metadata: run_metadata: 8 rows where devstage_curation = "Zygote" and experiment.library

8 rows where devstage_curation = "Zygote" and experiment.library_selection = "RANDOM"

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.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
8091	8091	ERR034124	ERX012650	ERS032265	ERP000635	PRJEB2512	The Zebrafish transcriptome during early development	KI-BN-JKE-DRERIO-RNASEQ-2011	Transcriptome Analysis	Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.			RNA extracted from zebrafish embryo at 1 cell stage	zebrafish embryo 1 cell	SAMEA791630	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	ENA first public:2011 06 09\|ENA last update:2018 03 08\|External Id:SAMEA791630\|INSDC center alias:KI BN\|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden\|INSDC first public:2011 06 09T11:04:10Z\|INSDC last update:2018 03 08T15:26:39Z\|INSDC status:public\|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 1cell\|common name:zebrafish\|sample name:KI BN JKE DRERIO RNASEQ 2011 1cell\|sex:mixed\|strain:Tuebingen								Transcriptome profiling of early zebrafish development	KI BN JKE DRERIO RNASEQ 2011 1cell	JKE Drerio rna seq	Transcriptome profiling of 1 cell stage of zebrafish embryos.	Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>	ERP000635	AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development	ENA FIRST PUBLIC:2011 06 09\|ENA LAST UPDATE:2018 11 16	KI-BN-JKE-DRERIO-RNASEQ-2011-1cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-1cell_QV.qual.gz	SOLiD_native SOLiD_native	3676380950.0	73527619.0	KI BN JKE DRERIO RNASEQ 2011 1cell	0:50		50							ERX012650	ERS032265	ERA029959	KI-BN\|Department of Biosciences and Nutrition	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	1	0.64855		0.08432		0.9052		0.74223		50		B		usable mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	Sweden	2011-06-09	Zygote	Embryo	Embryo Imprecise	All anatomical structures
51285	51285	SRR8663318	SRX5460015	SRS4433905	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466		ZF 0hpf rep2	GSM3638659		source name:embryo\|tissue:embryo\|developmental stage:0 hpf\|strain:wild type AB fish	ZF 0hpf rep2	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:0 hpf\|strain:wild type AB fish	GSM3638659	GSM3638659: ZF 0hpf rep2; Danio rerio; Bisulfite Seq	GSM3638659		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638659	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP187415					11732143200.0	39107144.0	GSM3638659 r1	0:150 1:150	A:4048603242;C:1827111316;G:1904770606;T:3949005244;N:2652792	150	150	4048603242	1827111316	1904770606	3949005244	2652792	SRX5460015	SRS4433905	SRA855736	GEO	Sun Yat-sen University	2	0.00152	0.00115	0.00043	0.00016	0.99928	0.99943	0.24509	0.81645	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Zygote	Embryo	Embryo Imprecise	All anatomical structures
51286	51286	SRR8663317	SRX5460014	SRS4433904	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466		ZF 0hpf rep1	GSM3638658		source name:embryo\|tissue:embryo\|developmental stage:0 hpf\|strain:wild type AB fish	ZF 0hpf rep1	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:0 hpf\|strain:wild type AB fish	GSM3638658	GSM3638658: ZF 0hpf rep1; Danio rerio; Bisulfite Seq	GSM3638658		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638658	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP187415					9931664700.0	33105549.0	GSM3638658 r1	0:150 1:150	A:3401474427;C:1566218806;G:1670547045;T:3291140367;N:2284055	150	150	3401474427	1566218806	1670547045	3291140367	2284055	SRX5460014	SRS4433904	SRA855736	GEO	Sun Yat-sen University	2	0.00196	0.00154	0.00071	0.00027	0.99928	0.99935	0.80263	0.85024	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Zygote	Embryo	Embryo Imprecise	All anatomical structures
53400	53400	SRR9849863	SRX6604465	SRS5169411	SRP216580	PRJNA556992	Global identification of circular RNAs during zebrafish embryogenesis	PRJNA556992	Other	Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.					0h		cultivar:Danio rerio\|age:0hpf stage:zygote\|sex:not determined\|tissue:not applicable\|BioSampleModel:Model organism or animal								circRNA 0h 1	0h 1	0h 1	circRNA sequence using embryo from zebrafish 0 hpf			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP216580			BN2-426_L3_52.R1.clean.fastq.gz BN2-426_L3_52.R2.clean.fastq.gz	fastq fastq	15572807100.0	51909357.0	BN2 426 L3 52.R1.clean.fastq.gz	0:150 1:150	A:2605617359;C:4885017797;G:5011849012;T:3067990728;N:2332204	150	150	2605617359	4885017797	5011849012	3067990728	2332204	SRX6604465	SRS5169411	SRA927972	Guangxi Academy of Fishery Sciences\|Guangxi Academy of Fishery Sciences	Guangxi Academy of Fishery Sciences	2	0.78804	0.77444	0.56081	0.54686	0.93348	0.93545	0.77104	0.62239	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-07-27	Zygote	Embryo	Embryo Imprecise	All anatomical structures
53401	53401	SRR9849864	SRX6604464	SRS5169411	SRP216580	PRJNA556992	Global identification of circular RNAs during zebrafish embryogenesis	PRJNA556992	Other	Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.					0h		cultivar:Danio rerio\|age:0hpf stage:zygote\|sex:not determined\|tissue:not applicable\|BioSampleModel:Model organism or animal								circRNA 0h 2	0h 2	0h 2	circRNA sequence using embryo from zebrafish 0 hpf			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP216580			0h_Clean_1.fq.gz 0h_Clean_2.fq.gz	fastq fastq	17258783034.0	57614191.0	0h Clean 1.fq.gz	0:149.78 1:149.78	A:3915507312;C:4601222856;G:4762519500;T:3977299451;N:2233915	149	149	3915507312	4601222856	4762519500	3977299451	2233915	SRX6604464	SRS5169411	SRA927972	Guangxi Academy of Fishery Sciences\|Guangxi Academy of Fishery Sciences	Guangxi Academy of Fishery Sciences	2	0.82486	0.82843	0.16023	0.14824	0.79971	0.80348	0.48785	0.48902	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-07-27	Zygote	Embryo	Embryo Imprecise	All anatomical structures
55860	55860	SRR10863001	SRX7533067	SRS5972255	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.			The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.		wt zygote 0hpf rep3		strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 3\|BioSampleModel:Model organism or animal								totalRNA of Zebrafish: zygote 0hpf	wt zygote 0hpf rep3 totalRNA	wt zygote 0hpf rep3 totalRNA	NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	NextSeq 550		SRP241074			09072018-wt_zygote_0hpf_rep3_totalRNA.R1.fastq.gz 09072018-wt_zygote_0hpf_rep3_totalRNA.R2.fastq.gz 30052018-wt_zygote_0hpf_rep3_totalRNA.R1.fastq.gz 30052018-wt_zygote_0hpf_rep3_totalRNA.R2.fastq.gz	fastq fastq fastq fastq	4458621474.0	30620736.0	09072018 wt zygote 0hpf rep3 totalRNA.R1.fastq.gz	0:72.80 1:72.80	A:1208331512;C:1036387532;G:1015612570;T:1198148120;N:141740	72	72	1208331512	1036387532	1015612570	1198148120	141740	SRX7533067	SRS5972255	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.95239	0.95309	0.06336	0.06309	0.77703	0.77901	0.70327	0.70174	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	unknown	unknown	Germany	2020-01-10	Zygote	Embryo	Whole Organism	All anatomical structures
55861	55861	SRR10863002	SRX7533066	SRS5972254	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.			The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.		wt zygote 0hpf rep2		strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal								totalRNA of Zebrafish: zygote 0hpf	wt zygote 0hpf rep2 totalRNA	wt zygote 0hpf rep2 totalRNA	NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	NextSeq 550		SRP241074			30052018-wt_zygote_0hpf_rep2_totalRNA.R2.fastq.gz 30052018-wt_zygote_0hpf_rep2_totalRNA.R1.fastq.gz 09072018-wt_zygote_0hpf_rep2_totalRNA.R2.fastq.gz 09072018-wt_zygote_0hpf_rep2_totalRNA.R1.fastq.gz	fastq fastq fastq fastq	4071628788.0	27966671.0	09072018 wt zygote 0hpf rep2 totalRNA.R1.fastq.gz	0:72.79 1:72.79	A:1109401096;C:941703799;G:920259964;T:1100136253;N:127676	72	72	1109401096	941703799	920259964	1100136253	127676	SRX7533066	SRS5972254	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.95344	0.95216	0.06464	0.064	0.77835	0.78086	0.70871	0.71004	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	unknown	unknown	Germany	2020-01-10	Zygote	Embryo	Whole Organism	All anatomical structures
55863	55863	SRR10863005	SRX7533064	SRS5972253	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.			The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.		wt zygote 0hpf rep1		strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal								totalRNA of Zebrafish: zygote 0hpf	wt zygote 0hpf rep1 totalRNA	wt zygote 0hpf rep1 totalRNA	NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	NextSeq 550		SRP241074			09072018-wt_zygote_0hpf_rep1_totalRNA.R1.fastq.gz 09072018-wt_zygote_0hpf_rep1_totalRNA.R2.fastq.gz 30052018-wt_zygote_0hpf_rep1_totalRNA.R1.fastq.gz 30052018-wt_zygote_0hpf_rep1_totalRNA.R2.fastq.gz	fastq fastq fastq fastq	4015382154.0	27584968.0	09072018 wt zygote 0hpf rep1 totalRNA.R1.fastq.gz	0:72.78 1:72.78	A:1092464298;C:930179967;G:907966263;T:1084644388;N:127238	72	72	1092464298	930179967	907966263	1084644388	127238	SRX7533064	SRS5972253	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.95247	0.95275	0.06393	0.0634	0.7782	0.7805	0.70719	0.70435	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	unknown	unknown	Germany	2020-01-10	Zygote	Embryo	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");;