metadata: run_metadata: 12 rows where experiment.library_selection = "cDNA", experiment.platform = "ABI_SOLID" and tissue

12 rows where experiment.library_selection = "cDNA", experiment.platform = "ABI_SOLID" and tissue_curation = "Fin"

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
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");;