rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_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,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
40599,SRR3231354,SRX1637105,SRS1342922,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,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,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:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4.1_R1_001.fastq.gz 8hpf_wt_Plate4.1_R2_001.fastq.gz,fastq fastq,2340114249.0,31038332.0,GSM2090871 r1,0:75.50 1:75.29,A:719873895;C:416010081;G:472221417;T:731461092;N:547764,75,75,,,719873895,416010081,472221417,731461092,547764,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",1,0.00529,,0.00355,,0.99655,,0.52173,,76,,T,,under 1.2% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40600,SRR3231355,SRX1637105,SRS1342922,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,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,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:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4.2_R1_001.fastq.gz 8hpf_wt_Plate4.2_R2_001.fastq.gz,fastq fastq,2340187687.0,31038332.0,GSM2090871 r2,0:75.50 1:75.29,A:718375391;C:414519064;G:478873036;T:728401149;N:19047,75,75,,,718375391,414519064,478873036,728401149,19047,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",1,0.00524,,0.00333,,0.99634,,0.47321,,76,,T,,under 1.2% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40601,SRR3231356,SRX1637105,SRS1342922,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,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,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:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4.3_R1_001.fastq.gz 8hpf_wt_Plate4.3_R2_001.fastq.gz,fastq fastq,2331948832.0,15464230.0,GSM2090871 r3,0:75.51 1:75.29,A:710801790;C:413559417;G:478178818;T:728790143;N:618664,75,75,,,710801790,413559417,478178818,728790143,618664,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00263,0.00843,0.0023,0.00555,0.99955,0.99437,0.37837,0.52459,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40602,SRR3231357,SRX1637105,SRS1342922,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,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,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:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4_R1_001.fastq.gz 8hpf_wt_Plate4_R2_001.fastq.gz,fastq fastq,2346532249.0,15562065.0,GSM2090871 r4,0:75.50 1:75.29,A:726362504;C:417435976;G:471522192;T:731180603;N:30974,75,75,,,726362504,417435976,471522192,731180603,30974,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0024,0.00837,0.00209,0.00548,0.99975,0.99409,0.2,0.53439,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40603,SRR3231350,SRX1637104,SRS1342923,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,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,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:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3.1_R2_001.fastq.gz 8hpf_wt_Plate3.1_R1_001.fastq.gz,fastq fastq,1401297283.0,9290433.0,GSM2090870 r1,0:75.49 1:75.34,A:419635887;C:271951633;G:296507210;T:413191086;N:11467,75,75,,,419635887,271951633,296507210,413191086,11467,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00163,0.00616,0.00116,0.00341,0.99951,0.99425,0.125,0.59722,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40604,SRR3231351,SRX1637104,SRS1342923,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,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,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:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3.2_R1_001.fastq.gz 8hpf_wt_Plate3.2_R2_001.fastq.gz,fastq fastq,1401701707.0,9293054.0,GSM2090870 r2,0:75.50 1:75.34,A:422173594;C:272799681;G:292195265;T:414209404;N:323763,75,75,,,422173594,272799681,292195265,414209404,323763,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00183,0.0057,0.00134,0.00307,0.99959,0.9948,0.18965,0.59402,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40605,SRR3231352,SRX1637104,SRS1342923,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,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,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:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3.3_R1_001.fastq.gz 8hpf_wt_Plate3.3_R2_001.fastq.gz,fastq fastq,1395747908.0,9253276.0,GSM2090870 r3,0:75.50 1:75.34,A:416176386;C:270989429;G:295563056;T:412655214;N:363823,75,75,,,416176386,270989429,295563056,412655214,363823,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00148,0.0058,0.00112,0.00312,0.99969,0.99476,0.16279,0.54093,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40606,SRR3231353,SRX1637104,SRS1342923,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,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,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:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3_R1_001.fastq.gz 8hpf_wt_Plate3_R2_001.fastq.gz,fastq fastq,1407551761.0,9332199.0,GSM2090870 r4,0:75.49 1:75.34,A:425795996;C:274090898;G:292401737;T:415244521;N:18609,75,75,,,425795996,274090898,292401737,415244521,18609,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00196,0.00615,0.00142,0.00325,0.99926,0.99403,0.39682,0.57712,74,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40607,SRR3231346,SRX1637103,SRS1342924,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,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,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:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2.1_R1_001.fastq.gz 8hpf_wt_Plate2.1_R2_001.fastq.gz,fastq fastq,952595024.0,6315631.0,GSM2090869 r1,0:75.47 1:75.36,A:302137554;C:151875219;G:168962721;T:329611160;N:8370,75,75,,,302137554,151875219,168962721,329611160,8370,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00829,0.04086,0.00683,0.01381,0.99898,0.97133,0.21481,0.68244,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40608,SRR3231347,SRX1637103,SRS1342924,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,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,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:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2.2_R1_001.fastq.gz 8hpf_wt_Plate2.2_R2_001.fastq.gz,fastq fastq,946451815.0,6274940.0,GSM2090869 r2,0:75.47 1:75.36,A:302374789;C:151074230;G:165028305;T:327758585;N:215906,75,75,,,302374789,151074230,165028305,327758585,215906,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00869,0.03997,0.00704,0.01272,0.99888,0.97183,0.24342,0.68028,75,74,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40609,SRR3231348,SRX1637103,SRS1342924,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,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,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:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2.3_R2_001.fastq.gz 8hpf_wt_Plate2.3_R1_001.fastq.gz,fastq fastq,947126047.0,6279272.0,GSM2090869 r3,0:75.48 1:75.36,A:299035197;C:150983123;G:168162807;T:328697140;N:247780,75,75,,,299035197,150983123,168162807,328697140,247780,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00868,0.03867,0.00717,0.01319,0.99864,0.97356,0.29285,0.66677,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40610,SRR3231349,SRX1637103,SRS1342924,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,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,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:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2_R1_001.fastq.gz 8hpf_wt_Plate2_R2_001.fastq.gz,fastq fastq,948028451.0,6285580.0,GSM2090869 r4,0:75.47 1:75.36,A:304286797;C:151414365;G:164490323;T:327824187;N:12779,75,75,,,304286797,151414365,164490323,327824187,12779,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0086,0.04012,0.00712,0.01343,0.99888,0.97177,0.29411,0.66575,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40611,SRR3231342,SRX1637102,SRS1342925,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,,8hpf wt Plate1.1,GSM2090868,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090868,GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090868,,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:GSM2090868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate1.1_R1_001.fastq.gz 8hpf_wt_Plate1.1_R2_001.fastq.gz,fastq fastq,1189452130.0,7888435.0,GSM2090868 r1,0:75.47 1:75.32,A:375847699;C:199289576;G:245818831;T:368358068;N:137956,75,75,,,375847699,199289576,245818831,368358068,137956,SRX1637102,SRS1342925,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00377,0.02162,0.00304,0.01018,0.99931,0.9848,0.29032,0.61771,75,73,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40612,SRR3231343,SRX1637102,SRS1342925,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,,8hpf wt Plate1.1,GSM2090868,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090868,GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090868,,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:GSM2090868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate1.2_R1_001.fastq.gz 8hpf_wt_Plate1.2_R2_001.fastq.gz,fastq fastq,1238856894.0,8215764.0,GSM2090868 r2,0:75.47 1:75.32,A:389215255;C:208182440;G:256176425;T:385173832;N:108942,75,75,,,389215255,208182440,256176425,385173832,108942,SRX1637102,SRS1342925,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00375,0.02269,0.00298,0.01135,0.99928,0.98423,0.40579,0.61686,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40613,SRR3231344,SRX1637102,SRS1342925,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,,8hpf wt Plate1.1,GSM2090868,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090868,GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090868,,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:GSM2090868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate1.3_R1_001.fastq.gz 8hpf_wt_Plate1.3_R2_001.fastq.gz,fastq fastq,1240573542.0,8227185.0,GSM2090868 r3,0:75.47 1:75.32,A:389703162;C:207657187;G:257329681;T:385780094;N:103418,75,75,,,389703162,207657187,257329681,385780094,103418,SRX1637102,SRS1342925,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00354,0.02325,0.00287,0.01111,0.99922,0.98309,0.47368,0.60449,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40614,SRR3231345,SRX1637102,SRS1342925,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,,8hpf wt Plate1.1,GSM2090868,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090868,GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090868,,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:GSM2090868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate1_R1_001.fastq.gz 8hpf_wt_Plate1_R2_001.fastq.gz,fastq fastq,1215460175.0,8061085.0,GSM2090868 r4,0:75.46 1:75.32,A:382475416;C:204057930;G:251490776;T:377293780;N:142273,75,75,,,382475416,204057930,251490776,377293780,142273,SRX1637102,SRS1342925,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00394,0.02131,0.00309,0.0101,0.99928,0.98472,0.34285,0.61368,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40615,SRR3231338,SRX1637101,SRS1342933,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,,8hpf Tdrd6a :  Plate4.1,GSM2090867,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090867,GSM2090867: 8hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090867,,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:GSM2090867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate4.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4.1_R2_001.fastq.gz,fastq fastq,660308475.0,4377096.0,GSM2090867 r1,0:75.49 1:75.36,A:203051507;C:115872485;G:122313924;T:219064434;N:6125,75,75,,,203051507,115872485,122313924,219064434,6125,SRX1637101,SRS1342933,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00239,0.00751,0.00191,0.00364,0.99941,0.99385,0.5625,0.71067,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40616,SRR3231339,SRX1637101,SRS1342933,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,,8hpf Tdrd6a :  Plate4.1,GSM2090867,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090867,GSM2090867: 8hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090867,,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:GSM2090867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate4.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4.2_R2_001.fastq.gz,fastq fastq,659386859.0,4370960.0,GSM2090867 r2,0:75.50 1:75.36,A:204037715;C:116060649;G:120151402;T:218981853;N:155240,75,75,,,204037715,116060649,120151402,218981853,155240,SRX1637101,SRS1342933,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00303,0.00736,0.00246,0.00371,0.99941,0.99429,0.45614,0.65738,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40617,SRR3231340,SRX1637101,SRS1342933,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,,8hpf Tdrd6a :  Plate4.1,GSM2090867,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090867,GSM2090867: 8hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090867,,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:GSM2090867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate4.3_R2_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4.3_R1_001.fastq.gz,fastq fastq,656929514.0,4354565.0,GSM2090867 r3,0:75.50 1:75.36,A:200970859;C:115371071;G:121921931;T:218498053;N:167600,75,75,,,200970859,115371071,121921931,218498053,167600,SRX1637101,SRS1342933,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00267,0.00746,0.00211,0.00354,0.99926,0.99371,0.58181,0.66467,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40618,SRR3231341,SRX1637101,SRS1342933,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,,8hpf Tdrd6a :  Plate4.1,GSM2090867,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090867,GSM2090867: 8hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090867,,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:GSM2090867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate4_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4_R2_001.fastq.gz,fastq fastq,659750831.0,4373567.0,GSM2090867 r4,0:75.49 1:75.36,A:205228191;C:116070031;G:119659384;T:218783801;N:9424,75,75,,,205228191,116070031,119659384,218783801,9424,SRX1637101,SRS1342933,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00286,0.00728,0.00232,0.00355,0.99945,0.99439,0.47169,0.69696,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40619,SRR3231334,SRX1637100,SRS1342932,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,,8hpf Tdrd6a :  Plate3.1,GSM2090866,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090866,GSM2090866: 8hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090866,,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:GSM2090866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate3.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3.1_R2_001.fastq.gz,fastq fastq,991807830.0,6574461.0,GSM2090866 r1,0:75.50 1:75.35,A:306057776;C:164673747;G:183621348;T:337443425;N:11534,75,75,,,306057776,164673747,183621348,337443425,11534,SRX1637100,SRS1342932,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00573,0.01848,0.00474,0.0066,0.99918,0.98362,0.36274,0.59804,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40620,SRR3231335,SRX1637100,SRS1342932,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,,8hpf Tdrd6a :  Plate3.1,GSM2090866,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090866,GSM2090866: 8hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090866,,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:GSM2090866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate3.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3.2_R2_001.fastq.gz,fastq fastq,985873592.0,6535185.0,GSM2090866 r2,0:75.50 1:75.35,A:306272693;C:164036011;G:179508984;T:335829272;N:226632,75,75,,,306272693,164036011,179508984,335829272,226632,SRX1637100,SRS1342932,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00561,0.0179,0.00465,0.00654,0.99918,0.98437,0.31,0.63328,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40621,SRR3231336,SRX1637100,SRS1342932,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,,8hpf Tdrd6a :  Plate3.1,GSM2090866,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090866,GSM2090866: 8hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090866,,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:GSM2090866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate3.3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3.3_R2_001.fastq.gz,fastq fastq,985261576.0,6530964.0,GSM2090866 r3,0:75.51 1:75.35,A:302874779;C:163594572;G:182423657;T:336116219;N:252349,75,75,,,302874779,163594572,182423657,336116219,252349,SRX1637100,SRS1342932,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0057,0.01777,0.00484,0.00661,0.99926,0.98482,0.3146,0.64967,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40622,SRR3231337,SRX1637100,SRS1342932,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,,8hpf Tdrd6a :  Plate3.1,GSM2090866,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090866,GSM2090866: 8hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090866,,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:GSM2090866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3_R2_001.fastq.gz,fastq fastq,988364061.0,6551921.0,GSM2090866 r4,0:75.50 1:75.35,A:308483971;C:164508093;G:179109944;T:336245723;N:16330,75,75,,,308483971,164508093,179109944,336245723,16330,SRX1637100,SRS1342932,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00558,0.0188,0.00462,0.00684,0.99912,0.98354,0.38775,0.62734,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40623,SRR3231330,SRX1637099,SRS1342934,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,,8hpf Tdrd6a :  Plate2.1,GSM2090865,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090865,GSM2090865: 8hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090865,,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:GSM2090865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate2.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2.1_R2_001.fastq.gz,fastq fastq,1347558297.0,8935001.0,GSM2090865 r1,0:75.49 1:75.32,A:428692990;C:233467157;G:260154804;T:425229674;N:13672,75,75,,,428692990,233467157,260154804,425229674,13672,SRX1637099,SRS1342934,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00717,0.02482,0.00583,0.01367,0.9977,0.98301,0.54347,0.62642,74,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40624,SRR3231331,SRX1637099,SRS1342934,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,,8hpf Tdrd6a :  Plate2.1,GSM2090865,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090865,GSM2090865: 8hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090865,,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:GSM2090865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate2.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2.2_R2_001.fastq.gz,fastq fastq,1347477358.0,8934352.0,GSM2090865 r2,0:75.50 1:75.32,A:431085993;C:234267083;G:255942417;T:425873702;N:308163,75,75,,,431085993,234267083,255942417,425873702,308163,SRX1637099,SRS1342934,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00723,0.02422,0.00571,0.01316,0.99748,0.9825,0.4935,0.61373,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40625,SRR3231332,SRX1637099,SRS1342934,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,,8hpf Tdrd6a :  Plate2.1,GSM2090865,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090865,GSM2090865: 8hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090865,,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:GSM2090865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate2.3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2.3_R2_001.fastq.gz,fastq fastq,1342511024.0,8901101.0,GSM2090865 r3,0:75.50 1:75.32,A:424536537;C:232976344;G:259737347;T:424897714;N:363082,75,75,,,424536537,232976344,259737347,424897714,363082,SRX1637099,SRS1342934,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00707,0.02424,0.00579,0.01341,0.99788,0.98277,0.3897,0.60237,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40626,SRR3231333,SRX1637099,SRS1342934,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,,8hpf Tdrd6a :  Plate2.1,GSM2090865,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090865,GSM2090865: 8hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090865,,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:GSM2090865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2_R2_001.fastq.gz,fastq fastq,1349985043.0,8951395.0,GSM2090865 r4,0:75.49 1:75.32,A:433870230;C:234813106;G:255398294;T:425882927;N:20486,75,75,,,433870230,234813106,255398294,425882927,20486,SRX1637099,SRS1342934,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00663,0.02406,0.00536,0.01336,0.99772,0.98281,0.48872,0.63184,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40627,SRR3231326,SRX1637098,SRS1342905,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,,8hpf Tdrd6a :  Plate1.1,GSM2090864,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090864,GSM2090864: 8hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090864,,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:GSM2090864,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate1.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1.1_R2_001.fastq.gz,fastq fastq,2529086421.0,16774294.0,GSM2090864 r1,0:75.43 1:75.34,A:796779684;C:413533280;G:487547543;T:830919763;N:306151,75,75,,,796779684,413533280,487547543,830919763,306151,SRX1637098,SRS1342905,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.05805,0.15018,0.04986,0.07872,0.98729,0.92443,0.5,0.46925,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40628,SRR3231327,SRX1637098,SRS1342905,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,,8hpf Tdrd6a :  Plate1.1,GSM2090864,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090864,GSM2090864: 8hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090864,,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:GSM2090864,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate1.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1.2_R2_001.fastq.gz,fastq fastq,2629569381.0,17440212.0,GSM2090864 r2,0:75.43 1:75.34,A:823719446;C:431439564;G:506909577;T:867265650;N:235144,75,75,,,823719446,431439564,506909577,867265650,235144,SRX1637098,SRS1342905,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0575,0.1556,0.04944,0.08069,0.98648,0.92245,0.5,0.58664,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40629,SRR3231328,SRX1637098,SRS1342905,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,,8hpf Tdrd6a :  Plate1.1,GSM2090864,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090864,GSM2090864: 8hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090864,,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:GSM2090864,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate1.3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1.3_R2_001.fastq.gz,fastq fastq,2626839769.0,17422028.0,GSM2090864 r3,0:75.43 1:75.35,A:822264952;C:429448970;G:507899334;T:867005630;N:220883,75,75,,,822264952,429448970,507899334,867005630,220883,SRX1637098,SRS1342905,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.05904,0.1574,0.05085,0.08206,0.98685,0.92133,0.50407,0.58481,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40630,SRR3231329,SRX1637098,SRS1342905,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,,8hpf Tdrd6a :  Plate1.1,GSM2090864,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf 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:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090864,GSM2090864: 8hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090864,,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:GSM2090864,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1_R2_001.fastq.gz,fastq fastq,2592347629.0,17194377.0,GSM2090864 r4,0:75.43 1:75.34,A:813940505;C:424856630;G:499860954;T:853378694;N:310846,75,75,,,813940505,424856630,499860954,853378694,310846,SRX1637098,SRS1342905,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0589,0.14612,0.05081,0.07706,0.98756,0.92829,0.52503,0.46498,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
50628,SRR8182164,SRX5002131,SRS4036794,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 7hpf RNA seq rep2,GSM3467114,,tissue:PGCs 7hpf RNA seq replicate 2|cell type:primordial germ cells|developmental stage:7hpf,PGC 7hpf 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 7hpf 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:7hpf,GSM3467114,GSM3467114: PGC 7hpf RNA seq rep2; Danio rerio; RNA Seq,GSM3467114,,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:GSM3467114,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP168473,,,PGC_7h_rep2_R1.fastq.gz PGC_7h_rep2_R2.fastq.gz,fastq fastq,9481475596.0,46937998.0,GSM3467114 r1,0:101 1:101,A:1668317872;C:3083330861;G:3080548352;T:1648694500;N:584011,101,101,,,1668317872,3083330861,3080548352,1648694500,584011,SRX5002131,SRS4036794,SRA808716,GEO,"Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute",2,0.97773,0.98127,0.25067,0.23496,0.88318,0.88306,0.85098,0.92027,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Australia,2018-11-13,Gastrula,Embryo,Gonad,Reproductive System
50629,SRR8182163,SRX5002130,SRS4036793,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 7hpf RNA seq rep1,GSM3467113,,tissue:PGCs 7hpf RNA seq replicate 1|cell type:primordial germ cells|developmental stage:7hpf,PGC 7hpf 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 7hpf 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:7hpf,GSM3467113,GSM3467113: PGC 7hpf RNA seq rep1; Danio rerio; RNA Seq,GSM3467113,,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:GSM3467113,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP168473,,,PGC_7h_rep1_R1.fastq.gz PGC_7h_rep1_R2.fastq.gz,fastq fastq,10088815058.0,49944629.0,GSM3467113 r1,0:101 1:101,A:1806152257;C:3225759540;G:3246771301;T:1809505955;N:626005,101,101,,,1806152257,3225759540,3246771301,1809505955,626005,SRX5002130,SRS4036793,SRA808716,GEO,"Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute",2,0.98127,0.98176,0.23978,0.22208,0.86902,0.86989,0.87272,0.90058,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Australia,2018-11-13,Gastrula,Embryo,Gonad,Reproductive System
51714,SRR8799027,SRX5587878,SRS4549125,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 7hpf RNA seq rep2 RUN2,GSM3689554,,tissue:PGCs 7hpf RNA seq replicate 2 RUN2|cell type:primordial germ cells|developmental stage:7hpf,PGC 7hpf 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 7hpf 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:7hpf,GSM3689554,GSM3689554: PGC 7hpf RNA seq rep2 RUN2; Danio rerio; RNA Seq,GSM3689554,,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:GSM3689554,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP189741,,,PGC_7h_rep2_R2_001.fastq.gz PGC_7h_rep2_R1_001.fastq.gz,fastq fastq,20195621044.0,99978322.0,GSM3689554 r1,0:101 1:101,A:3507319398;C:6608277226;G:6608106633;T:3471819746;N:98041,101,101,,,3507319398,6608277226,6608106633,3471819746,98041,SRX5587878,SRS4549125,SRA867175,GEO,"Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute",2,0.97952,0.982,0.24309,0.22928,0.88527,0.88517,0.89923,0.92505,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Australia,2019-03-28,Gastrula,Embryo,Gonad,Reproductive System
51715,SRR8799026,SRX5587877,SRS4549124,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 7hpf RNA seq rep1 RUN2,GSM3689553,,tissue:PGCs 7hpf RNA seq replicate 1 RUN2|cell type:primordial germ cells|developmental stage:7hpf,PGC 7hpf 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 7hpf 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:7hpf,GSM3689553,GSM3689553: PGC 7hpf RNA seq rep1 RUN2; Danio rerio; RNA Seq,GSM3689553,,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:GSM3689553,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP189741,,,PGC_7h_rep1_R2_001.fastq.gz PGC_7h_rep1_R1_001.fastq.gz,fastq fastq,22036293726.0,109090563.0,GSM3689553 r1,0:101 1:101,A:3894674712;C:7087458592;G:7147309454;T:3906742891;N:108077,101,101,,,3894674712,7087458592,7147309454,3906742891,108077,SRX5587877,SRS4549124,SRA867175,GEO,"Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute",2,0.98233,0.98249,0.22995,0.21519,0.87176,0.87233,0.79764,0.90655,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Australia,2019-03-28,Gastrula,Embryo,Gonad,Reproductive System
60891,SRR12628230,SRX9110493,SRS7353476,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,,h6 2: PGCs 6hpf repeat2,GSM4777190,,source name:PGCs|cell type:primordial germ cells|strain:AB|tissue:gonad,h6 2: PGCs 6hpf 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,GSM4777190,GSM4777190: h6 2: PGCs 6hpf repeat2; Danio rerio; miRNA Seq,GSM4777190,,1,PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.,GEO Accession:GSM4777190,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,HiSeq X Ten,,SRP282187,,,h6_2.fastq,fastq,2330922150.0,15539481.0,GSM4777190 r1,0:150 1:0,A:563758043;C:619336180;G:552040747;T:595747277;N:39903,150,0,,,563758043,619336180,552040747,595747277,39903,SRX9110493,SRS7353476,SRA1124474,GEO,"Shanghai Institute of Biochemistry and Cell Biology,CAS",1,0.00014,,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,Gastrula,Embryo,Gonad,Reproductive System
60892,SRR12628229,SRX9110492,SRS7353475,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,,h6 1: PGCs 6hpf repeat1,GSM4777189,,source name:PGCs|cell type:primordial germ cells|strain:AB|tissue:gonad,h6 1: PGCs 6hpf 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,GSM4777189,GSM4777189: h6 1: PGCs 6hpf repeat1; Danio rerio; miRNA Seq,GSM4777189,,1,PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.,GEO Accession:GSM4777189,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,HiSeq X Ten,,SRP282187,,,h6_1.fastq,fastq,1979588400.0,13197256.0,GSM4777189 r1,0:150 1:0,A:453046525;C:471873747;G:495904656;T:558729697;N:33775,150,0,,,453046525,471873747,495904656,558729697,33775,SRX9110492,SRS7353475,SRA1124474,GEO,"Shanghai Institute of Biochemistry and Cell Biology,CAS",1,0.00028,,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,Gastrula,Embryo,Gonad,Reproductive System