20101014_Gong_1_SetA_F3_0_2DMSO.csfasta solid0518_20101014_Gong_1_SetA_F3_QV_0_2DMSO.qual	SOLiD_native SOLiD_native	409327205.0	11695063.0	GSM1209643 r1	0:35	0:136723730;1:95263220;2:87949986;3:88818989;.:571280	35						SRX335554	SRS470625	SRA098000	GEO	National University of Singapore	1	0.01735	0.00647	0.9946	0.51324	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2013-08-15	Adult	Adult	Liver	Liver and Biliary System
37131	37131	SRR952909	SRX335553	SRS470624	SRP028848	PRJNA215326	Transcriptomic analyses of TCDD treated zebrafish liver	GSE49915	Transcriptome Analysis	To fully understand molecular toxicity of TCDD in an in vivo animal model adult zebrafish were exposed to TCDD at xxx nM for xxx h and the livers were sampled for RNA sequencing based transcriptomic profiling. A total of 1 058 differently expressed genes were identified based on fold change>2 and TPM transcripts per million >10. Among the top 20 up regulated genes 10 novel responsive genes were identified and verified by qRT PCR analysis on independent samples. Transcriptomic analysis indicated several deregulated pathways associated with cell cycle endocrine disruptors signal transduction and immune systems. Comparative analyses of TCDD induced transcriptomic changes between fish and mammalian models revealed that proteomic pathway is consistently up regulated while calcium signaling pathway and several immune related pathways are generally down regulated. Overall design: Transcriptome profiling of treated sample TCDD and control sample DMSO were generated by deep sequencing using three prime RNA SAGE with SOLiD system	pubmed:24204792	TCDD	GSM1209642	source name:liver\|tissue:liver\|genotype:wildtype sibling\|treatment:TCDD	TCDD	The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Supplementary files format and content: The mapped transcripts were listed with GI and expression levels in TPM.	liver	3 mpf wildtype zebrafish were treated for 96 hrs. TCDD or DMSO treatment was conducted in 3 L tanks with around 15 adult and water was changed every day.	Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.		tissue:liver\|genotype:wildtype sibling\|treatment:TCDD	GSM1209642	GSM1209642: TCDD; Danio rerio; RNA Seq	GSM1209642	1	Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.	GEO Accession:GSM1209642	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	SRP028848		solid0518_20101014_Gong_1_SetA_F3_QV_1_2TCDD.qual solid0518_20101014_Gong_1_SetA_F3_1_2TCDD.csfasta	SOLiD_native SOLiD_native	627514895.0	17928997.0	GSM1209642 r1	0:35	0:214639659;1:142538233;2:131819822;3:137625000;.:892181	35						SRX335553	SRS470624	SRA098000	GEO	National University of Singapore	1	0.01773	0.00917	0.99646	0.56398	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2013-08-15	Adult	Adult	Liver	Liver and Biliary System
37271	37271	SRR1050719	SRX392663	SRS515660	SRP034513	PRJNA231764	Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer	GSE53342	Transcriptome Analysis	To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system	pubmed:24633177	X+M D+	GSM1289483	source name:liver tumor\|tissue:liver\|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP\|agent:doxycycline	X+M D+	The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	liver tumor	Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.	Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.		tissue:liver\|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP\|agent:doxycycline	GSM1289483	GSM1289483: X+M D+; Danio rerio; RNA Seq	GSM1289483	1	Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.	GEO Accession:GSM1289483	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	SRP034513		X+M-D+.csfasta.gz X+M-D+.qual	SOLiD_native SOLiD_native	367532585.0	10500931.0	GSM1289483 r1	0:35	0:113917936;1:90770860;2:74839037;3:87267038;.:737714	35						SRX392663	SRS515660	SRA117588	GEO	National University of Singapore	1	0.03142	0.01041	0.99115	0.47722	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2013-12-16	Adult	Adult	Liver	Liver and Biliary System
37272	37272	SRR1050718	SRX392662	SRS515661	SRP034513	PRJNA231764	Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer	GSE53342	Transcriptome Analysis	To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system	pubmed:24633177	X M+D+	GSM1289482	source name:liver tumor\|tissue:liver\|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP\|agent:doxycycline	X M+D+	The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	liver tumor	Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.	Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.		tissue:liver\|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP\|agent:doxycycline	GSM1289482	GSM1289482: X M+D+; Danio rerio; RNA Seq	GSM1289482	1	Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.	GEO Accession:GSM1289482	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	SRP034513		X-M+D+.csfasta.gz X-M+D+.qual	SOLiD_native SOLiD_native	524940885.0	14998311.0	GSM1289482 r1	0:35	0:177873348;1:126792787;2:107434769;3:111636161;.:1203820	35						SRX392662	SRS515661	SRA117588	GEO	National University of Singapore	1	0.04433	0.02519	0.99456	0.5443	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2013-12-16	Adult	Adult	Liver	Liver and Biliary System
37273	37273	SRR1050717	SRX392661	SRS515658	SRP034513	PRJNA231764	Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer	GSE53342	Transcriptome Analysis	To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system	pubmed:24633177	X M D+	GSM1289481	source name:control liver\|tissue:liver\|genotype:wildtype sibling\|agent:doxycycline	X M D+	The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	control liver	Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.	Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.		tissue:liver\|genotype:wildtype sibling\|agent:doxycycline	GSM1289481	GSM1289481: X M D+; Danio rerio; RNA Seq	GSM1289481	1	Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.	GEO Accession:GSM1289481	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	SRP034513		X-M-D+.csfasta.gz X-M-D+.qual	SOLiD_native SOLiD_native	503677265.0	14390779.0	GSM1289481 r1	0:35	0:153190412;1:124381654;2:106372352;3:118615876;.:1116971	35						SRX392661	SRS515658	SRA117588	GEO	National University of Singapore	1	0.03136	0.01201	0.99356	0.49598	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2013-12-16	Adult	Adult	Liver	Liver and Biliary System
37274	37274	SRR1050716	SRX392660	SRS515659	SRP034513	PRJNA231764	Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer	GSE53342	Transcriptome Analysis	To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system	pubmed:24633177	X+M D	GSM1289480	source name:control liver\|tissue:liver\|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP\|agent:n1	X+M D	The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	control liver	Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.	Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.		tissue:liver\|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP\|agent:n1	GSM1289480	GSM1289480: X+M D ; Danio rerio; RNA Seq	GSM1289480	1	Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.	GEO Accession:GSM1289480	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	SRP034513		X+M-D-.csfasta.gz X+M-D-.qual	SOLiD_native SOLiD_native	634523960.0	18129256.0	GSM1289480 r1	0:35	0:234010528;1:135057441;2:132344184;3:131577105;.:1534702	35						SRX392660	SRS515659	SRA117588	GEO	National University of Singapore	1	0.06814	0.05142	0.99579	0.6174	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2013-12-16	Adult	Adult	Liver	Liver and Biliary System
37275	37275	SRR1050715	SRX392659	SRS515657	SRP034513	PRJNA231764	Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer	GSE53342	Transcriptome Analysis	To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system	pubmed:24633177	X M+D	GSM1289479	source name:control liver\|tissue:liver\|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP\|agent:n1	X M+D	The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	control liver	Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.	Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.		tissue:liver\|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP\|agent:n1	GSM1289479	GSM1289479: X M+D ; Danio rerio; RNA Seq	GSM1289479	1	Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.	GEO Accession:GSM1289479	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	SRP034513		X-M+D-.csfasta.gz X-M+D-.qual	SOLiD_native SOLiD_native	417548565.0	11929959.0	GSM1289479 r1	0:35	0:114209112;1:103552786;2:91302789;3:107590004;.:893874	35						SRX392659	SRS515657	SRA117588	GEO	National University of Singapore	1	0.02253	0.00519	0.99218	0.61466	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2013-12-16	Adult	Adult	Liver	Liver and Biliary System
37276	37276	SRR1050714	SRX392658	SRS515656	SRP034513	PRJNA231764	Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer	GSE53342	Transcriptome Analysis	To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system	pubmed:24633177	X M D	GSM1289478	source name:control liver\|tissue:liver\|genotype:wildtype sibling\|agent:n1	X M D	The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	control liver	Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.	Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.		tissue:liver\|genotype:wildtype sibling\|agent:n1	GSM1289478	GSM1289478: X M D ; Danio rerio; RNA Seq	GSM1289478	1	Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.	GEO Accession:GSM1289478	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	SRP034513		X-M-D-.csfasta.gz X-M-D-.qual	SOLiD_native SOLiD_native	522827305.0	14937923.0	GSM1289478 r1	0:35	0:143962506;1:130748449;2:106995057;3:140038917;.:1082376	35						SRX392658	SRS515656	SRA117588	GEO	National University of Singapore	1	0.02926	0.00817	0.99022	0.53421	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2013-12-16	Adult	Adult	Liver	Liver and Biliary System
48021	48021	SRR6915090	SRX3862779	SRS3104834	SRP136710	PRJNA447984	RNA seq data from adult zebrafish caudal fin regeneration	GSE112498	Transcriptome Analysis	Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.	pubmed:30031067	10dpa replicate3	GSM3071386	source name:caudal fin tissue 10 dy post amputation\|tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	10dpa replicate3	SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample	caudal fin tissue 10 dy post amputation	Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction.	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.	tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	GSM3071386	GSM3071386: 10dpa replicate3; Danio rerio; RNA Seq	GSM3071386	1	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	GEO Accession:GSM3071386	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB 5500 Genetic Analyzer	SRP136710	options: accept hard clip	Solid5500_2014_11_07_1_L03-1-Idx_10-10.bam	bam	682375516.0	14088728.0	GSM3071386 r1	0:48.43	A:140419665;C:148759068;G:176799261;T:168695522;N:47702000	48	140419665	148759068	176799261	168695522	47702000	SRX3862779	SRS3104834	SRA676352	GEO	Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon	1	0.76603	0.04459	0.79752	0.50424	50	B	usable mapping rate	legacy	early	full_length	random_priming	lexogen	bulk	unknown	unknown	France	2018-03-29	Adult	Adult	Fin	Surface Structure
48022	48022	SRR6915089	SRX3862778	SRS3104833	SRP136710	PRJNA447984	RNA seq data from adult zebrafish caudal fin regeneration	GSE112498	Transcriptome Analysis	Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.	pubmed:30031067	3dpa replicate3	GSM3071385	source name:caudal fin tissue 3 dy post amputation\|tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	3dpa replicate3	SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample	caudal fin tissue 3 dy post amputation	Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction.	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.	tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	GSM3071385	GSM3071385: 3dpa replicate3; Danio rerio; RNA Seq	GSM3071385	1	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	GEO Accession:GSM3071385	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB 5500 Genetic Analyzer	SRP136710	options: accept hard clip	Solid5500_2014_11_07_1_L03-1-Idx_12-12.bam	bam	901887293.0	18522789.0	GSM3071385 r1	0:48.69	A:184300673;C:193849264;G:243428119;T:224471972;N:55837265	48	184300673	193849264	243428119	224471972	55837265	SRX3862778	SRS3104833	SRA676352	GEO	Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon	1	0.78632	0.03154	0.79707	0.51779	50	B	usable mapping rate	legacy	early	full_length	random_priming	lexogen	bulk	unknown	unknown	France	2018-03-29	Adult	Adult	Fin	Surface Structure
48023	48023	SRR6915088	SRX3862777	SRS3104832	SRP136710	PRJNA447984	RNA seq data from adult zebrafish caudal fin regeneration	GSE112498	Transcriptome Analysis	Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.	pubmed:30031067	2dpa replicate3	GSM3071384	source name:caudal fin tissue 2 dy post amputation\|tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	2dpa replicate3	SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample	caudal fin tissue 2 dy post amputation	Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction.	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.	tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	GSM3071384	GSM3071384: 2dpa replicate3; Danio rerio; RNA Seq	GSM3071384	1	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	GEO Accession:GSM3071384	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB 5500 Genetic Analyzer	SRP136710	options: accept hard clip	Solid5500_2014_11_07_1_L03-1-Idx_11-11.bam	bam	850810410.0	17462158.0	GSM3071384 r1	0:48.72	A:176186499;C:182052044;G:228063922;T:213571294;N:50936651	48	176186499	182052044	228063922	213571294	50936651	SRX3862777	SRS3104832	SRA676352	GEO	Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon	1	0.77804	0.03462	0.80229	0.49822	43	B	usable mapping rate	legacy	early	full_length	random_priming	lexogen	bulk	unknown	unknown	France	2018-03-29	Adult	Adult	Fin	Surface Structure
48024	48024	SRR6915087	SRX3862776	SRS3104831	SRP136710	PRJNA447984	RNA seq data from adult zebrafish caudal fin regeneration	GSE112498	Transcriptome Analysis	Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.	pubmed:30031067	0dpa replicate3	GSM3071383	source name:caudal fin tissue 0 dy post amputation\|tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	0dpa replicate3	SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample	caudal fin tissue 0 dy post amputation	Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction.	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.	tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	GSM3071383	GSM3071383: 0dpa replicate3; Danio rerio; RNA Seq	GSM3071383	1	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	GEO Accession:GSM3071383	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB 5500 Genetic Analyzer	SRP136710	options: accept hard clip	Solid5500_2014_11_07_1_L03-1-Idx_9-9.bam	bam	598710241.0	12328728.0	GSM3071383 r1	0:48.56	A:121889198;C:129444719;G:158430979;T:150128070;N:38817275	48	121889198	129444719	158430979	150128070	38817275	SRX3862776	SRS3104831	SRA676352	GEO	Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon	1	0.77	0.03334	0.799	0.45925	50	B	usable mapping rate	legacy	early	full_length	random_priming	lexogen	bulk	unknown	unknown	France	2018-03-29	Adult	Adult	Fin	Surface Structure
48025	48025	SRR6915086	SRX3862775	SRS3104830	SRP136710	PRJNA447984	RNA seq data from adult zebrafish caudal fin regeneration	GSE112498	Transcriptome Analysis	Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.	pubmed:30031067	10dpa replicate2	GSM3071382	source name:caudal fin tissue 10 dy post amputation\|tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	10dpa replicate2	SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample	caudal fin tissue 10 dy post amputation	Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction.	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.	tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	GSM3071382	GSM3071382: 10dpa replicate2; Danio rerio; RNA Seq	GSM3071382	1	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	GEO Accession:GSM3071382	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB 5500 Genetic Analyzer	SRP136710	options: accept hard clip	Solid5500_2014_11_07_1_L02-1-Idx_8-8.bam	bam	1205021238.0	24639106.0	GSM3071382 r1	0:48.91	A:255022070;C:275793907;G:309172527;T:294800027;N:70232707	48	255022070	275793907	309172527	294800027	70232707	SRX3862775	SRS3104830	SRA676352	GEO	Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon	1	0.80398	0.05829	0.78644	0.4993	50	B	usable mapping rate	legacy	early	full_length	random_priming	lexogen	bulk	unknown	unknown	France	2018-03-29	Adult	Adult	Fin	Surface Structure
48026	48026	SRR6915085	SRX3862774	SRS3104829	SRP136710	PRJNA447984	RNA seq data from adult zebrafish caudal fin regeneration	GSE112498	Transcriptome Analysis	Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.	pubmed:30031067	3dpa replicate2	GSM3071381	source name:caudal fin tissue 3 dy post amputation\|tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	3dpa replicate2	SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample	caudal fin tissue 3 dy post amputation	Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction.	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.	tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	GSM3071381	GSM3071381: 3dpa replicate2; Danio rerio; RNA Seq	GSM3071381	1	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	GEO Accession:GSM3071381	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB 5500 Genetic Analyzer	SRP136710	options: accept hard clip	Solid5500_2014_11_07_1_L02-1-Idx_10-10.bam	bam	1479531813.0	30219937.0	GSM3071381 r1	0:48.96	A:314793261;C:331769330;G:384109921;T:369987947;N:78871354	48	314793261	331769330	384109921	369987947	78871354	SRX3862774	SRS3104829	SRA676352	GEO	Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon	1	0.81777	0.03195	0.7821	0.49263	50	B	usable mapping rate	legacy	early	full_length	random_priming	lexogen	bulk	unknown	unknown	France	2018-03-29	Adult	Adult	Fin	Surface Structure
48027	48027	SRR6915084	SRX3862773	SRS3104828	SRP136710	PRJNA447984	RNA seq data from adult zebrafish caudal fin regeneration	GSE112498	Transcriptome Analysis	Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.	pubmed:30031067	2dpa replicate2	GSM3071380	source name:caudal fin tissue 2 dy post amputation\|tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	2dpa replicate2	SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample	caudal fin tissue 2 dy post amputation	Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction.	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.	tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	GSM3071380	GSM3071380: 2dpa replicate2; Danio rerio; RNA Seq	GSM3071380	1	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	GEO Accession:GSM3071380	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB 5500 Genetic Analyzer	SRP136710	options: accept hard clip	Solid5500_2014_11_07_1_L02-1-Idx_9-9.bam	bam	834856811.0	17079585.0	GSM3071380 r1	0:48.88	A:179851654;C:186667201;G:209784080;T:212166083;N:46387793	48	179851654	186667201	209784080	212166083	46387793	SRX3862773	SRS3104828	SRA676352	GEO	Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon	1	0.80341	0.02786	0.78031	0.49876	50	B	usable mapping rate	legacy	early	full_length	random_priming	lexogen	bulk	unknown	unknown	France	2018-03-29	Adult	Adult	Fin	Surface Structure
48028	48028	SRR6915083	SRX3862772	SRS3104827	SRP136710	PRJNA447984	RNA seq data from adult zebrafish caudal fin regeneration	GSE112498	Transcriptome Analysis	Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.	pubmed:30031067	0dpa replicate2	GSM3071379	source name:caudal fin tissue 0 dy post amputation\|tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	0dpa replicate2	SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample	caudal fin tissue 0 dy post amputation	Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction.	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.	tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	GSM3071379	GSM3071379: 0dpa replicate2; Danio rerio; RNA Seq	GSM3071379	1	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	GEO Accession:GSM3071379	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB 5500 Genetic Analyzer	SRP136710	options: accept hard clip	Solid5500_2014_11_07_1_L02-1-Idx_7-7.bam	bam	821645371.0	16824250.0	GSM3071379 r1	0:48.84	A:169383232;C:176200663;G:223364159;T:207905438;N:44791879	48	169383232	176200663	223364159	207905438	44791879	SRX3862772	SRS3104827	SRA676352	GEO	Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon	1	0.79697	0.04152	0.79513	0.48078	34	B	usable mapping rate	legacy	early	full_length	random_priming	lexogen	bulk	unknown	unknown	France	2018-03-29	Adult	Adult	Fin	Surface Structure
48029	48029	SRR6915082	SRX3862771	SRS3104826	SRP136710	PRJNA447984	RNA seq data from adult zebrafish caudal fin regeneration	GSE112498	Transcriptome Analysis	Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.	pubmed:30031067	10dpa replicate1	GSM3071378	source name:caudal fin tissue 10 dy post amputation\|tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	10dpa replicate1	SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample	caudal fin tissue 10 dy post amputation	Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction.	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.	tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	GSM3071378	GSM3071378: 10dpa replicate1; Danio rerio; RNA Seq	GSM3071378	1	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	GEO Accession:GSM3071378	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB 5500 Genetic Analyzer	SRP136710	options: accept hard clip	Solid5500_2014_11_07_1_L01-1-Idx_4-4.bam	bam	1056921416.0	21553661.0	GSM3071378 r1	0:49.04	A:223138065;C:233998717;G:286278215;T:261736901;N:51769518	49	223138065	233998717	286278215	261736901	51769518	SRX3862771	SRS3104826	SRA676352	GEO	Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon	1	0.81372	0.06015	0.79017	0.49818	50	B	usable mapping rate	legacy	early	full_length	random_priming	lexogen	bulk	unknown	unknown	France	2018-03-29	Adult	Adult	Fin	Surface Structure
48030	48030	SRR6915081	SRX3862770	SRS3104824	SRP136710	PRJNA447984	RNA seq data from adult zebrafish caudal fin regeneration	GSE112498	Transcriptome Analysis	Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.	pubmed:30031067	3dpa replicate1	GSM3071377	source name:caudal fin tissue 3 dy post amputation\|tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	3dpa replicate1	SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample	caudal fin tissue 3 dy post amputation	Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction.	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.	tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	GSM3071377	GSM3071377: 3dpa replicate1; Danio rerio; RNA Seq	GSM3071377	1	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	GEO Accession:GSM3071377	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB 5500 Genetic Analyzer	SRP136710	options: accept hard clip	Solid5500_2014_11_07_1_L01-1-Idx_6-6.bam	bam	614372216.0	12531168.0	GSM3071377 r1	0:49.03	A:129828689;C:133826356;G:168985348;T:153858339;N:27873484	49	129828689	133826356	168985348	153858339	27873484	SRX3862770	SRS3104824	SRA676352	GEO	Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon	1	0.81659	0.02803	0.78987	0.49295	50	B	usable mapping rate	legacy	early	full_length	random_priming	lexogen	bulk	unknown	unknown	France	2018-03-29	Adult	Adult	Fin	Surface Structure
48031	48031	SRR6915080	SRX3862769	SRS3104825	SRP136710	PRJNA447984	RNA seq data from adult zebrafish caudal fin regeneration	GSE112498	Transcriptome Analysis	Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.	pubmed:30031067	2dpa replicate1	GSM3071376	source name:caudal fin tissue 2 dy post amputation\|tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	2dpa replicate1	SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample	caudal fin tissue 2 dy post amputation	Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction.	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.	tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	GSM3071376	GSM3071376: 2dpa replicate1; Danio rerio; RNA Seq	GSM3071376	1	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	GEO Accession:GSM3071376	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB 5500 Genetic Analyzer	SRP136710	options: accept hard clip	Solid5500_2014_11_07_1_L01-1-Idx_5-5.bam	bam	1317408760.0	26870813.0	GSM3071376 r1	0:49.03	A:278980295;C:285236037;G:357022664;T:334390621;N:61779143	49	278980295	285236037	357022664	334390621	61779143	SRX3862769	SRS3104825	SRA676352	GEO	Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon	1	0.81546	0.02559	0.79328	0.48857	50	B	usable mapping rate	legacy	early	full_length	random_priming	lexogen	bulk	unknown	unknown	France	2018-03-29	Adult	Adult	Fin	Surface Structure
48032	48032	SRR6915079	SRX3862768	SRS3104823	SRP136710	PRJNA447984	RNA seq data from adult zebrafish caudal fin regeneration	GSE112498	Transcriptome Analysis	Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.	pubmed:30031067	0dpa replicate1	GSM3071375	source name:caudal fin tissue 0 dy post amputation\|tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	0dpa replicate1	SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample	caudal fin tissue 0 dy post amputation	Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction.	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.	tissue:caudal fin\|strain:AB Tu\|age:adults between 8 mpf and 18 mpf	GSM3071375	GSM3071375: 0dpa replicate1; Danio rerio; RNA Seq	GSM3071375	1	RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.	GEO Accession:GSM3071375	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB 5500 Genetic Analyzer	SRP136710	options: accept hard clip	Solid5500_2014_11_07_1_L01-1-Idx_3-3.bam	bam	975324708.0	19881338.0	GSM3071375 r1	0:49.06	A:203549346;C:215407985;G:265949502;T:244027187;N:46390688	49	203549346	215407985	265949502	244027187	46390688	SRX3862768	SRS3104823	SRA676352	GEO	Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon	1	0.80817	0.05047	0.79569	0.47149	50	B	usable mapping rate	legacy	early	full_length	random_priming	lexogen	bulk	unknown	unknown	France	2018-03-29	Adult	Adult	Fin	Surface Structure

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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");;