metadata: run_metadata: 46 rows where devstage_curation = "Pharyngula" and tissue

46 rows where devstage_curation = "Pharyngula" and tissue_curation = "Gonad"

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.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.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
40631	40631	SRR3231322	SRX1637097	SRS1342906	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	8and24hpf wt Plate1.1	GSM2090863	tissue:Germ cells\|cell line:Primary cells\|developmental stage:8and24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	8and24hpf wt Plate1.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:8and24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090863	GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq	GSM2090863	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090863	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	8and24hpf_wt_Plate1.1_R1_001.fastq.gz 8and24hpf_wt_Plate1.1_R2_001.fastq.gz	fastq fastq	354951269.0	2354572.0	GSM2090863 r1	0:75.37 1:75.38	A:109255676;C:46649925;G:56800706;T:142212324;N:32638	75	75	109255676	46649925	56800706	142212324	32638	SRX1637097	SRS1342906	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.08814	0.58586	0.05414	0.12777	0.98236	0.8253	0.52224	0.5333	75	55	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40632	40632	SRR3231323	SRX1637097	SRS1342906	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	8and24hpf wt Plate1.1	GSM2090863	tissue:Germ cells\|cell line:Primary cells\|developmental stage:8and24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	8and24hpf wt Plate1.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:8and24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090863	GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq	GSM2090863	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090863	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	8and24hpf_wt_Plate1.2_R1_001.fastq.gz 8and24hpf_wt_Plate1.2_R2_001.fastq.gz	fastq fastq	373175186.0	2475371.0	GSM2090863 r2	0:75.37 1:75.38	A:114080796;C:49251081;G:59964869;T:149836843;N:41597	75	75	114080796	49251081	59964869	149836843	41597	SRX1637097	SRS1342906	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.0895	0.59282	0.05309	0.12622	0.9811	0.82185	0.51449	0.52518	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40633	40633	SRR3231324	SRX1637097	SRS1342906	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	8and24hpf wt Plate1.1	GSM2090863	tissue:Germ cells\|cell line:Primary cells\|developmental stage:8and24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	8and24hpf wt Plate1.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:8and24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090863	GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq	GSM2090863	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090863	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	8and24hpf_wt_Plate1.3_R1_001.fastq.gz 8and24hpf_wt_Plate1.3_R2_001.fastq.gz	fastq fastq	376796544.0	2499144.0	GSM2090863 r3	0:75.38 1:75.39	A:114262594;C:49685044;G:61341084;T:151464220;N:43602	75	75	114262594	49685044	61341084	151464220	43602	SRX1637097	SRS1342906	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.08885	0.60874	0.05444	0.12569	0.98177	0.81233	0.51071	0.53112	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40634	40634	SRR3231325	SRX1637097	SRS1342906	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	8and24hpf wt Plate1.1	GSM2090863	tissue:Germ cells\|cell line:Primary cells\|developmental stage:8and24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	8and24hpf wt Plate1.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:8and24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090863	GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq	GSM2090863	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090863	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	8and24hpf_wt_Plate1_R1_001.fastq.gz 8and24hpf_wt_Plate1_R2_001.fastq.gz	fastq fastq	370852802.0	2459988.0	GSM2090863 r4	0:75.37 1:75.38	A:113706258;C:48924259;G:59523739;T:148663433;N:35113	75	75	113706258	48924259	59523739	148663433	35113	SRX1637097	SRS1342906	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.08962	0.59214	0.05376	0.12667	0.98226	0.82142	0.53851	0.52744	75	32	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40669	40669	SRR3231284	SRX1637085	SRS1342918	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate5.1	GSM2090851	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate5.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090851	GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq	GSM2090851	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090851	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate5.1_R1_001.fastq.gz 24hpf_wt_Plate5.1_R2_001.fastq.gz	fastq fastq	558605417.0	3704499.0	GSM2090851 r1	0:75.45 1:75.34	A:170059730;C:87004627;G:101477517;T:200008732;N:54811	75	75	170059730	87004627	101477517	200008732	54811	SRX1637085	SRS1342918	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01541	0.18137	0.00841	0.03816	0.99206	0.90047	0.55425	0.56591	76	32	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40670	40670	SRR3231285	SRX1637085	SRS1342918	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate5.1	GSM2090851	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate5.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090851	GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq	GSM2090851	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090851	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate5.2_R1_001.fastq.gz 24hpf_wt_Plate5.2_R2_001.fastq.gz	fastq fastq	581533785.0	3856402.0	GSM2090851 r2	0:75.45 1:75.34	A:176436951;C:90826765;G:105424561;T:208785606;N:59902	75	75	176436951	90826765	105424561	208785606	59902	SRX1637085	SRS1342918	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01519	0.18239	0.0089	0.03729	0.99306	0.89917	0.59594	0.573	74	75	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40671	40671	SRR3231286	SRX1637085	SRS1342918	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate5.1	GSM2090851	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate5.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090851	GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq	GSM2090851	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090851	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate5.3_R1_001.fastq.gz 24hpf_wt_Plate5.3_R2_001.fastq.gz	fastq fastq	581069691.0	3853089.0	GSM2090851 r3	0:75.45 1:75.35	A:175088129;C:90460041;G:106640639;T:208812858;N:68024	75	75	175088129	90460041	106640639	208812858	68024	SRX1637085	SRS1342918	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01551	0.19274	0.00932	0.0399	0.99289	0.89319	0.57195	0.56478	74	75	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40672	40672	SRR3231287	SRX1637085	SRS1342918	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate5.1	GSM2090851	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate5.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090851	GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq	GSM2090851	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090851	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate5_R1_001.fastq.gz 24hpf_wt_Plate5_R2_001.fastq.gz	fastq fastq	576677563.0	3824304.0	GSM2090851 r4	0:75.45 1:75.34	A:175248120;C:90164865;G:104482050;T:206728496;N:54032	75	75	175248120	90164865	104482050	206728496	54032	SRX1637085	SRS1342918	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01561	0.18528	0.00921	0.03947	0.99302	0.8981	0.60185	0.58278	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40673	40673	SRR3231280	SRX1637084	SRS1342920	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate4.1	GSM2090850	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate4.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090850	GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq	GSM2090850	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090850	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate4.1_R1_001.fastq.gz 24hpf_wt_Plate4.1_R2_001.fastq.gz	fastq fastq	739151929.0	4905477.0	GSM2090850 r1	0:75.40 1:75.28	A:237453179;C:120215450;G:139806121;T:241606048;N:71131	75	75	237453179	120215450	139806121	241606048	71131	SRX1637084	SRS1342920	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01446	0.18296	0.00907	0.03633	0.99442	0.91147	0.57858	0.55259	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40674	40674	SRR3231281	SRX1637084	SRS1342920	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate4.1	GSM2090850	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate4.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090850	GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq	GSM2090850	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090850	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate4.2_R1_001.fastq.gz 24hpf_wt_Plate4.2_R2_001.fastq.gz	fastq fastq	769081502.0	5103797.0	GSM2090850 r2	0:75.40 1:75.29	A:245920087;C:125753713;G:145142187;T:252183239;N:82276	75	75	245920087	125753713	145142187	252183239	82276	SRX1637084	SRS1342920	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01429	0.18495	0.00907	0.0378	0.99435	0.91181	0.60136	0.5509	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40675	40675	SRR3231282	SRX1637084	SRS1342920	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate4.1	GSM2090850	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate4.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090850	GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq	GSM2090850	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090850	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate4.3_R1_001.fastq.gz 24hpf_wt_Plate4.3_R2_001.fastq.gz	fastq fastq	763478256.0	5066455.0	GSM2090850 r3	0:75.40 1:75.29	A:242520066;C:123970168;G:146100841;T:250803049;N:84132	75	75	242520066	123970168	146100841	250803049	84132	SRX1637084	SRS1342920	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01481	0.1935	0.0093	0.03777	0.99448	0.90526	0.5546	0.56044	74	75	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40676	40676	SRR3231283	SRX1637084	SRS1342920	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate4.1	GSM2090850	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate4.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090850	GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq	GSM2090850	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090850	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate4_R1_001.fastq.gz 24hpf_wt_Plate4_R2_001.fastq.gz	fastq fastq	762348830.0	5059335.0	GSM2090850 r4	0:75.40 1:75.28	A:244240563;C:124701855;G:143859660;T:249474441;N:72311	75	75	244240563	124701855	143859660	249474441	72311	SRX1637084	SRS1342920	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01537	0.18668	0.00965	0.03681	0.99407	0.91066	0.54926	0.55097	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40677	40677	SRR3231276	SRX1637083	SRS1342919	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate3.1	GSM2090849	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate3.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090849	GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq	GSM2090849	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090849	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate3.1_R1_001.fastq.gz 24hpf_wt_Plate3.1_R2_001.fastq.gz	fastq fastq	692753746.0	4593127.0	GSM2090849 r1	0:75.47 1:75.35	A:200412235;C:124307113;G:146191995;T:221774807;N:67596	75	75	200412235	124307113	146191995	221774807	67596	SRX1637083	SRS1342919	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.00405	0.02858	0.00276	0.00696	0.99752	0.9722	0.64935	0.55705	76	74	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40678	40678	SRR3231277	SRX1637083	SRS1342919	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate3.1	GSM2090849	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate3.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090849	GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq	GSM2090849	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090849	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate3.2_R1_001.fastq.gz 24hpf_wt_Plate3.2_R2_001.fastq.gz	fastq fastq	701569969.0	4651611.0	GSM2090849 r2	0:75.47 1:75.35	A:203675895;C:126097325;G:146891489;T:224837147;N:68113	75	75	203675895	126097325	146891489	224837147	68113	SRX1637083	SRS1342919	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.00395	0.0305	0.0027	0.00699	0.9976	0.97088	0.4863	0.57133	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40679	40679	SRR3231278	SRX1637083	SRS1342919	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate3.1	GSM2090849	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate3.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090849	GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq	GSM2090849	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090849	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate3.3_R1_001.fastq.gz 24hpf_wt_Plate3.3_R2_001.fastq.gz	fastq fastq	688668111.0	4566244.0	GSM2090849 r3	0:75.47 1:75.35	A:199652330;C:123454100;G:144848134;T:220657099;N:56448	75	75	199652330	123454100	144848134	220657099	56448	SRX1637083	SRS1342919	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.00369	0.02792	0.00272	0.00658	0.99803	0.9727	0.50427	0.55885	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40680	40680	SRR3231279	SRX1637083	SRS1342919	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate3.1	GSM2090849	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate3.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090849	GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq	GSM2090849	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090849	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate3_R1_001.fastq.gz 24hpf_wt_Plate3_R2_001.fastq.gz	fastq fastq	702507993.0	4657860.0	GSM2090849 r4	0:75.47 1:75.35	A:203715514;C:126718380;G:147182176;T:224817151;N:74772	75	75	203715514	126718380	147182176	224817151	74772	SRX1637083	SRS1342919	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.00392	0.0275	0.00279	0.00707	0.99778	0.97297	0.46666	0.56022	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40681	40681	SRR3231272	SRX1637082	SRS1342921	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate2.1	GSM2090848	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate2.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090848	GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq	GSM2090848	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090848	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate2.1_R1_001.fastq.gz 24hpf_wt_Plate2.1_R2_001.fastq.gz	fastq fastq	298994170.0	1982738.0	GSM2090848 r1	0:75.44 1:75.35	A:93083508;C:44907251;G:52817440;T:108158577;N:27394	75	75	93083508	44907251	52817440	108158577	27394	SRX1637082	SRS1342921	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01409	0.02745	0.01105	0.00689	0.99847	0.97512	0.14754	0.54124	75	75	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40682	40682	SRR3231273	SRX1637082	SRS1342921	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate2.1	GSM2090848	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate2.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090848	GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq	GSM2090848	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090848	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate2.2_R1_001.fastq.gz 24hpf_wt_Plate2.2_R2_001.fastq.gz	fastq fastq	306815504.0	2034672.0	GSM2090848 r2	0:75.44 1:75.36	A:95967069;C:46066723;G:53601976;T:111150011;N:29725	75	75	95967069	46066723	53601976	111150011	29725	SRX1637082	SRS1342921	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01382	0.03079	0.01075	0.00723	0.99859	0.97344	0.14334	0.56436	75	76	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40683	40683	SRR3231274	SRX1637082	SRS1342921	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate2.1	GSM2090848	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate2.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090848	GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq	GSM2090848	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090848	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate2.3_R1_001.fastq.gz 24hpf_wt_Plate2.3_R2_001.fastq.gz	fastq fastq	300764521.0	1994537.0	GSM2090848 r3	0:75.44 1:75.35	A:93852241;C:45007343;G:52938896;T:108939437;N:26604	75	75	93852241	45007343	52938896	108939437	26604	SRX1637082	SRS1342921	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.0141	0.02918	0.01084	0.0072	0.99853	0.97437	0.12264	0.55403	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40684	40684	SRR3231275	SRX1637082	SRS1342921	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate2.1	GSM2090848	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate2.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090848	GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq	GSM2090848	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090848	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate2_R1_001.fastq.gz 24hpf_wt_Plate2_R2_001.fastq.gz	fastq fastq	302297329.0	2004669.0	GSM2090848 r4	0:75.44 1:75.35	A:94284770;C:45616868;G:52928512;T:109434957;N:32222	75	75	94284770	45616868	52928512	109434957	32222	SRX1637082	SRS1342921	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01369	0.02852	0.01069	0.00705	0.99874	0.97526	0.10472	0.56414	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40685	40685	SRR3231268	SRX1637081	SRS1342935	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate1.1	GSM2090847	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate1.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090847	GSM2090847: 24hpf wt Plate1.1; Danio rerio; RNA Seq	GSM2090847	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090847	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate1.1_R1_001.fastq.gz 24hpf_wt_Plate1.1_R2_001.fastq.gz	fastq fastq	836011252.0	5542746.0	GSM2090847 r1	0:75.49 1:75.34	A:254663944;C:151442656;G:167697929;T:262199779;N:6944	75	75	254663944	151442656	167697929	262199779	6944	SRX1637081	SRS1342935	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.03375	0.07314	0.02792	0.0396	0.98882	0.95753	0.54559	0.53265	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40686	40686	SRR3231269	SRX1637081	SRS1342935	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate1.1	GSM2090847	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate1.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090847	GSM2090847: 24hpf wt Plate1.1; Danio rerio; RNA Seq	GSM2090847	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090847	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate1.2_R1_001.fastq.gz 24hpf_wt_Plate1.2_R2_001.fastq.gz	fastq fastq	830338169.0	5505101.0	GSM2090847 r2	0:75.49 1:75.34	A:254439239;C:150818963;G:164159782;T:260734365;N:185820	75	75	254439239	150818963	164159782	260734365	185820	SRX1637081	SRS1342935	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.03438	0.07482	0.02833	0.04098	0.98867	0.95868	0.55778	0.56233	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40687	40687	SRR3231270	SRX1637081	SRS1342935	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate1.1	GSM2090847	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate1.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090847	GSM2090847: 24hpf wt Plate1.1; Danio rerio; RNA Seq	GSM2090847	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090847	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate1.3_R1_001.fastq.gz 24hpf_wt_Plate1.3_R2_001.fastq.gz	fastq fastq	832999933.0	5522579.0	GSM2090847 r3	0:75.49 1:75.34	A:252395960;C:151022816;G:167338952;T:262031054;N:211151	75	75	252395960	151022816	167338952	262031054	211151	SRX1637081	SRS1342935	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.0331	0.07425	0.02697	0.04008	0.98817	0.95862	0.53915	0.54556	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40688	40688	SRR3231271	SRX1637081	SRS1342935	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf wt Plate1.1	GSM2090847	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf wt Plate1.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:wildtype\|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090847	GSM2090847: 24hpf wt Plate1.1; Danio rerio; RNA Seq	GSM2090847	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090847	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_wt_Plate1_R1_001.fastq.gz 24hpf_wt_Plate1_R2_001.fastq.gz	fastq fastq	838188458.0	5557389.0	GSM2090847 r4	0:75.48 1:75.34	A:257879266;C:152322486;G:165090591;T:262885421;N:10694	75	75	257879266	152322486	165090591	262885421	10694	SRX1637081	SRS1342935	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.03416	0.07497	0.0282	0.04152	0.98871	0.95927	0.49844	0.55123	75	75	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40689	40689	SRR3231264	SRX1637080	SRS1342936	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf Tdrd6a : Plate3.1	GSM2090846	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf Tdrd6a : Plate3.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090846	GSM2090846: 24hpf Tdrd6a : Plate3.1; Danio rerio; RNA Seq	GSM2090846	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090846	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_Tdrd6a-:-_Plate3.1_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate3.1_R2_001.fastq.gz	fastq fastq	1371297393.0	9095769.0	GSM2090846 r1	0:75.42 1:75.35	A:425284978;C:236010283;G:260994358;T:448883843;N:123931	75	75	425284978	236010283	260994358	448883843	123931	SRX1637080	SRS1342936	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01833	0.04333	0.01582	0.01601	0.99594	0.96871	0.43243	0.56321	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40690	40690	SRR3231265	SRX1637080	SRS1342936	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf Tdrd6a : Plate3.1	GSM2090846	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf Tdrd6a : Plate3.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090846	GSM2090846: 24hpf Tdrd6a : Plate3.1; Danio rerio; RNA Seq	GSM2090846	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090846	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_Tdrd6a-:-_Plate3.2_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate3.2_R2_001.fastq.gz	fastq fastq	1397660189.0	9270812.0	GSM2090846 r2	0:75.42 1:75.34	A:435127552;C:240183852;G:263594089;T:458617665;N:137031	75	75	435127552	240183852	263594089	458617665	137031	SRX1637080	SRS1342936	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01782	0.04718	0.01547	0.01691	0.9963	0.96737	0.46382	0.54605	75	76	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40691	40691	SRR3231266	SRX1637080	SRS1342936	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf Tdrd6a : Plate3.1	GSM2090846	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf Tdrd6a : Plate3.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090846	GSM2090846: 24hpf Tdrd6a : Plate3.1; Danio rerio; RNA Seq	GSM2090846	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090846	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_Tdrd6a-:-_Plate3.3_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate3.3_R2_001.fastq.gz	fastq fastq	1369635087.0	9085243.0	GSM2090846 r3	0:75.41 1:75.34	A:425335498;C:234980221;G:259843705;T:449365378;N:110285	75	75	425335498	234980221	259843705	449365378	110285	SRX1637080	SRS1342936	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01833	0.04405	0.01594	0.01596	0.99636	0.9694	0.49166	0.56044	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40692	40692	SRR3231267	SRX1637080	SRS1342936	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf Tdrd6a : Plate3.1	GSM2090846	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf Tdrd6a : Plate3.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090846	GSM2090846: 24hpf Tdrd6a : Plate3.1; Danio rerio; RNA Seq	GSM2090846	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090846	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_Tdrd6a-:-_Plate3_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate3_R2_001.fastq.gz	fastq fastq	1410682920.0	9356966.0	GSM2090846 r4	0:75.42 1:75.34	A:436822225;C:244639009;G:267991531;T:461073192;N:156963	75	75	436822225	244639009	267991531	461073192	156963	SRX1637080	SRS1342936	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.01761	0.04359	0.01513	0.01603	0.99584	0.96871	0.46718	0.55856	75	75	T	T	mates < 9% mapping rate	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40693	40693	SRR3231260	SRX1637079	SRS1342937	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf Tdrd6a : Plate2.1	GSM2090845	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf Tdrd6a : Plate2.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090845	GSM2090845: 24hpf Tdrd6a : Plate2.1; Danio rerio; RNA Seq	GSM2090845	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090845	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_Tdrd6a-:-_Plate2.1_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate2.1_R2_001.fastq.gz	fastq fastq	908747232.0	6024927.0	GSM2090845 r1	0:75.47 1:75.36	A:280168278;C:154557506;G:169723057;T:304291004;N:7387	75	75	280168278	154557506	169723057	304291004	7387	SRX1637079	SRS1342937	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.18399	0.33806	0.16099	0.20721	0.95846	0.87878	0.49734	0.53532	76	75	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40694	40694	SRR3231261	SRX1637079	SRS1342937	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf Tdrd6a : Plate2.1	GSM2090845	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf Tdrd6a : Plate2.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090845	GSM2090845: 24hpf Tdrd6a : Plate2.1; Danio rerio; RNA Seq	GSM2090845	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090845	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_Tdrd6a-:-_Plate2.2_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate2.2_R2_001.fastq.gz	fastq fastq	899928650.0	5966433.0	GSM2090845 r2	0:75.47 1:75.36	A:279603733;C:153512612;G:165252396;T:301355799;N:204110	75	75	279603733	153512612	165252396	301355799	204110	SRX1637079	SRS1342937	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.18665	0.33654	0.16315	0.20612	0.95812	0.87641	0.48791	0.53087	75	75	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40695	40695	SRR3231262	SRX1637079	SRS1342937	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf Tdrd6a : Plate2.1	GSM2090845	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf Tdrd6a : Plate2.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090845	GSM2090845: 24hpf Tdrd6a : Plate2.1; Danio rerio; RNA Seq	GSM2090845	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090845	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_Tdrd6a-:-_Plate2.3_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate2.3_R2_001.fastq.gz	fastq fastq	910589284.0	6036899.0	GSM2090845 r3	0:75.47 1:75.36	A:279344268;C:154985581;G:170329370;T:305702456;N:227609	75	75	279344268	154985581	170329370	305702456	227609	SRX1637079	SRS1342937	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.1847	0.33529	0.16159	0.20809	0.95806	0.88101	0.48203	0.53309	76	75	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40696	40696	SRR3231263	SRX1637079	SRS1342937	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf Tdrd6a : Plate2.1	GSM2090845	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf Tdrd6a : Plate2.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090845	GSM2090845: 24hpf Tdrd6a : Plate2.1; Danio rerio; RNA Seq	GSM2090845	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090845	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_Tdrd6a-:-_Plate2_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate2_R2_001.fastq.gz	fastq fastq	911364231.0	6042507.0	GSM2090845 r4	0:75.46 1:75.36	A:284483499;C:155490114;G:166537185;T:304841630;N:11803	75	75	284483499	155490114	166537185	304841630	11803	SRX1637079	SRS1342937	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.1873	0.33611	0.16336	0.20573	0.95812	0.87554	0.48685	0.52933	76	76	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40697	40697	SRR3231256	SRX1637078	SRS1342938	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf Tdrd6a : Plate1.1	GSM2090844	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf Tdrd6a : Plate1.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090844	GSM2090844: 24hpf Tdrd6a : Plate1.1; Danio rerio; RNA Seq	GSM2090844	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090844	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_Tdrd6a-:-_Plate1.1_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate1.1_R2_001.fastq.gz	fastq fastq	604973130.0	4010320.0	GSM2090844 r1	0:75.46 1:75.39	A:187609294;C:95230616;G:105121464;T:217006596;N:5160	75	75	187609294	95230616	105121464	217006596	5160	SRX1637078	SRS1342938	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.24179	0.45155	0.21128	0.26362	0.95475	0.84183	0.54132	0.53298	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40698	40698	SRR3231257	SRX1637078	SRS1342938	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf Tdrd6a : Plate1.1	GSM2090844	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf Tdrd6a : Plate1.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090844	GSM2090844: 24hpf Tdrd6a : Plate1.1; Danio rerio; RNA Seq	GSM2090844	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090844	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_Tdrd6a-:-_Plate1.2_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate1.2_R2_001.fastq.gz	fastq fastq	597266507.0	3959286.0	GSM2090844 r2	0:75.46 1:75.39	A:186751324;C:94261867;G:101806474;T:214309214;N:137628	75	75	186751324	94261867	101806474	214309214	137628	SRX1637078	SRS1342938	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.24002	0.44945	0.20966	0.26222	0.95595	0.84313	0.53005	0.52366	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40699	40699	SRR3231258	SRX1637078	SRS1342938	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf Tdrd6a : Plate1.1	GSM2090844	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf Tdrd6a : Plate1.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090844	GSM2090844: 24hpf Tdrd6a : Plate1.1; Danio rerio; RNA Seq	GSM2090844	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090844	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_Tdrd6a-:-_Plate1.3_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate1.3_R2_001.fastq.gz	fastq fastq	600809103.0	3982665.0	GSM2090844 r3	0:75.47 1:75.39	A:185579699;C:94586895;G:104466591;T:216021526;N:154392	75	75	185579699	94586895	104466591	216021526	154392	SRX1637078	SRS1342938	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.24004	0.44637	0.21044	0.26336	0.95619	0.84991	0.52752	0.53543	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
40700	40700	SRR3231259	SRX1637078	SRS1342938	SRP071848	PRJNA315399	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]	GSE79283	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: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.	parent bioproject:PRJNA315403	pubmed:30086300	24hpf Tdrd6a : Plate1.1	GSM2090844	tissue:Germ cells\|cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	24hpf Tdrd6a : Plate1.1	post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.	Germ cells	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	Zebrafish were maintained under standard conditions.	cell line:Primary cells\|developmental stage:24hpf\|genotype/variation:Tdrd6a : \|protocol:CEL seq Hashimshony et al. Cell reports 2012	GSM2090844	GSM2090844: 24hpf Tdrd6a : Plate1.1; Danio rerio; RNA Seq	GSM2090844	1	mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.	GEO Accession:GSM2090844	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP071848	24hpf_Tdrd6a-:-_Plate1_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate1_R2_001.fastq.gz	fastq fastq	599838493.0	3976457.0	GSM2090844 r4	0:75.46 1:75.39	A:188491793;C:94714801;G:101689123;T:214934949;N:7827	75	75	188491793	94714801	101689123	214934949	7827	SRX1637078	SRS1342938	SRA385812	GEO	Rene Ketting, RNA silencing, IMB	2	0.23905	0.44741	0.2093	0.26277	0.95619	0.84196	0.53501	0.52664	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2016-03-16	Pharyngula	Embryo	Gonad	Reproductive System
50624	50624	SRR8182168	SRX5002135	SRS4036798	SRP168473	PRJNA505329	Retention of paternal epigenetic memory in the developing teleost germline [RNA Seq]	GSE122480	Transcriptome Analysis	Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: Using low input RNA seq we have profiled transcriptomes of zebrafish primordial germ cells PGCs and age matched somatic cells at 4 blastula 7 gastrula 24 pharyngula prim 5 and 36 pharyngula prim 25 hpf	parent bioproject:PRJNA506076	pubmed:31296860	PGC 36hpf RNA seq rep2	GSM3467118	tissue:PGCs 36hpf RNA seq replicate 2\|cell type:primordial germ cells\|developmental stage:36hpf	PGC 36hpf RNA seq rep2	Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Differential gene expression analysis was performed using edgeR Robinson et al 2010; Bioinformatics; McCarthy et al 2012; Nucleic Acids Research Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 4 developmental stages in replicates.	PGCs 36hpf RNA seq replicate 2	PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp		cell type:primordial germ cells\|developmental stage:36hpf	GSM3467118	GSM3467118: PGC 36hpf RNA seq rep2; Danio rerio; RNA Seq	GSM3467118	1	PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp	GEO Accession:GSM3467118	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP168473	PGC_36h_rep2_R1.fastq.gz PGC_36h_rep2_R2.fastq.gz	fastq fastq	9702849214.0	48033907.0	GSM3467118 r1	0:101 1:101	A:1957602439;C:2881656243;G:2916349837;T:1946652829;N:587866	101	101	1957602439	2881656243	2916349837	1946652829	587866	SRX5002135	SRS4036798	SRA808716	GEO	Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute	2	0.95843	0.95704	0.25621	0.23569	0.7666	0.76926	0.78788	0.83187	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	Australia	2018-11-13	Pharyngula	Embryo	Gonad	Reproductive System
50625	50625	SRR8182167	SRX5002134	SRS4036797	SRP168473	PRJNA505329	Retention of paternal epigenetic memory in the developing teleost germline [RNA Seq]	GSE122480	Transcriptome Analysis	Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: Using low input RNA seq we have profiled transcriptomes of zebrafish primordial germ cells PGCs and age matched somatic cells at 4 blastula 7 gastrula 24 pharyngula prim 5 and 36 pharyngula prim 25 hpf	parent bioproject:PRJNA506076	pubmed:31296860	PGC 36hpf RNA seq rep1	GSM3467117	tissue:PGCs 36hpf RNA seq replicate 1\|cell type:primordial germ cells\|developmental stage:36hpf	PGC 36hpf RNA seq rep1	Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Differential gene expression analysis was performed using edgeR Robinson et al 2010; Bioinformatics; McCarthy et al 2012; Nucleic Acids Research Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 4 developmental stages in replicates.	PGCs 36hpf RNA seq replicate 1	PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp		cell type:primordial germ cells\|developmental stage:36hpf	GSM3467117	GSM3467117: PGC 36hpf RNA seq rep1; Danio rerio; RNA Seq	GSM3467117	1	PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp	GEO Accession:GSM3467117	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP168473	PGC_36h_rep1_R1.fastq.gz PGC_36h_rep1_R2.fastq.gz	fastq fastq	13534965358.0	67004779.0	GSM3467117 r1	0:101 1:101	A:2801419410;C:3934724172;G:3989620478;T:2808370955;N:830343	101	101	2801419410	3934724172	3989620478	2808370955	830343	SRX5002134	SRS4036797	SRA808716	GEO	Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute	2	0.96071	0.95932	0.25676	0.24882	0.77824	0.78102	0.74887	0.76013	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	Australia	2018-11-13	Pharyngula	Embryo	Gonad	Reproductive System
50626	50626	SRR8182166	SRX5002133	SRS4036796	SRP168473	PRJNA505329	Retention of paternal epigenetic memory in the developing teleost germline [RNA Seq]	GSE122480	Transcriptome Analysis	Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: Using low input RNA seq we have profiled transcriptomes of zebrafish primordial germ cells PGCs and age matched somatic cells at 4 blastula 7 gastrula 24 pharyngula prim 5 and 36 pharyngula prim 25 hpf	parent bioproject:PRJNA506076	pubmed:31296860	PGC 24hpf RNA seq rep2	GSM3467116	tissue:PGCs 24hpf RNA seq replicate 2\|cell type:primordial germ cells\|developmental stage:24hpf	PGC 24hpf RNA seq rep2	Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Differential gene expression analysis was performed using edgeR Robinson et al 2010; Bioinformatics; McCarthy et al 2012; Nucleic Acids Research Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 4 developmental stages in replicates.	PGCs 24hpf RNA seq replicate 2	PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp		cell type:primordial germ cells\|developmental stage:24hpf	GSM3467116	GSM3467116: PGC 24hpf RNA seq rep2; Danio rerio; RNA Seq	GSM3467116	1	PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp	GEO Accession:GSM3467116	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP168473	PGC_24h_rep2_R1.fastq.gz PGC_24h_rep2_R2.fastq.gz	fastq fastq	11932456130.0	59071565.0	GSM3467116 r1	0:101 1:101	A:2215999785;C:3735562796;G:3758529225;T:2221638795;N:725529	101	101	2215999785	3735562796	3758529225	2221638795	725529	SRX5002133	SRS4036796	SRA808716	GEO	Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute	2	0.97602	0.97703	0.23352	0.22993	0.83737	0.8394	0.79621	0.8174	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	Australia	2018-11-13	Pharyngula	Embryo	Gonad	Reproductive System
50627	50627	SRR8182165	SRX5002132	SRS4036795	SRP168473	PRJNA505329	Retention of paternal epigenetic memory in the developing teleost germline [RNA Seq]	GSE122480	Transcriptome Analysis	Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: Using low input RNA seq we have profiled transcriptomes of zebrafish primordial germ cells PGCs and age matched somatic cells at 4 blastula 7 gastrula 24 pharyngula prim 5 and 36 pharyngula prim 25 hpf	parent bioproject:PRJNA506076	pubmed:31296860	PGC 24hpf RNA seq rep1	GSM3467115	tissue:PGCs 24hpf RNA seq replicate 1\|cell type:primordial germ cells\|developmental stage:24hpf	PGC 24hpf RNA seq rep1	Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Differential gene expression analysis was performed using edgeR Robinson et al 2010; Bioinformatics; McCarthy et al 2012; Nucleic Acids Research Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 4 developmental stages in replicates.	PGCs 24hpf RNA seq replicate 1	PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp		cell type:primordial germ cells\|developmental stage:24hpf	GSM3467115	GSM3467115: PGC 24hpf RNA seq rep1; Danio rerio; RNA Seq	GSM3467115	1	PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp	GEO Accession:GSM3467115	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP168473	PGC_24h_rep1_R2.fastq.gz PGC_24h_rep1_R1.fastq.gz	fastq fastq	11647052956.0	57658678.0	GSM3467115 r1	0:101 1:101	A:2169149120;C:3642548842;G:3659465614;T:2175179501;N:709879	101	101	2169149120	3642548842	3659465614	2175179501	709879	SRX5002132	SRS4036795	SRA808716	GEO	Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute	2	0.97553	0.97628	0.22987	0.22664	0.82891	0.82927	0.7894	0.8166	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	Australia	2018-11-13	Pharyngula	Embryo	Gonad	Reproductive System
51713	51713	SRR8799028	SRX5587879	SRS4549126	SRP189741	PRJNA529645	Retention of paternal epigenetic memory in the developing teleost germline [alt splicing]	GSE128986	Transcriptome Analysis	Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: In order to perform alternative splicing analysis PGC 7 hpf PGC 24 hpf Soma 7 hpf and Soma 24 hpf low input RNA seq samples have been sequenced on an additional lane of Nova seq 6000 and analyzed together with the previous RNA seq run GSE122480.	parent bioproject:PRJNA506076	pubmed:31296860	PGC 24hpf RNA seq rep1 RUN2	GSM3689555	tissue:PGCs 24hpf RNA seq replicate 1 RUN2\|cell type:primordial germ cells\|developmental stage:24hpf	PGC 24hpf RNA seq rep1 RUN2	Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 2 developmental stages in replicates.	PGCs 24hpf RNA seq replicate 1 RUN2	PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp		cell type:primordial germ cells\|developmental stage:24hpf	GSM3689555	GSM3689555: PGC 24hpf RNA seq rep1 RUN2; Danio rerio; RNA Seq	GSM3689555	1	PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp	GEO Accession:GSM3689555	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP189741	PGC_24h_rep1_R2_001.fastq.gz PGC_24h_rep1_R1_001.fastq.gz	fastq fastq	23657278682.0	117115241.0	GSM3689555 r1	0:101 1:101	A:4349199519;C:7446484673;G:7492936033;T:4368542331;N:116126	101	101	4349199519	7446484673	7492936033	4368542331	116126	SRX5587879	SRS4549126	SRA867175	GEO	Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute	2	0.97789	0.97672	0.22125	0.22042	0.83195	0.83358	0.76619	0.81524	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	Australia	2019-03-28	Pharyngula	Embryo	Gonad	Reproductive System
51720	51720	SRR8799029	SRX5587872	SRS4549119	SRP189741	PRJNA529645	Retention of paternal epigenetic memory in the developing teleost germline [alt splicing]	GSE128986	Transcriptome Analysis	Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: In order to perform alternative splicing analysis PGC 7 hpf PGC 24 hpf Soma 7 hpf and Soma 24 hpf low input RNA seq samples have been sequenced on an additional lane of Nova seq 6000 and analyzed together with the previous RNA seq run GSE122480.	parent bioproject:PRJNA506076	pubmed:31296860	PGC 24hpf RNA seq rep2 RUN2	GSM3689556	tissue:PGCs 24hpf RNA seq replicate 2 RUN2\|cell type:primordial germ cells\|developmental stage:24hpf	PGC 24hpf RNA seq rep2 RUN2	Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 2 developmental stages in replicates.	PGCs 24hpf RNA seq replicate 2 RUN2	PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp		cell type:primordial germ cells\|developmental stage:24hpf	GSM3689556	GSM3689556: PGC 24hpf RNA seq rep2 RUN2; Danio rerio; RNA Seq	GSM3689556	1	PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp	GEO Accession:GSM3689556	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP189741	PGC_24h_rep2_R2_001.fastq.gz PGC_24h_rep2_R1_001.fastq.gz	fastq fastq	24057891142.0	119098471.0	GSM3689556 r1	0:101 1:101	A:4413753037;C:7580010114;G:7634880573;T:4429128675;N:118743	101	101	4413753037	7580010114	7634880573	4429128675	118743	SRX5587872	SRS4549119	SRA867175	GEO	Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute	2	0.97726	0.97716	0.22877	0.22609	0.84228	0.84319	0.79575	0.73876	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	Australia	2019-03-28	Pharyngula	Embryo	Gonad	Reproductive System
53007	53007	SRR9662032	SRX6422908	SRS5079698	SRP213938	PRJNA553572	A map of cis regulatory elements and 3D genome structures in zebrafish	GSE134055	Other	The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.		pubmed:33239788;pubmed:35649578	YueLab RNA Seq Testis rep2	GSM3934900	source name:Tissue\|strain:Tuebingen\|tissue:Testis	YueLab RNA Seq Testis rep2	RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged	Tissue	For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.	Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions	strain:Tuebingen\|tissue:Testis	GSM3934900	GSM3934900: YueLab RNA Seq Testis rep2; Danio rerio; RNA Seq	GSM3934900	1	For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.	GEO Accession:GSM3934900	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina Genome Analyzer	SRP213938	YueLab-RNA-Seq-Testis-rep2_1.fastq.gz YueLab-RNA-Seq-Testis-rep2_2.fastq.gz	fastq fastq	2436875302.0	18371528.0	GSM3934900 r1	0:66.32 1:66.33	A:653432595;C:557313995;G:543148700;T:682901514;N:78498	66	66	653432595	557313995	543148700	682901514	78498	SRX6422908	SRS5079698	SRA919194	GEO	Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine	2	0.96211	0.96932	0.15423	0.15585	0.63698	0.63203	0.48854	0.48734	64	65	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2019-07-09	Pharyngula	Embryo	Gonad	Reproductive System
53008	53008	SRR9662031	SRX6422907	SRS5079697	SRP213938	PRJNA553572	A map of cis regulatory elements and 3D genome structures in zebrafish	GSE134055	Other	The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.		pubmed:33239788;pubmed:35649578	YueLab RNA Seq Testis rep1	GSM3934899	source name:Tissue\|strain:Tuebingen\|tissue:Testis	YueLab RNA Seq Testis rep1	RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged	Tissue	For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.	Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions	strain:Tuebingen\|tissue:Testis	GSM3934899	GSM3934899: YueLab RNA Seq Testis rep1; Danio rerio; RNA Seq	GSM3934899	1	For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.	GEO Accession:GSM3934899	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina Genome Analyzer	SRP213938	YueLab-RNA-Seq-Testis-rep1_1.fastq.gz YueLab-RNA-Seq-Testis-rep1_2.fastq.gz	fastq fastq	4260409405.0	35273156.0	GSM3934899 r1	0:60.49 1:60.29	A:1116411235;C:981833820;G:983285862;T:1178815187;N:63301	60	60	1116411235	981833820	983285862	1178815187	63301	SRX6422907	SRS5079697	SRA919194	GEO	Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine	2	0.97089	0.97484	0.14016	0.14077	0.62658	0.63051	0.496	0.49774	61	59	B	B	biological fallback assumption	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2019-07-09	Pharyngula	Embryo	Gonad	Reproductive System
60887	60887	SRR12628234	SRX9110497	SRS7353480	SRP282187	PRJNA663091	Characterization of small RNAs in early zebrafish PGCs	GSE157865	Transcriptome Analysis	Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs		pubmed:33506864	h24 2: PGCs 24hpf repeat2	GSM4777194	source name:PGCs\|cell type:primordial germ cells\|strain:AB\|tissue:gonad	h24 2: PGCs 24hpf repeat2	Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample …	PGCs	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.		cell type:primordial germ cells\|strain:AB\|tissue:gonad	GSM4777194	GSM4777194: h24 2: PGCs 24hpf repeat2; Danio rerio; miRNA Seq	GSM4777194	1	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.	GEO Accession:GSM4777194	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	HiSeq X Ten	SRP282187	h24_2.fastq	fastq	4024398750.0	26829325.0	GSM4777194 r1	0:150 1:0	A:1030703487;C:1025857271;G:1004392553;T:963376583;N:68856	150	0	1030703487	1025857271	1004392553	963376583	68856	SRX9110497	SRS7353480	SRA1124474	GEO	Shanghai Institute of Biochemistry and Cell Biology,CAS	1	0.00025		0.0		0.99997		1.0		150		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2020-09-12	Pharyngula	Embryo	Gonad	Reproductive System
60888	60888	SRR12628233	SRX9110496	SRS7353479	SRP282187	PRJNA663091	Characterization of small RNAs in early zebrafish PGCs	GSE157865	Transcriptome Analysis	Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs		pubmed:33506864	h24 1: PGCs 24hpf repeat1	GSM4777193	source name:PGCs\|cell type:primordial germ cells\|strain:AB\|tissue:gonad	h24 1: PGCs 24hpf repeat1	Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample …	PGCs	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.		cell type:primordial germ cells\|strain:AB\|tissue:gonad	GSM4777193	GSM4777193: h24 1: PGCs 24hpf repeat1; Danio rerio; miRNA Seq	GSM4777193	1	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.	GEO Accession:GSM4777193	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	HiSeq X Ten	SRP282187	h24_1.fastq	fastq	2223111450.0	14820743.0	GSM4777193 r1	0:150 1:0	A:510125618;C:561938103;G:577742482;T:573267493;N:37754	150	0	510125618	561938103	577742482	573267493	37754	SRX9110496	SRS7353479	SRA1124474	GEO	Shanghai Institute of Biochemistry and Cell Biology,CAS	1	0.0004		0.0		0.99993		1.0		150		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2020-09-12	Pharyngula	Embryo	Gonad	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");;