metadata: run_metadata: 12 rows where devstage_curation = "Larval" and experiment.platform = "ABI

12 rows where devstage_curation = "Larval" 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.attributes	study.PMIDs	sample.description	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.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	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
36506	36506	SRR566696	SRX185761	SRS361914	SRP015680	PRJNA174800	Transcriptomic analyses of Myc induced zebrafish liver cancer	GSE40745	Transcriptome Analysis	To study the characteristics and mechanisms of Myc 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 ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.		pubmed:23038063	source: liver tumor M+D+	GSM1000561: M+D+ 2	GSM1000561	genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP\|tissue:liver\|treatment:doxycycline	M+D+ 2	The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	liver tumor M+D+	Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.	Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.		genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP\|tissue:liver\|treatment:doxycycline	GSM1000561	GSM1000561: M+D+ 2; Danio rerio; RNA Seq	GSM1000561 1	1		GEO Accession:GSM1000561	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD 3 Plus System	SRP015680	M+D+_2_QV.qual M+D+_2.csfasta	SOLiD_native SOLiD_native	1493416960.0	42669056.0	GSM1000561 r1	0:35	0:377247910;1:348861020;2:522134600;3:237405266;.:7768164	35	SRX185761	SRS361914	SRA058618	GEO	National University of Singapore	1	0.06244	0.00306	0.99567	0.34618	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2012-09-10	Larval	Larval	Liver	Liver and Biliary System
36507	36507	SRR566695	SRX185760	SRS361913	SRP015680	PRJNA174800	Transcriptomic analyses of Myc induced zebrafish liver cancer	GSE40745	Transcriptome Analysis	To study the characteristics and mechanisms of Myc 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 ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.		pubmed:23038063	source: liver tumor M+D+	GSM1000560: M+D+ 1	GSM1000560	genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP\|tissue:liver\|treatment:doxycycline	M+D+ 1	The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	liver tumor M+D+	Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.	Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.		genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP\|tissue:liver\|treatment:doxycycline	GSM1000560	GSM1000560: M+D+ 1; Danio rerio; RNA Seq	GSM1000560 1	1		GEO Accession:GSM1000560	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD 3 Plus System	SRP015680			1291539515.0	36901129.0	GSM1000560 r1	0:35	0:266006021;1:328523841;2:440474617;3:254266912;.:2268124	35	SRX185760	SRS361913	SRA058618	GEO	National University of Singapore	1	0.10629	0.0044	0.99239	0.31953	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2012-09-10	Larval	Larval	Liver	Liver and Biliary System
36508	36508	SRR566694	SRX185759	SRS361912	SRP015680	PRJNA174800	Transcriptomic analyses of Myc induced zebrafish liver cancer	GSE40745	Transcriptome Analysis	To study the characteristics and mechanisms of Myc 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 ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.		pubmed:23038063	source: control liver M D+	GSM1000559: M D+ 2	GSM1000559	genotype:wildtype\|tissue:liver\|treatment:doxycycline	M D+ 2	The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	control liver M D+	Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.	Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.		genotype:wildtype\|tissue:liver\|treatment:doxycycline	GSM1000559	GSM1000559: M D+ 2; Danio rerio; RNA Seq	GSM1000559 1	1		GEO Accession:GSM1000559	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD 3 Plus System	SRP015680	M-D+_2_QV.qual	SOLiD_native	1438423910.0	41097826.0	GSM1000559 r1	0:35	0:353104627;1:349496969;2:433338629;3:275089557;.:27394128	35	SRX185759	SRS361912	SRA058618	GEO	National University of Singapore	1	0.04748	0.00442	0.99425	0.53794	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2012-09-10	Larval	Larval	Liver	Liver and Biliary System
36509	36509	SRR566693	SRX185758	SRS361911	SRP015680	PRJNA174800	Transcriptomic analyses of Myc induced zebrafish liver cancer	GSE40745	Transcriptome Analysis	To study the characteristics and mechanisms of Myc 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 ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.		pubmed:23038063	source: control liver M D+	GSM1000558: M D+ 1	GSM1000558	genotype:wildtype\|tissue:liver\|treatment:doxycycline	M D+ 1	The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	control liver M D+	Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.	Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.		genotype:wildtype\|tissue:liver\|treatment:doxycycline	GSM1000558	GSM1000558: M D+ 1; Danio rerio; RNA Seq	GSM1000558 1	1		GEO Accession:GSM1000558	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD 3 Plus System	SRP015680	M-D+_1.csfasta	SOLiD_native	1284638285.0	36703951.0	GSM1000558 r1	0:35	0:328871758;1:317693850;2:402981931;3:233637468;.:1453278	35	SRX185758	SRS361911	SRA058618	GEO	National University of Singapore	1	0.10539	0.00562	0.99141	0.37635	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2012-09-10	Larval	Larval	Liver	Liver and Biliary System
36510	36510	SRR566692	SRX185757	SRS361910	SRP015680	PRJNA174800	Transcriptomic analyses of Myc induced zebrafish liver cancer	GSE40745	Transcriptome Analysis	To study the characteristics and mechanisms of Myc 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 ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.		pubmed:23038063	source: control liver M+D	GSM1000557: M+D 2	GSM1000557	genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP\|tissue:liver\|treatment:n1	M+D 2	The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	control liver M+D	Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.	Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.		genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP\|tissue:liver\|treatment:n1	GSM1000557	GSM1000557: M+D 2; Danio rerio; RNA Seq	GSM1000557 1	1		GEO Accession:GSM1000557	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD 3 Plus System	SRP015680	M+D-_2_QV.qual	SOLiD_native	1404966080.0	40141888.0	GSM1000557 r1	0:35	0:371691603;1:354481639;2:405221861;3:271978812;.:1592165	35	SRX185757	SRS361910	SRA058618	GEO	National University of Singapore	1	0.07869	0.00455	0.99253	0.51508	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2012-09-10	Larval	Larval	Liver	Liver and Biliary System
36511	36511	SRR566691	SRX185756	SRS361909	SRP015680	PRJNA174800	Transcriptomic analyses of Myc induced zebrafish liver cancer	GSE40745	Transcriptome Analysis	To study the characteristics and mechanisms of Myc 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 ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.		pubmed:23038063	source: control liver M+D	GSM1000556: M+D 1	GSM1000556	genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP\|tissue:liver\|treatment:n1	M+D 1	The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	control liver M+D	Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.	Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.		genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP\|tissue:liver\|treatment:n1	GSM1000556	GSM1000556: M+D 1; Danio rerio; RNA Seq	GSM1000556 1	1		GEO Accession:GSM1000556	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD 3 Plus System	SRP015680	M+D-_1_QV.qual M+D-_1.csfasta	SOLiD_native SOLiD_native	1286706820.0	36763052.0	GSM1000556 r1	0:35	0:252864341;1:338709089;2:436928155;3:256235022;.:1970213	35	SRX185756	SRS361909	SRA058618	GEO	National University of Singapore	1	0.12399	0.00617	0.98752	0.50351	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2012-09-10	Larval	Larval	Liver	Liver and Biliary System
36512	36512	SRR566690	SRX185755	SRS361908	SRP015680	PRJNA174800	Transcriptomic analyses of Myc induced zebrafish liver cancer	GSE40745	Transcriptome Analysis	To study the characteristics and mechanisms of Myc 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 ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.		pubmed:23038063	source: control liver M D	GSM1000555: M D 2	GSM1000555	genotype:wildtype\|tissue:liver\|treatment:n1	M D 2	The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	control liver M D	Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.	Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.		genotype:wildtype\|tissue:liver\|treatment:n1	GSM1000555	GSM1000555: M D 2; Danio rerio; RNA Seq	GSM1000555 1	1		GEO Accession:GSM1000555	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD 3 Plus System	SRP015680	M-D-_2_QV.qual M-D-_2.csfasta	SOLiD_native SOLiD_native	1337952770.0	38227222.0	GSM1000555 r1	0:35	0:391863829;1:347720340;2:312814682;3:283542736;.:2011183	35	SRX185755	SRS361908	SRA058618	GEO	National University of Singapore	1	0.04605	0.00365	0.99494	0.51825	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2012-09-10	Larval	Larval	Liver	Liver and Biliary System
36513	36513	SRR566689	SRX185754	SRS361907	SRP015680	PRJNA174800	Transcriptomic analyses of Myc induced zebrafish liver cancer	GSE40745	Transcriptome Analysis	To study the characteristics and mechanisms of Myc 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 ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.		pubmed:23038063	source: control liver M D	GSM1000554: M D 1	GSM1000554	genotype:wildtype\|tissue:liver\|treatment:n1	M D 1	The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	control liver M D	Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.	Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.		genotype:wildtype\|tissue:liver\|treatment:n1	GSM1000554	GSM1000554: M D 1; Danio rerio; RNA Seq	GSM1000554 1	1		GEO Accession:GSM1000554	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD 3 Plus System	SRP015680	M-D-_1.csfasta	SOLiD_native	1395143680.0	39861248.0	GSM1000554 r1	0:35	0:439852883;1:355203725;2:298639546;3:299770820;.:1676706	35	SRX185754	SRS361907	SRA058618	GEO	National University of Singapore	1	0.02094	0.00123	0.99784	0.58426	35	B	usable mapping rate	legacy	early	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2012-09-10	Larval	Larval	Liver	Liver and Biliary System
36685	36685	SRR801688	SRX258168	SRS406299	SRP020469	PRJNA195909	RNA sequencing project for zebrafish embryo and larva development	GSE45706	Transcriptome Analysis	Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish		pubmed:23700457;pubmed:26891128	source: Zebrafish 1 wpf larvae	GSM1112163: larva 1 week	GSM1112163	strain:AB\|developmental stage:larva 1 week\|tissue:larva	larva 1 week	Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly	Zebrafish 1 wpf larvae	Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.	Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.	Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995	strain:AB\|developmental stage:larva 1 week\|tissue:larva	GSM1112163	GSM1112163: larva 1 week; Danio rerio; RNA Seq	GSM1112163 1	1		GEO Accession:GSM1112163	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	SRP020469	D_rerio_1week_F3.csfasta.bz2 D_rerio_1week_F3_QV.qual.bz2	SOLiD_native SOLiD_native	18866346300.0	377326926.0	GSM1112163 r1	0:50	0:4319577052;1:5210931849;2:5202393345;3:4013865803;.:119578251	50	SRX258168	SRS406299	SRA072427	GEO	Shanghai Chenshan Botanical Garden	1	0.60649	0.05524	0.86746	0.51092	50	B	usable mapping rate	legacy	early	unknown	poly_a	unknown	bulk	unknown	unknown	China	2013-04-02	Larval	Larval	Embryo Imprecise	All anatomical structures
36686	36686	SRR801687	SRX258167	SRS406298	SRP020469	PRJNA195909	RNA sequencing project for zebrafish embryo and larva development	GSE45706	Transcriptome Analysis	Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish		pubmed:23700457;pubmed:26891128	source: Zebrafish embryos at the Protruding mouth stage	GSM1112162: Protruding mouth 72hpf	GSM1112162	strain:AB\|developmental stage:Protruding mouth 72hpf\|tissue:embryo	Protruding mouth 72hpf	Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly	Zebrafish embryos at the Protruding mouth stage	Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.	Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.	Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995	strain:AB\|developmental stage:Protruding mouth 72hpf\|tissue:embryo	GSM1112162	GSM1112162: Protruding mouth 72hpf; Danio rerio; RNA Seq	GSM1112162 1	1		GEO Accession:GSM1112162	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	SRP020469	D_rerio_72hpf_F3.csfasta.bz2 D_rerio_72hpf_F3_QV.qual.bz2	SOLiD_native SOLiD_native	19339397750.0	386787955.0	GSM1112162 r1	0:50	0:4755453154;1:5011845177;2:5110574744;3:4002085043;.:459439632	50	SRX258167	SRS406298	SRA072427	GEO	Shanghai Chenshan Botanical Garden	1	0.34099	0.03045	0.92409	0.49783	50	B	usable mapping rate	legacy	early	unknown	poly_a	unknown	bulk	unknown	unknown	China	2013-04-02	Larval	Larval	Embryo Imprecise	All anatomical structures
37907	37907	SRR1104969	SRX424037	SRS527958	SRP035264	PRJNA236557	Genome wide analysis of gene expression and intron retention during development in a U12 type splicing deficient zebrafish mutant [RNA seq]	GSE53758	Transcriptome Analysis	To determine the global impact of the clbn mutation on gene expression and efficiency of U2 and U12 type splicing we analyzed the transcriptome of 108hpf wt and clbn mutant larvae by microarrays and RNA sequencing. RNAseq data was used to characterize intron retention of U2 type and U12 type intron on a genome wide scale to confirm that rnpc3 deficiency specifically impairs U12 type splicing. RNAseq and microarray data were combined to yield high confidence lists of differentially expressed genes which show that impaired U12 type splicing has a wide ranging effect on the developing transcriptome. Overall design: RNAseq libraries prepared from 108 hpf zebrafish larvae approx. 60 embryos each genotyped homozygous wildtype and homozygous clbns841 mutants respectively	parent bioproject:PRJNA236230	pubmed:24516132		108hpf clbn	GSM1303831	source name:108hpf clbn larvae\|genotype/variation:clbns841\|development stage:108 hpf\|tissue:whole larvae	108hpf clbn	50bp single end reads were mapped using the X MATE recursive mapping pipeline 42 allowing for 5 color space mismatches per 50bp read CS 50 5 The uniquely mappable regions uniqueome of the ZV9 assembly were calculated using the same mapping parameters CS 50 5 For intron retention analysis RPKM were calculated for annotated Refseq introns + manually annotated U12 type introns using Galaxy For gene expression analysis RPKM were calculated for annotated Refseq coding regions using Galaxy Genome build: Zebrafish Zv9	108hpf clbn larvae	Starting at 24 hpf embryos were transferred into egg water containing 0.003% 1 Phenyl 2 thiourea PTU to prevent pigmentation	Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first and aqueous phases of all homozygous wildtype and mutant larvae respectively were pooled prior to RNA precipiation with isopropanol. For RNA sequencing RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD™ Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F 08/2009. 8μl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37°C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50μl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5μl by centrifuging under vacuum at 40°C. 1μl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5’ end of the sense strand. post o/n ligation samples were reverse transcribed for 30min at 42°C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide 8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.	Embryos for all experiments were produced by natural spawning transferred into petri dishes with pre warmed egg water 60mg of sea salt/1L ddH20 and placed in a 28.5°C incubator on a 12h light/dark cycle.	genotype/variation:clbns841\|developmental stage:108 hpf\|tissue:whole larvae	GSM1303831	GSM1303831: 108hpf clbn; Danio rerio; RNA Seq	GSM1303831	1	Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first and aqueous phases of all homozygous wildtype and mutant larvae respectively were pooled prior to RNA precipiation with isopropanol. For RNA sequencing RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD™ Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F 08/2009. 8μl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37°C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50μl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5μl by centrifuging under vacuum at 40°C. 1μl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5’ end of the sense strand. post o/n ligation samples were reverse transcribed for 30min at 42°C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide 8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.	GEO Accession:GSM1303831	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	SRP035264	108hpf_clbn_F3_QV.qual.bz2 108hpf_clbn_F3.csfasta.bz2	SOLiD_native SOLiD_native	2698882700.0	53977654.0	GSM1303831 r1	0:50	0:653022205;1:711705790;2:753066133;3:571973990;.:9114582	50	SRX424037	SRS527958	SRA123959	GEO	Heath Laboratory, Development and Cancer, Walter and Eliza Hall Institute of Medical Research	1	0.56134	0.05842	0.84303	0.49093	50	B	usable mapping rate	legacy	early	full_length	poly_a	unknown	bulk	unknown	unknown	Australia	2014-01-09	Larval	Larval	Whole Organism	All anatomical structures
37908	37908	SRR1104968	SRX424036	SRS527957	SRP035264	PRJNA236557	Genome wide analysis of gene expression and intron retention during development in a U12 type splicing deficient zebrafish mutant [RNA seq]	GSE53758	Transcriptome Analysis	To determine the global impact of the clbn mutation on gene expression and efficiency of U2 and U12 type splicing we analyzed the transcriptome of 108hpf wt and clbn mutant larvae by microarrays and RNA sequencing. RNAseq data was used to characterize intron retention of U2 type and U12 type intron on a genome wide scale to confirm that rnpc3 deficiency specifically impairs U12 type splicing. RNAseq and microarray data were combined to yield high confidence lists of differentially expressed genes which show that impaired U12 type splicing has a wide ranging effect on the developing transcriptome. Overall design: RNAseq libraries prepared from 108 hpf zebrafish larvae approx. 60 embryos each genotyped homozygous wildtype and homozygous clbns841 mutants respectively	parent bioproject:PRJNA236230	pubmed:24516132		108hpf wt	GSM1303830	source name:108hpf wt larvae\|genotype/variation:wildtype\|development stage:108 hpf\|tissue:whole larvae	108hpf wt	50bp single end reads were mapped using the X MATE recursive mapping pipeline 42 allowing for 5 color space mismatches per 50bp read CS 50 5 The uniquely mappable regions uniqueome of the ZV9 assembly were calculated using the same mapping parameters CS 50 5 For intron retention analysis RPKM were calculated for annotated Refseq introns + manually annotated U12 type introns using Galaxy For gene expression analysis RPKM were calculated for annotated Refseq coding regions using Galaxy Genome build: Zebrafish Zv9	108hpf wt larvae	Starting at 24 hpf embryos were transferred into egg water containing 0.003% 1 Phenyl 2 thiourea PTU to prevent pigmentation	Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first and aqueous phases of all homozygous wildtype and mutant larvae respectively were pooled prior to RNA precipiation with isopropanol. For RNA sequencing RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD™ Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F 08/2009. 8μl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37°C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50μl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5μl by centrifuging under vacuum at 40°C. 1μl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5’ end of the sense strand. post o/n ligation samples were reverse transcribed for 30min at 42°C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide 8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.	Embryos for all experiments were produced by natural spawning transferred into petri dishes with pre warmed egg water 60mg of sea salt/1L ddH20 and placed in a 28.5°C incubator on a 12h light/dark cycle.	genotype/variation:wildtype\|developmental stage:108 hpf\|tissue:whole larvae	GSM1303830	GSM1303830: 108hpf wt; Danio rerio; RNA Seq	GSM1303830	1	Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first and aqueous phases of all homozygous wildtype and mutant larvae respectively were pooled prior to RNA precipiation with isopropanol. For RNA sequencing RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD™ Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F 08/2009. 8μl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37°C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50μl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5μl by centrifuging under vacuum at 40°C. 1μl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5’ end of the sense strand. post o/n ligation samples were reverse transcribed for 30min at 42°C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide 8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.	GEO Accession:GSM1303830	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	SRP035264	108hpf_wt_F3_QV.qual.bz2 108hpf_wt_F3.csfasta.bz2	SOLiD_native SOLiD_native	2835473700.0	56709474.0	GSM1303830 r1	0:50	0:697915785;1:748317376;2:781024795;3:605838541;.:2377203	50	SRX424036	SRS527957	SRA123959	GEO	Heath Laboratory, Development and Cancer, Walter and Eliza Hall Institute of Medical Research	1	0.57033	0.05759	0.8384	0.49692	50	B	usable mapping rate	legacy	early	full_length	poly_a	unknown	bulk	unknown	unknown	Australia	2014-01-09	Larval	Larval	Whole Organism	All anatomical structures

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