metadata: run_metadata: 18 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "other" and tissue_curation

18 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "other" and tissue_curation_coarse = "Reproductive System"

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.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.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
36285	36285	SRR363985	SRX105298	SRS270141	SRP009275	PRJNA148581	Hen1 analysis in zebrafish	GSE33582	Transcriptome Analysis	small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel the small RNA libraries wre made.		pubmed:20859253	wildtype ligation	GSM830247	source name:testis\|strain:TL\|genotype/variation:Hen1 wildtype\|tissue:testis\|small rna library prep method:adapter ligation	wildtype ligation	three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8	testis		Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. Adaptors were ligated to the five prime and three prime ends of the isolated RNA and the product was converted to cDNA using a primer on the three prime adaptor. post 15 cycles PCR amplification of the library the product was gel purified and sequenced on a Solexa platform.		strain:TL\|genotype/variation:Hen1 wildtype\|tissue:testis\|small rna library prep method:adapter ligation	GSM830247	GSM830247: wildtype ligation	GSM830247: wildtype ligation	GSM830247: wildtype ligation	1		GEO Accession:GSM830247	RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP009275	read name barcode proc directive:ignore	WTTESTIS.fastq	fastq	395791130.0	8604155.0	GSM830247 1	0:46	A:79045664;C:90489917;G:99082007;T:127024229;N:149313	46		79045664	90489917	99082007	127024229	149313	SRX105298	SRS270141	SRA047996	GEO	European Research Institute for the Biology of Ageing, University Medical Center Groningen	1	0.00021	0.00015	0.99989	0.0	46	T	under 1.2% mapping rate	illumina	early_illumina	5prime	poly_a	unknown	bulk	unknown	unknown	Netherlands	2011-11-09	Undetermined	Undetermined	Gonad	Reproductive System
36286	36286	SRR363984	SRX105297	SRS270140	SRP009275	PRJNA148581	Hen1 analysis in zebrafish	GSE33582	Transcriptome Analysis	small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel the small RNA libraries wre made.		pubmed:20859253	hen1 mutant ligation	GSM830246	source name:testis\|strain:TL\|genotype/variation:Hen1 mutant\|tissue:testis\|small rna library prep method:adapter ligation	hen1 mutant ligation	three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8	testis		Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. Adaptors were ligated to the five prime and three prime ends of the isolated RNA and the product was converted to cDNA using a primer on the three prime adaptor. post 15 cycles PCR amplification of the library the product was gel purified and sequenced on a Solexa platform.		strain:TL\|genotype/variation:Hen1 mutant\|tissue:testis\|small rna library prep method:adapter ligation	GSM830246	GSM830246: hen1 mutant ligation	GSM830246: hen1 mutant ligation	GSM830246: hen1 mutant ligation	1		GEO Accession:GSM830246	RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP009275	read name barcode proc directive:ignore	HEN1TESTIS.fastq	fastq	440876374.0	9584269.0	GSM830246 1	0:46	A:91693980;C:99515953;G:105634029;T:143841954;N:190458	46		91693980	99515953	105634029	143841954	190458	SRX105297	SRS270140	SRA047996	GEO	European Research Institute for the Biology of Ageing, University Medical Center Groningen	1	0.00039	0.00033	0.99995	0.0	46	T	under 1.2% mapping rate	illumina	early_illumina	5prime	poly_a	unknown	bulk	unknown	unknown	Netherlands	2011-11-09	Undetermined	Undetermined	Gonad	Reproductive System
36287	36287	SRR363983	SRX105296	SRS270139	SRP009275	PRJNA148581	Hen1 analysis in zebrafish	GSE33582	Transcriptome Analysis	small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel the small RNA libraries wre made.		pubmed:20859253	wildtype polyA	GSM830245	source name:testis\|strain:TL\|genotype/variation:Hen1 wildtype\|tissue:testis\|small rna library prep method:polyA tailing	wildtype polyA	three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8	testis		Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. RNA was polyA tailed using polyA polymerase followed by ligation of a RNA adaptor to the five prime phosphate of the small RNAs. First strand cDNA synthesis was performed using an oligodT linker primer and M MLV RNase H reverse transcriptase. post amplification the cDNA was sent for sequencing on an Illumina/Solexa platform.		strain:TL\|genotype/variation:Hen1 wildtype\|tissue:testis\|small rna library prep method:polyA tailing	GSM830245	GSM830245: wildtype polyA	GSM830245: wildtype polyA	GSM830245: wildtype polyA	1		GEO Accession:GSM830245	RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>44</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP009275	read name barcode proc directive:ignore	VASAGFPHEN1plusMALE.fastq	fastq	167344144.0	3803276.0	GSM830245 1	0:44	A:87935982;C:21182538;G:19081938;T:34474815;N:4668871	44		87935982	21182538	19081938	34474815	4668871	SRX105296	SRS270139	SRA047996	GEO	European Research Institute for the Biology of Ageing, University Medical Center Groningen	1	0.06642	0.05042	0.99226	0.38346	44	B	usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	Netherlands	2011-11-09	Undetermined	Undetermined	Gonad	Reproductive System
40701	40701	SRR3231363	SRX1637111	SRS1342926	SRP071849	PRJNA315400	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]	GSE79161	Transcriptome Analysis	Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.	parent bioproject:PRJNA315403	pubmed:30086300	Input 3	GSM2087141	tissue:Zebrafish Zygotes\|fraction:Input	Input 3	Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.	Zebrafish Zygotes		mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	Zebrafish were maintained under standard conditions.	fraction:Input	GSM2087141	GSM2087141: Input 3; Danio rerio; RIP Seq	GSM2087141		1	mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	GEO Accession:GSM2087141	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP071849		WT_Input_3.fastq.gz	fastq	1902296226.0	37299926.0	GSM2087141 r1	0:51	A:466290166;C:465344039;G:486942278;T:483240280;N:479463	51		466290166	465344039	486942278	483240280	479463	SRX1637111	SRS1342926	SRA385813	GEO	Rene Ketting, RNA silencing, IMB	1	0.85793	0.14814	0.79941	0.55214	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2016-03-13	Zygote	Embryo	Oocyte	Reproductive System
40702	40702	SRR3231362	SRX1637110	SRS1342927	SRP071849	PRJNA315400	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]	GSE79161	Transcriptome Analysis	Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.	parent bioproject:PRJNA315403	pubmed:30086300	Input 2	GSM2087140	tissue:Zebrafish Zygotes\|fraction:Input	Input 2	Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.	Zebrafish Zygotes		mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	Zebrafish were maintained under standard conditions.	fraction:Input	GSM2087140	GSM2087140: Input 2; Danio rerio; RIP Seq	GSM2087140		1	mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	GEO Accession:GSM2087140	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP071849		WT_Input_2.fastq.gz	fastq	1540737999.0	30210549.0	GSM2087140 r1	0:51	A:380481772;C:379741192;G:395453141;T:384675313;N:386581	51		380481772	379741192	395453141	384675313	386581	SRX1637110	SRS1342927	SRA385813	GEO	Rene Ketting, RNA silencing, IMB	1	0.8787	0.14935	0.79202	0.54381	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2016-03-13	Zygote	Embryo	Oocyte	Reproductive System
40703	40703	SRR3231361	SRX1637109	SRS1342928	SRP071849	PRJNA315400	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]	GSE79161	Transcriptome Analysis	Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.	parent bioproject:PRJNA315403	pubmed:30086300	Input 1	GSM2087139	tissue:Zebrafish Zygotes\|fraction:Input	Input 1	Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.	Zebrafish Zygotes		mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	Zebrafish were maintained under standard conditions.	fraction:Input	GSM2087139	GSM2087139: Input 1; Danio rerio; RIP Seq	GSM2087139		1	mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	GEO Accession:GSM2087139	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP071849		WT_Input_1.fastq.gz	fastq	1109818905.0	21761155.0	GSM2087139 r1										SRX1637109	SRS1342928	SRA385813	GEO	Rene Ketting, RNA silencing, IMB	1	0.87467	0.18794	0.79411	0.63378	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2016-03-13	Zygote	Embryo	Oocyte	Reproductive System
40704	40704	SRR3231360	SRX1637108	SRS1342929	SRP071849	PRJNA315400	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]	GSE79161	Transcriptome Analysis	Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.	parent bioproject:PRJNA315403	pubmed:30086300	Tdrd6a IP 3	GSM2087138	tissue:Zebrafish Zygotes\|fraction:Tdrd6a IP	Tdrd6a IP 3	Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.	Zebrafish Zygotes		mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	Zebrafish were maintained under standard conditions.	fraction:Tdrd6a IP	GSM2087138	GSM2087138: Tdrd6a IP 3; Danio rerio; RIP Seq	GSM2087138		1	mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	GEO Accession:GSM2087138	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP071849		WT_Tdrd6a_IP_3.fastq.gz	fastq	843641439.0	16541989.0	GSM2087138 r1	0:51	A:216465581;C:196892096;G:207722567;T:222361382;N:199813	51		216465581	196892096	207722567	222361382	199813	SRX1637108	SRS1342929	SRA385813	GEO	Rene Ketting, RNA silencing, IMB	1	0.84615	0.08957	0.78768	0.50612	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2016-03-13	Zygote	Embryo	Oocyte	Reproductive System
40705	40705	SRR3231359	SRX1637107	SRS1342930	SRP071849	PRJNA315400	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]	GSE79161	Transcriptome Analysis	Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.	parent bioproject:PRJNA315403	pubmed:30086300	Tdrd6a IP 2	GSM2087137	tissue:Zebrafish Zygotes\|fraction:Tdrd6a IP	Tdrd6a IP 2	Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.	Zebrafish Zygotes		mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	Zebrafish were maintained under standard conditions.	fraction:Tdrd6a IP	GSM2087137	GSM2087137: Tdrd6a IP 2; Danio rerio; RIP Seq	GSM2087137		1	mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	GEO Accession:GSM2087137	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP071849		WT_Tdrd6a_IP_2.fastq.gz	fastq	391198050.0	7670550.0	GSM2087137 r1	0:51	A:99015594;C:91525929;G:97155710;T:103371571;N:129246	51		99015594	91525929	97155710	103371571	129246	SRX1637107	SRS1342930	SRA385813	GEO	Rene Ketting, RNA silencing, IMB	1	0.85778	0.12015	0.80515	0.47541	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2016-03-13	Zygote	Embryo	Oocyte	Reproductive System
40706	40706	SRR3231358	SRX1637106	SRS1342931	SRP071849	PRJNA315400	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]	GSE79161	Transcriptome Analysis	Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.	parent bioproject:PRJNA315403	pubmed:30086300	Tdrd6a IP 1	GSM2087136	tissue:Zebrafish Zygotes\|fraction:Tdrd6a IP	Tdrd6a IP 1	Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.	Zebrafish Zygotes		mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	Zebrafish were maintained under standard conditions.	fraction:Tdrd6a IP	GSM2087136	GSM2087136: Tdrd6a IP 1; Danio rerio; RIP Seq	GSM2087136		1	mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	GEO Accession:GSM2087136	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP071849		WT_Tdrd6a_IP_1.fastq.gz	fastq	1927415052.0	37792452.0	GSM2087136 r1	0:51	A:498125298;C:444860381;G:468826607;T:515142356;N:460410	51		498125298	444860381	468826607	515142356	460410	SRX1637106	SRS1342931	SRA385813	GEO	Rene Ketting, RNA silencing, IMB	1	0.86194	0.09753	0.80146	0.47808	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2016-03-13	Zygote	Embryo	Oocyte	Reproductive System
44644	44644	SRR6268204	SRX3374372	SRS2671596	SRP124609	PRJNA417597	Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation	GSE106677	Other	The stability of mRNAs is regulated by signals within their sequences but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR Seq a combination of massively parallel reporter assays and regression models to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment a single sample was collected every hour between 1h to 10h and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A reporters in two separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment rep samples were coll…		pubmed:29225039	oocyte A+ 7h	GSM2845358	source name:zebrafish oocyte\|developmental stage:7h\|tissue:oocyte	oocyte A+ 7h	Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg lowest 3.125fg and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels	zebrafish oocyte	Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.	Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors	Fertilized zebrafish eggs or oocytes were collected at 28C and kept in culture medium 5.03mM NaCl 0.17mM KCl 0.33mM CaCl2 0.33mM MgSo4 0.1% Methylene blue. A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.	developmental stage:7h\|tissue:oocyte	GSM2845358	GSM2845358: oocyte A+ 7h; Danio rerio; OTHER	GSM2845358		1	Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors	GEO Accession:GSM2845358	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina MiSeq		SRP124609		AR22-SL21.fastq.gz	fastq	463495840.0	2896849.0	GSM2845358 r1	0:160 1:0	A:145685088;C:104925443;G:89232572;T:123650704;N:2033	160	0	145685088	104925443	89232572	123650704	2033	SRX3374372	SRS2671596	SRA629220	GEO	Broad Institute	1	4e-05	1e-05	0.99991	0.5	160	T	under 1.2% mapping rate	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-11-08	Gastrula	Embryo	Oocyte	Reproductive System
44645	44645	SRR6268203	SRX3374371	SRS2671594	SRP124609	PRJNA417597	Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation	GSE106677	Other	The stability of mRNAs is regulated by signals within their sequences but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR Seq a combination of massively parallel reporter assays and regression models to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment a single sample was collected every hour between 1h to 10h and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A reporters in two separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment rep samples were coll…		pubmed:29225039	oocyte A+ 4h	GSM2845357	source name:zebrafish oocyte\|developmental stage:4h\|tissue:oocyte	oocyte A+ 4h	Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg lowest 3.125fg and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels	zebrafish oocyte	Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.	Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors	Fertilized zebrafish eggs or oocytes were collected at 28C and kept in culture medium 5.03mM NaCl 0.17mM KCl 0.33mM CaCl2 0.33mM MgSo4 0.1% Methylene blue. A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.	developmental stage:4h\|tissue:oocyte	GSM2845357	GSM2845357: oocyte A+ 4h; Danio rerio; OTHER	GSM2845357		1	Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors	GEO Accession:GSM2845357	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina MiSeq		SRP124609		AR21-SL41.fastq.gz	fastq	474802240.0	2967514.0	GSM2845357 r1	0:160 1:0	A:145810423;C:111330144;G:93000312;T:124660574;N:787	160	0	145810423	111330144	93000312	124660574	787	SRX3374371	SRS2671594	SRA629220	GEO	Broad Institute	1	2e-05	0.0	0.99997	0.0	160	T	under 1.2% mapping rate	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-11-08	Blastula	Embryo	Oocyte	Reproductive System
44646	44646	SRR6268202	SRX3374370	SRS2671595	SRP124609	PRJNA417597	Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation	GSE106677	Other	The stability of mRNAs is regulated by signals within their sequences but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR Seq a combination of massively parallel reporter assays and regression models to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment a single sample was collected every hour between 1h to 10h and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A reporters in two separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment rep samples were coll…		pubmed:29225039	oocyte A+ 1h	GSM2845356	source name:zebrafish oocyte\|developmental stage:1h\|tissue:oocyte	oocyte A+ 1h	Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg lowest 3.125fg and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels	zebrafish oocyte	Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.	Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors	Fertilized zebrafish eggs or oocytes were collected at 28C and kept in culture medium 5.03mM NaCl 0.17mM KCl 0.33mM CaCl2 0.33mM MgSo4 0.1% Methylene blue. A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.	developmental stage:1h\|tissue:oocyte	GSM2845356	GSM2845356: oocyte A+ 1h; Danio rerio; OTHER	GSM2845356		1	Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors	GEO Accession:GSM2845356	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina MiSeq		SRP124609		AR20.fastq.gz	fastq	647004960.0	4043781.0	GSM2845356 r1	0:160 1:0	A:196358573;C:155899107;G:129095192;T:165649225;N:2863	160	0	196358573	155899107	129095192	165649225	2863	SRX3374370	SRS2671595	SRA629220	GEO	Broad Institute	1	1e-05	0.0	0.99997	0.0	160	T	under 1.2% mapping rate	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-11-08	Cleavage	Embryo	Oocyte	Reproductive System
44647	44647	SRR6268201	SRX3374369	SRS2671601	SRP124609	PRJNA417597	Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation	GSE106677	Other	The stability of mRNAs is regulated by signals within their sequences but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR Seq a combination of massively parallel reporter assays and regression models to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment a single sample was collected every hour between 1h to 10h and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A reporters in two separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment rep samples were coll…		pubmed:29225039	oocyte A 7h	GSM2845355	source name:zebrafish oocyte\|developmental stage:7h\|tissue:oocyte	oocyte A 7h	Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg lowest 3.125fg and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels	zebrafish oocyte	Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.	Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors	Fertilized zebrafish eggs or oocytes were collected at 28C and kept in culture medium 5.03mM NaCl 0.17mM KCl 0.33mM CaCl2 0.33mM MgSo4 0.1% Methylene blue. A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.	developmental stage:7h\|tissue:oocyte	GSM2845355	GSM2845355: oocyte A 7h; Danio rerio; OTHER	GSM2845355		1	Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors	GEO Accession:GSM2845355	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina MiSeq		SRP124609		AR19-SL40.fastq.gz	fastq	437084640.0	2731779.0	GSM2845355 r1	0:160 1:0	A:138575507;C:98512376;G:80808399;T:119186452;N:1906	160	0	138575507	98512376	80808399	119186452	1906	SRX3374369	SRS2671601	SRA629220	GEO	Broad Institute	1	2e-05	0.0	0.99995	1.0	160	T	under 1.2% mapping rate	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-11-08	Gastrula	Embryo	Oocyte	Reproductive System
44648	44648	SRR6268200	SRX3374368	SRS2671593	SRP124609	PRJNA417597	Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation	GSE106677	Other	The stability of mRNAs is regulated by signals within their sequences but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR Seq a combination of massively parallel reporter assays and regression models to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment a single sample was collected every hour between 1h to 10h and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A reporters in two separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment rep samples were coll…		pubmed:29225039	oocyte A 4h	GSM2845354	source name:zebrafish oocyte\|developmental stage:4h\|tissue:oocyte	oocyte A 4h	Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg lowest 3.125fg and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels	zebrafish oocyte	Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.	Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors	Fertilized zebrafish eggs or oocytes were collected at 28C and kept in culture medium 5.03mM NaCl 0.17mM KCl 0.33mM CaCl2 0.33mM MgSo4 0.1% Methylene blue. A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.	developmental stage:4h\|tissue:oocyte	GSM2845354	GSM2845354: oocyte A 4h; Danio rerio; OTHER	GSM2845354		1	Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors	GEO Accession:GSM2845354	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina MiSeq		SRP124609		AR18-SL39.fastq.gz	fastq	533958880.0	3337243.0	GSM2845354 r1	0:160 1:0	A:163118236;C:125487590;G:106580813;T:138769793;N:2448	160	0	163118236	125487590	106580813	138769793	2448	SRX3374368	SRS2671593	SRA629220	GEO	Broad Institute	1	1e-05	0.0	0.99997	0.0	160	T	under 1.2% mapping rate	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-11-08	Blastula	Embryo	Oocyte	Reproductive System
44649	44649	SRR6268199	SRX3374367	SRS2671602	SRP124609	PRJNA417597	Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation	GSE106677	Other	The stability of mRNAs is regulated by signals within their sequences but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR Seq a combination of massively parallel reporter assays and regression models to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment a single sample was collected every hour between 1h to 10h and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A reporters in two separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment rep samples were coll…		pubmed:29225039	oocyte A 1h	GSM2845353	source name:zebrafish oocyte\|developmental stage:1h\|tissue:oocyte	oocyte A 1h	Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg lowest 3.125fg and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels	zebrafish oocyte	Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.	Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors	Fertilized zebrafish eggs or oocytes were collected at 28C and kept in culture medium 5.03mM NaCl 0.17mM KCl 0.33mM CaCl2 0.33mM MgSo4 0.1% Methylene blue. A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.	developmental stage:1h\|tissue:oocyte	GSM2845353	GSM2845353: oocyte A 1h; Danio rerio; OTHER	GSM2845353		1	Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors	GEO Accession:GSM2845353	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina MiSeq		SRP124609		AR17-SL38.fastq.gz	fastq	532076160.0	3325476.0	GSM2845353 r1	0:160 1:0	A:162057480;C:125858627;G:108494717;T:135663057;N:2279	160	0	162057480	125858627	108494717	135663057	2279	SRX3374367	SRS2671602	SRA629220	GEO	Broad Institute	1	2e-05	0.0	0.99995	1.0	160	T	under 1.2% mapping rate	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-11-08	Cleavage	Embryo	Oocyte	Reproductive System
59512	59512	SRR11924307	SRX8469983	SRS6770634	SRP265951	PRJNA637293	The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites	GSE151797	Other	A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.		pubmed:32912962	Unf egg 3	GSM4591051	source name:unfertilized egg\|tissue:unfertilized egg\|rna fraction:size fractionated 20 40 nt whole cell RNA	Unf egg 3	Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.	unfertilized egg		Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description		tissue:unfertilized egg\|rna fraction:size fractionated 20 40 nt whole cell RNA	GSM4591051	GSM4591051: Unf egg 3; Danio rerio; OTHER	GSM4591051		1	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	GEO Accession:GSM4591051	OTHER	TRANSCRIPTOMIC	other	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP265951	intentional duplicate	GSE151797_Reference_sequence.fa Unf_egg_3.bam	bam bam	149835556.0	5777340.0	GSM4591051 r1	0:25.94	A:27873539;C:50837956;G:37710769;T:33413292;N:0	25		27873539	50837956	37710769	33413292	0	SRX8469983	SRS6770634	SRA1083099	GEO	RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen	1	0.74561	0.22616	0.89441	0.76897	34	B	usable mapping rate	ion_torrent	ion_torrent	5prime	small_rna	unknown	bulk	unknown	unknown	Denmark	2020-06-04	Zygote	Embryo	Oocyte	Reproductive System
59513	59513	SRR11924305	SRX8469982	SRS6770633	SRP265951	PRJNA637293	The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites	GSE151797	Other	A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.		pubmed:32912962	Unf egg 2	GSM4591050	source name:unfertilized egg\|tissue:unfertilized egg\|rna fraction:size fractionated 20 40 nt whole cell RNA	Unf egg 2	Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.	unfertilized egg		Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description		tissue:unfertilized egg\|rna fraction:size fractionated 20 40 nt whole cell RNA	GSM4591050	GSM4591050: Unf egg 2; Danio rerio; OTHER	GSM4591050		1	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	GEO Accession:GSM4591050	OTHER	TRANSCRIPTOMIC	other	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP265951	intentional duplicate	GSE151797_Reference_sequence.fa Unf_egg_2.bam	bam bam	235014832.0	8915586.0	GSM4591050 r1	0:26.36	A:43825969;C:79775479;G:60531219;T:50882165;N:0	26		43825969	79775479	60531219	50882165	0	SRX8469982	SRS6770633	SRA1083099	GEO	RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen	1	0.78414	0.23044	0.90352	0.76934	40	B	usable mapping rate	ion_torrent	ion_torrent	5prime	small_rna	unknown	bulk	unknown	unknown	Denmark	2020-06-04	Zygote	Embryo	Oocyte	Reproductive System
59514	59514	SRR11924304	SRX8469981	SRS6770632	SRP265951	PRJNA637293	The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites	GSE151797	Other	A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.		pubmed:32912962	Unf egg 1	GSM4591049	source name:unfertilized egg\|tissue:unfertilized egg\|rna fraction:size fractionated 20 40 nt whole cell RNA	Unf egg 1	Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.	unfertilized egg		Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description		tissue:unfertilized egg\|rna fraction:size fractionated 20 40 nt whole cell RNA	GSM4591049	GSM4591049: Unf egg 1; Danio rerio; OTHER	GSM4591049		1	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	GEO Accession:GSM4591049	OTHER	TRANSCRIPTOMIC	other	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP265951	intentional duplicate	GSE151797_Reference_sequence.fa Unf_egg_1.bam	bam bam	245529952.0	9182415.0	GSM4591049 r1	0:26.74	A:46557080;C:80893860;G:66050448;T:52028564;N:0	26		46557080	80893860	66050448	52028564	0	SRX8469981	SRS6770632	SRA1083099	GEO	RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen	1	0.87423	0.27943	0.91721	0.76816	37	B	usable mapping rate	ion_torrent	ion_torrent	5prime	small_rna	unknown	bulk	unknown	unknown	Denmark	2020-06-04	Zygote	Embryo	Oocyte	Reproductive System

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