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
40631,SRR3231322,SRX1637097,SRS1342906,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8and24hpf wt Plate1.1,GSM2090863,,tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8and24hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090863,GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090863,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090863,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8and24hpf_wt_Plate1.1_R1_001.fastq.gz 8and24hpf_wt_Plate1.1_R2_001.fastq.gz,fastq fastq,354951269.0,2354572.0,GSM2090863 r1,0:75.37 1:75.38,A:109255676;C:46649925;G:56800706;T:142212324;N:32638,75,75,,,109255676,46649925,56800706,142212324,32638,SRX1637097,SRS1342906,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.08814,0.58586,0.05414,0.12777,0.98236,0.8253,0.52224,0.5333,75,55,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40632,SRR3231323,SRX1637097,SRS1342906,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8and24hpf wt Plate1.1,GSM2090863,,tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8and24hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090863,GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090863,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090863,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8and24hpf_wt_Plate1.2_R1_001.fastq.gz 8and24hpf_wt_Plate1.2_R2_001.fastq.gz,fastq fastq,373175186.0,2475371.0,GSM2090863 r2,0:75.37 1:75.38,A:114080796;C:49251081;G:59964869;T:149836843;N:41597,75,75,,,114080796,49251081,59964869,149836843,41597,SRX1637097,SRS1342906,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0895,0.59282,0.05309,0.12622,0.9811,0.82185,0.51449,0.52518,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40633,SRR3231324,SRX1637097,SRS1342906,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8and24hpf wt Plate1.1,GSM2090863,,tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8and24hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090863,GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090863,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090863,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8and24hpf_wt_Plate1.3_R1_001.fastq.gz 8and24hpf_wt_Plate1.3_R2_001.fastq.gz,fastq fastq,376796544.0,2499144.0,GSM2090863 r3,0:75.38 1:75.39,A:114262594;C:49685044;G:61341084;T:151464220;N:43602,75,75,,,114262594,49685044,61341084,151464220,43602,SRX1637097,SRS1342906,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.08885,0.60874,0.05444,0.12569,0.98177,0.81233,0.51071,0.53112,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40634,SRR3231325,SRX1637097,SRS1342906,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8and24hpf wt Plate1.1,GSM2090863,,tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8and24hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090863,GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090863,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090863,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8and24hpf_wt_Plate1_R1_001.fastq.gz 8and24hpf_wt_Plate1_R2_001.fastq.gz,fastq fastq,370852802.0,2459988.0,GSM2090863 r4,0:75.37 1:75.38,A:113706258;C:48924259;G:59523739;T:148663433;N:35113,75,75,,,113706258,48924259,59523739,148663433,35113,SRX1637097,SRS1342906,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.08962,0.59214,0.05376,0.12667,0.98226,0.82142,0.53851,0.52744,75,32,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40635,SRR3231318,SRX1637096,SRS1342907,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,,3.5hpf wt Plate5.1,GSM2090862,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090862,GSM2090862: 3.5hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090862,,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:GSM2090862,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate5.1_R1_001.fastq.gz 3.5hpf_wt_Plate5.1_R2_001.fastq.gz,fastq fastq,465283988.0,3083951.0,GSM2090862 r1,0:75.46 1:75.41,A:131913263;C:74557873;G:91090052;T:167720369;N:2431,75,75,,,131913263,74557873,91090052,167720369,2431,SRX1637096,SRS1342907,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00196,0.01756,0.00174,0.00396,0.99981,0.97512,0.4375,0.58617,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40636,SRR3231319,SRX1637096,SRS1342907,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,,3.5hpf wt Plate5.1,GSM2090862,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090862,GSM2090862: 3.5hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090862,,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:GSM2090862,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate5.2_R1_001.fastq.gz 3.5hpf_wt_Plate5.2_R2_001.fastq.gz,fastq fastq,492787533.0,3266133.0,GSM2090862 r2,0:75.46 1:75.41,A:138920634;C:79266412;G:96252502;T:178340643;N:7342,75,75,,,138920634,79266412,96252502,178340643,7342,SRX1637096,SRS1342907,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00175,0.01711,0.00149,0.00417,0.99965,0.9754,0.28571,0.59079,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40637,SRR3231320,SRX1637096,SRS1342907,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,,3.5hpf wt Plate5.1,GSM2090862,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090862,GSM2090862: 3.5hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090862,,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:GSM2090862,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate5.3_R1_001.fastq.gz 3.5hpf_wt_Plate5.3_R2_001.fastq.gz,fastq fastq,478302056.0,3170122.0,GSM2090862 r3,0:75.46 1:75.41,A:134552769;C:76719834;G:94014994;T:173009599;N:4860,75,75,,,134552769,76719834,94014994,173009599,4860,SRX1637096,SRS1342907,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0018,0.01735,0.00154,0.00386,0.99967,0.97429,0.23809,0.55019,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40638,SRR3231321,SRX1637096,SRS1342907,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,,3.5hpf wt Plate5.1,GSM2090862,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090862,GSM2090862: 3.5hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090862,,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:GSM2090862,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate5_R1_001.fastq.gz 3.5hpf_wt_Plate5_R2_001.fastq.gz,fastq fastq,487978460.0,3234287.0,GSM2090862 r4,0:75.46 1:75.41,A:138127249;C:78568068;G:95022582;T:176256804;N:3757,75,75,,,138127249,78568068,95022582,176256804,3757,SRX1637096,SRS1342907,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00178,0.01711,0.00155,0.00374,0.99975,0.97457,0.38888,0.54467,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40639,SRR3231314,SRX1637095,SRS1342908,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,,3.5hpf wt Plate4.1,GSM2090861,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090861,GSM2090861: 3.5hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090861,,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:GSM2090861,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate4.1_R1_001.fastq.gz 3.5hpf_wt_Plate4.1_R2_001.fastq.gz,fastq fastq,1165572863.0,7724698.0,GSM2090861 r1,0:75.47 1:75.42,A:341597187;C:187300441;G:218487967;T:418181251;N:6017,75,75,,,341597187,187300441,218487967,418181251,6017,SRX1637095,SRS1342908,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0024,0.05972,0.00175,0.01107,0.99894,0.93363,0.46268,0.54466,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40640,SRR3231315,SRX1637095,SRS1342908,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,,3.5hpf wt Plate4.1,GSM2090861,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090861,GSM2090861: 3.5hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090861,,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:GSM2090861,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate4.2_R1_001.fastq.gz 3.5hpf_wt_Plate4.2_R2_001.fastq.gz,fastq fastq,1231311328.0,8160147.0,GSM2090861 r2,0:75.48 1:75.42,A:359044176;C:198664662;G:229959438;T:443624264;N:18788,75,75,,,359044176,198664662,229959438,443624264,18788,SRX1637095,SRS1342908,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0022,0.06116,0.00155,0.01128,0.99888,0.93229,0.40298,0.54742,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40641,SRR3231316,SRX1637095,SRS1342908,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,,3.5hpf wt Plate4.1,GSM2090861,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090861,GSM2090861: 3.5hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090861,,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:GSM2090861,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate4.3_R1_001.fastq.gz 3.5hpf_wt_Plate4.3_R2_001.fastq.gz,fastq fastq,1197590912.0,7936665.0,GSM2090861 r3,0:75.48 1:75.42,A:348626376;C:192686213;G:225139549;T:431126048;N:12726,75,75,,,348626376,192686213,225139549,431126048,12726,SRX1637095,SRS1342908,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00247,0.06111,0.00168,0.01107,0.9987,0.9318,0.41176,0.55782,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40642,SRR3231317,SRX1637095,SRS1342908,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,,3.5hpf wt Plate4.1,GSM2090861,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090861,GSM2090861: 3.5hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090861,,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:GSM2090861,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate4_R1_001.fastq.gz 3.5hpf_wt_Plate4_R2_001.fastq.gz,fastq fastq,1224213980.0,8113208.0,GSM2090861 r4,0:75.48 1:75.42,A:358299358;C:197501927;G:228122097;T:440281285;N:9313,75,75,,,358299358,197501927,228122097,440281285,9313,SRX1637095,SRS1342908,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00255,0.06199,0.00181,0.0116,0.9989,0.93326,0.48684,0.54385,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40643,SRR3231310,SRX1637094,SRS1342909,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,,3.5hpf wt Plate3.1,GSM2090860,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090860,GSM2090860: 3.5hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090860,,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:GSM2090860,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate3.1_R1_001.fastq.gz 3.5hpf_wt_Plate3.1_R2_001.fastq.gz,fastq fastq,626596035.0,4155091.0,GSM2090860 r1,0:75.44 1:75.37,A:192353640;C:87072147;G:109704935;T:237462123;N:3190,75,75,,,192353640,87072147,109704935,237462123,3190,SRX1637094,SRS1342909,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00677,0.07893,0.00548,0.01598,0.99898,0.92987,0.43902,0.58089,73,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40644,SRR3231311,SRX1637094,SRS1342909,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,,3.5hpf wt Plate3.1,GSM2090860,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090860,GSM2090860: 3.5hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090860,,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:GSM2090860,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate3.2_R1_001.fastq.gz 3.5hpf_wt_Plate3.2_R2_001.fastq.gz,fastq fastq,662952483.0,4396049.0,GSM2090860 r2,0:75.44 1:75.37,A:202110673;C:92410890;G:116053839;T:252366901;N:10180,75,75,,,202110673,92410890,116053839,252366901,10180,SRX1637094,SRS1342909,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00616,0.08027,0.00497,0.01696,0.99896,0.9277,0.50649,0.58134,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40645,SRR3231312,SRX1637094,SRS1342909,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,,3.5hpf wt Plate3.1,GSM2090860,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090860,GSM2090860: 3.5hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090860,,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:GSM2090860,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate3.3_R1_001.fastq.gz 3.5hpf_wt_Plate3.3_R2_001.fastq.gz,fastq fastq,647301548.0,4292251.0,GSM2090860 r3,0:75.44 1:75.37,A:197180599;C:89984465;G:113867175;T:246262732;N:6577,75,75,,,197180599,89984465,113867175,246262732,6577,SRX1637094,SRS1342909,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00689,0.08136,0.00549,0.01688,0.99876,0.92654,0.54347,0.58937,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40646,SRR3231313,SRX1637094,SRS1342909,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,,3.5hpf wt Plate3.1,GSM2090860,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090860,GSM2090860: 3.5hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090860,,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:GSM2090860,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate3_R1_001.fastq.gz 3.5hpf_wt_Plate3_R2_001.fastq.gz,fastq fastq,656915830.0,4356034.0,GSM2090860 r4,0:75.44 1:75.37,A:201028065;C:91591416;G:114616914;T:249674244;N:5191,75,75,,,201028065,91591416,114616914,249674244,5191,SRX1637094,SRS1342909,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00611,0.08116,0.0049,0.01729,0.99892,0.92661,0.37662,0.45981,75,74,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40647,SRR3231306,SRX1637093,SRS1342910,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,,3.5hpf wt Plate2.1,GSM2090859,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090859,GSM2090859: 3.5hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090859,,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:GSM2090859,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate2.1_R1_001.fastq.gz 3.5hpf_wt_Plate2.1_R2_001.fastq.gz,fastq fastq,885364409.0,5869953.0,GSM2090859 r1,0:75.43 1:75.40,A:267732586;C:139479978;G:161193259;T:316954042;N:4544,75,75,,,267732586,139479978,161193259,316954042,4544,SRX1637093,SRS1342910,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0027,0.09073,0.00136,0.01929,0.99801,0.92275,0.52678,0.59397,75,74,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40648,SRR3231307,SRX1637093,SRS1342910,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,,3.5hpf wt Plate2.1,GSM2090859,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090859,GSM2090859: 3.5hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090859,,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:GSM2090859,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate2.2_R1_001.fastq.gz 3.5hpf_wt_Plate2.2_R2_001.fastq.gz,fastq fastq,935453664.0,6201750.0,GSM2090859 r2,0:75.44 1:75.40,A:280574811;C:147981655;G:170370395;T:336513026;N:13777,75,75,,,280574811,147981655,170370395,336513026,13777,SRX1637093,SRS1342910,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00297,0.09176,0.00155,0.01869,0.99809,0.91946,0.46666,0.59074,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40649,SRR3231308,SRX1637093,SRS1342910,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,,3.5hpf wt Plate2.1,GSM2090859,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090859,GSM2090859: 3.5hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090859,,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:GSM2090859,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate2.3_R1_001.fastq.gz 3.5hpf_wt_Plate2.3_R2_001.fastq.gz,fastq fastq,912201099.0,6047636.0,GSM2090859 r3,0:75.44 1:75.40,A:273615357;C:143852122;G:166864092;T:327859891;N:9637,75,75,,,273615357,143852122,166864092,327859891,9637,SRX1637093,SRS1342910,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00346,0.0931,0.00171,0.01934,0.99728,0.91975,0.64238,0.59662,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40650,SRR3231309,SRX1637093,SRS1342910,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,,3.5hpf wt Plate2.1,GSM2090859,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090859,GSM2090859: 3.5hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090859,,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:GSM2090859,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate2_R1_001.fastq.gz 3.5hpf_wt_Plate2_R2_001.fastq.gz,fastq fastq,926760672.0,6144176.0,GSM2090859 r4,0:75.44 1:75.40,A:278868658;C:146660825;G:168550011;T:332674041;N:7137,75,75,,,278868658,146660825,168550011,332674041,7137,SRX1637093,SRS1342910,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00323,0.09308,0.00182,0.01911,0.99786,0.91999,0.52892,0.59305,76,73,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40651,SRR3231304,SRX1637092,SRS1342911,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,,3.5hpf wt Plate1.1,GSM2090858,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090858,GSM2090858: 3.5hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090858,,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:GSM2090858,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate1.1_R1_001.fastq.gz 3.5hpf_wt_Plate1.1_R2_001.fastq.gz,fastq fastq,1401396768.0,13739184.0,GSM2090858 r1,0:51 1:51,A:347756042;C:255264101;G:254249668;T:529161525;N:14965432,51,51,,,347756042,255264101,254249668,529161525,14965432,SRX1637092,SRS1342911,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00267,0.00682,0.00252,0.0043,0.99975,0.99407,0.5909,0.36136,51,51,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40652,SRR3231305,SRX1637092,SRS1342911,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,,3.5hpf wt Plate1.1,GSM2090858,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090858,GSM2090858: 3.5hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090858,,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:GSM2090858,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate1_R1_001.fastq.gz 3.5hpf_wt_Plate1_R2_001.fastq.gz,fastq fastq,1363312518.0,13365809.0,GSM2090858 r2,0:51 1:51,A:338101381;C:247778705;G:246079568;T:516046779;N:15306085,51,51,,,338101381,247778705,246079568,516046779,15306085,SRX1637092,SRS1342911,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00301,0.00726,0.0028,0.00467,0.99963,0.99387,0.53125,0.39461,51,51,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40653,SRR3231300,SRX1637091,SRS1342912,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,,3.5hpf Tdrd6a :  Plate5.1,GSM2090857,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090857,GSM2090857: 3.5hpf Tdrd6a :  Plate5.1; Danio rerio; RNA Seq,GSM2090857,,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:GSM2090857,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate5.1_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate5.1_R2_001.fastq.gz,fastq fastq,530054811.0,3515786.0,GSM2090857 r1,0:75.42 1:75.34,A:170905056;C:77131049;G:91888905;T:190127099;N:2702,75,75,,,170905056,77131049,91888905,190127099,2702,SRX1637091,SRS1342912,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.02617,0.05634,0.01838,0.01758,0.99754,0.95448,0.23693,0.5735,76,74,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40654,SRR3231301,SRX1637091,SRS1342912,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,,3.5hpf Tdrd6a :  Plate5.1,GSM2090857,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090857,GSM2090857: 3.5hpf Tdrd6a :  Plate5.1; Danio rerio; RNA Seq,GSM2090857,,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:GSM2090857,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate5.2_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate5.2_R2_001.fastq.gz,fastq fastq,557894343.0,3700294.0,GSM2090857 r2,0:75.43 1:75.35,A:178074028;C:81692578;G:96833862;T:201285418;N:8457,75,75,,,178074028,81692578,96833862,201285418,8457,SRX1637091,SRS1342912,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.02111,0.05616,0.01461,0.01725,0.99738,0.95172,0.26252,0.56747,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40655,SRR3231302,SRX1637091,SRS1342912,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,,3.5hpf Tdrd6a :  Plate5.1,GSM2090857,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090857,GSM2090857: 3.5hpf Tdrd6a :  Plate5.1; Danio rerio; RNA Seq,GSM2090857,,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:GSM2090857,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate5.3_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate5.3_R2_001.fastq.gz,fastq fastq,542585088.0,3598766.0,GSM2090857 r3,0:75.42 1:75.35,A:173334337;C:79046469;G:94586129;T:195612312;N:5841,75,75,,,173334337,79046469,94586129,195612312,5841,SRX1637091,SRS1342912,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.02344,0.05621,0.01663,0.01767,0.9974,0.95327,0.24376,0.57321,76,74,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40656,SRR3231303,SRX1637091,SRS1342912,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,,3.5hpf Tdrd6a :  Plate5.1,GSM2090857,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090857,GSM2090857: 3.5hpf Tdrd6a :  Plate5.1; Danio rerio; RNA Seq,GSM2090857,,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:GSM2090857,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate5_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate5_R2_001.fastq.gz,fastq fastq,553684137.0,3672462.0,GSM2090857 r4,0:75.42 1:75.34,A:177515943;C:81065494;G:95795614;T:199302825;N:4261,75,75,,,177515943,81065494,95795614,199302825,4261,SRX1637091,SRS1342912,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.02234,0.05529,0.01558,0.01742,0.99758,0.95377,0.24158,0.56936,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40657,SRR3231296,SRX1637090,SRS1342913,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,,3.5hpf Tdrd6a :  Plate4.1,GSM2090856,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090856,GSM2090856: 3.5hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090856,,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:GSM2090856,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate4.1_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate4.1_R2_001.fastq.gz,fastq fastq,758489825.0,5027396.0,GSM2090856 r1,0:75.47 1:75.41,A:223477381;C:119338529;G:141593308;T:274076559;N:4048,75,75,,,223477381,119338529,141593308,274076559,4048,SRX1637090,SRS1342913,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00426,0.0881,0.00214,0.01568,0.99703,0.92527,0.49494,0.60675,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40658,SRR3231297,SRX1637090,SRS1342913,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,,3.5hpf Tdrd6a :  Plate4.1,GSM2090856,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090856,GSM2090856: 3.5hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090856,,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:GSM2090856,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate4.2_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate4.2_R2_001.fastq.gz,fastq fastq,802062750.0,5316073.0,GSM2090856 r2,0:75.47 1:75.41,A:234800617;C:126749965;G:149363757;T:291136187;N:12224,75,75,,,234800617,126749965,149363757,291136187,12224,SRX1637090,SRS1342913,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00408,0.09004,0.00226,0.01667,0.99742,0.92216,0.5337,0.60822,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40659,SRR3231298,SRX1637090,SRS1342913,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,,3.5hpf Tdrd6a :  Plate4.1,GSM2090856,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090856,GSM2090856: 3.5hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090856,,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:GSM2090856,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate4.3_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate4.3_R2_001.fastq.gz,fastq fastq,781265465.0,5178193.0,GSM2090856 r3,0:75.47 1:75.41,A:228400304;C:123116486;G:146409916;T:283330556;N:8203,75,75,,,228400304,123116486,146409916,283330556,8203,SRX1637090,SRS1342913,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00418,0.09132,0.00184,0.01663,0.99683,0.92285,0.5066,0.5994,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40660,SRR3231299,SRX1637090,SRS1342913,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,,3.5hpf Tdrd6a :  Plate4.1,GSM2090856,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090856,GSM2090856: 3.5hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090856,,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:GSM2090856,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate4_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate4_R2_001.fastq.gz,fastq fastq,796243663.0,5277519.0,GSM2090856 r4,0:75.47 1:75.41,A:233877044;C:125841514;G:147929074;T:288590102;N:5929,75,75,,,233877044,125841514,147929074,288590102,5929,SRX1637090,SRS1342913,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00412,0.09175,0.00213,0.01649,0.99722,0.92243,0.47916,0.60143,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40661,SRR3231294,SRX1637089,SRS1342914,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,,3.5hpf Tdrd6a :  Plate3.1,GSM2090855,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090855,GSM2090855: 3.5hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090855,,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:GSM2090855,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate3.1_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate3.1_R2_001.fastq.gz,fastq fastq,1252913022.0,12283461.0,GSM2090855 r1,0:51 1:51,A:323874510;C:195258080;G:204580544;T:514382561;N:14817327,51,51,,,323874510,195258080,204580544,514382561,14817327,SRX1637089,SRS1342914,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00518,0.04289,0.00473,0.01518,0.99926,0.95412,0.41935,0.41704,51,51,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40662,SRR3231295,SRX1637089,SRS1342914,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,,3.5hpf Tdrd6a :  Plate3.1,GSM2090855,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090855,GSM2090855: 3.5hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090855,,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:GSM2090855,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate3_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate3_R2_001.fastq.gz,fastq fastq,1241394468.0,12170534.0,GSM2090855 r2,0:51 1:51,A:320378911;C:193092040;G:202025341;T:508939554;N:16958622,51,51,,,320378911,193092040,202025341,508939554,16958622,SRX1637089,SRS1342914,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00484,0.04293,0.00447,0.01494,0.99951,0.95452,0.42,0.41403,51,51,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40663,SRR3231292,SRX1637088,SRS1342915,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,,3.5hpf Tdrd6a :  Plate2.1,GSM2090854,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090854,GSM2090854: 3.5hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090854,,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:GSM2090854,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate2.1_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate2.1_R2_001.fastq.gz,fastq fastq,978116046.0,9589373.0,GSM2090854 r1,0:51 1:51,A:235926359;C:165980181;G:173164459;T:392643478;N:10401569,51,51,,,235926359,165980181,173164459,392643478,10401569,SRX1637088,SRS1342915,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00854,0.17952,0.00744,0.06281,0.99855,0.90017,0.4892,0.66386,51,51,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40664,SRR3231293,SRX1637088,SRS1342915,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,,3.5hpf Tdrd6a :  Plate2.1,GSM2090854,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090854,GSM2090854: 3.5hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090854,,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:GSM2090854,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate2_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate2_R2_001.fastq.gz,fastq fastq,957502560.0,9387280.0,GSM2090854 r2,0:51 1:51,A:230320241;C:162167341;G:169171883;T:384426371;N:11416724,51,51,,,230320241,162167341,169171883,384426371,11416724,SRX1637088,SRS1342915,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00896,0.17968,0.008,0.06282,0.9987,0.89899,0.55645,0.65931,51,51,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40665,SRR3231290,SRX1637087,SRS1342916,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,,3.5hpf Tdrd6a :  Plate1.1,GSM2090853,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090853,GSM2090853: 3.5hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090853,,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:GSM2090853,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate1.1_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate1.1_R2_001.fastq.gz,fastq fastq,1086532458.0,10652279.0,GSM2090853 r1,0:51 1:51,A:251396959;C:181408258;G:195341853;T:446862283;N:11523105,51,51,,,251396959,181408258,195341853,446862283,11523105,SRX1637087,SRS1342916,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0136,0.1857,0.01211,0.06822,0.99829,0.90585,0.59239,0.72278,51,51,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40666,SRR3231291,SRX1637087,SRS1342916,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,,3.5hpf Tdrd6a :  Plate1.1,GSM2090853,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf 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:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090853,GSM2090853: 3.5hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090853,,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:GSM2090853,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate1_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate1_R2_001.fastq.gz,fastq fastq,1066918470.0,10459985.0,GSM2090853 r2,0:51 1:51,A:246360010;C:177989653;G:191393960;T:438501621;N:12673226,51,51,,,246360010,177989653,191393960,438501621,12673226,SRX1637087,SRS1342916,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01365,0.18567,0.01228,0.06729,0.99831,0.90347,0.55029,0.35593,51,51,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40667,SRR3231288,SRX1637086,SRS1342917,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,,2wpf wt 1,GSM2090852,,tissue:Germ cells|cell line:Primary cells|developmental stage:2wpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,2wpf wt 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:2wpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090852,GSM2090852: 2wpf wt 1; Danio rerio; RNA Seq,GSM2090852,,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:GSM2090852,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,2wpf_wt_1_R1_001.fastq.gz 2wpf_wt_1_R2_001.fastq.gz,fastq fastq,899083386.0,8814543.0,GSM2090852 r1,0:51 1:51,A:211455925;C:158092908;G:163752155;T:355377184;N:10405214,51,51,,,211455925,158092908,163752155,355377184,10405214,SRX1637086,SRS1342917,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0051,0.10904,0.00468,0.0257,0.99912,0.90145,0.47272,0.47949,51,51,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Larval,Larval,Gonad,Reproductive System
40668,SRR3231289,SRX1637086,SRS1342917,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,,2wpf wt 1,GSM2090852,,tissue:Germ cells|cell line:Primary cells|developmental stage:2wpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,2wpf wt 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:2wpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090852,GSM2090852: 2wpf wt 1; Danio rerio; RNA Seq,GSM2090852,,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:GSM2090852,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,2wpf_wt_R1_001.fastq.gz 2wpf_wt_R2_001.fastq.gz,fastq fastq,895174134.0,8776217.0,GSM2090852 r2,0:51 1:51,A:210034767;C:157173531;G:162557633;T:353624192;N:11784011,51,51,,,210034767,157173531,162557633,353624192,11784011,SRX1637086,SRS1342917,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00514,0.10967,0.00459,0.0262,0.9991,0.90516,0.47887,0.49885,51,51,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Larval,Larval,Gonad,Reproductive System
40669,SRR3231284,SRX1637085,SRS1342918,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate5.1,GSM2090851,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090851,GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090851,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090851,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate5.1_R1_001.fastq.gz 24hpf_wt_Plate5.1_R2_001.fastq.gz,fastq fastq,558605417.0,3704499.0,GSM2090851 r1,0:75.45 1:75.34,A:170059730;C:87004627;G:101477517;T:200008732;N:54811,75,75,,,170059730,87004627,101477517,200008732,54811,SRX1637085,SRS1342918,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01541,0.18137,0.00841,0.03816,0.99206,0.90047,0.55425,0.56591,76,32,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40670,SRR3231285,SRX1637085,SRS1342918,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate5.1,GSM2090851,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090851,GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090851,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090851,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate5.2_R1_001.fastq.gz 24hpf_wt_Plate5.2_R2_001.fastq.gz,fastq fastq,581533785.0,3856402.0,GSM2090851 r2,0:75.45 1:75.34,A:176436951;C:90826765;G:105424561;T:208785606;N:59902,75,75,,,176436951,90826765,105424561,208785606,59902,SRX1637085,SRS1342918,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01519,0.18239,0.0089,0.03729,0.99306,0.89917,0.59594,0.573,74,75,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40671,SRR3231286,SRX1637085,SRS1342918,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate5.1,GSM2090851,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090851,GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090851,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090851,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate5.3_R1_001.fastq.gz 24hpf_wt_Plate5.3_R2_001.fastq.gz,fastq fastq,581069691.0,3853089.0,GSM2090851 r3,0:75.45 1:75.35,A:175088129;C:90460041;G:106640639;T:208812858;N:68024,75,75,,,175088129,90460041,106640639,208812858,68024,SRX1637085,SRS1342918,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01551,0.19274,0.00932,0.0399,0.99289,0.89319,0.57195,0.56478,74,75,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40672,SRR3231287,SRX1637085,SRS1342918,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate5.1,GSM2090851,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090851,GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090851,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090851,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate5_R1_001.fastq.gz 24hpf_wt_Plate5_R2_001.fastq.gz,fastq fastq,576677563.0,3824304.0,GSM2090851 r4,0:75.45 1:75.34,A:175248120;C:90164865;G:104482050;T:206728496;N:54032,75,75,,,175248120,90164865,104482050,206728496,54032,SRX1637085,SRS1342918,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01561,0.18528,0.00921,0.03947,0.99302,0.8981,0.60185,0.58278,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40673,SRR3231280,SRX1637084,SRS1342920,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate4.1,GSM2090850,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090850,GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090850,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090850,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate4.1_R1_001.fastq.gz 24hpf_wt_Plate4.1_R2_001.fastq.gz,fastq fastq,739151929.0,4905477.0,GSM2090850 r1,0:75.40 1:75.28,A:237453179;C:120215450;G:139806121;T:241606048;N:71131,75,75,,,237453179,120215450,139806121,241606048,71131,SRX1637084,SRS1342920,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01446,0.18296,0.00907,0.03633,0.99442,0.91147,0.57858,0.55259,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40674,SRR3231281,SRX1637084,SRS1342920,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate4.1,GSM2090850,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090850,GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090850,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090850,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate4.2_R1_001.fastq.gz 24hpf_wt_Plate4.2_R2_001.fastq.gz,fastq fastq,769081502.0,5103797.0,GSM2090850 r2,0:75.40 1:75.29,A:245920087;C:125753713;G:145142187;T:252183239;N:82276,75,75,,,245920087,125753713,145142187,252183239,82276,SRX1637084,SRS1342920,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01429,0.18495,0.00907,0.0378,0.99435,0.91181,0.60136,0.5509,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40675,SRR3231282,SRX1637084,SRS1342920,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate4.1,GSM2090850,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090850,GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090850,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090850,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate4.3_R1_001.fastq.gz 24hpf_wt_Plate4.3_R2_001.fastq.gz,fastq fastq,763478256.0,5066455.0,GSM2090850 r3,0:75.40 1:75.29,A:242520066;C:123970168;G:146100841;T:250803049;N:84132,75,75,,,242520066,123970168,146100841,250803049,84132,SRX1637084,SRS1342920,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01481,0.1935,0.0093,0.03777,0.99448,0.90526,0.5546,0.56044,74,75,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40676,SRR3231283,SRX1637084,SRS1342920,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate4.1,GSM2090850,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090850,GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090850,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090850,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate4_R1_001.fastq.gz 24hpf_wt_Plate4_R2_001.fastq.gz,fastq fastq,762348830.0,5059335.0,GSM2090850 r4,0:75.40 1:75.28,A:244240563;C:124701855;G:143859660;T:249474441;N:72311,75,75,,,244240563,124701855,143859660,249474441,72311,SRX1637084,SRS1342920,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01537,0.18668,0.00965,0.03681,0.99407,0.91066,0.54926,0.55097,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40677,SRR3231276,SRX1637083,SRS1342919,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate3.1,GSM2090849,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090849,GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090849,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090849,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate3.1_R1_001.fastq.gz 24hpf_wt_Plate3.1_R2_001.fastq.gz,fastq fastq,692753746.0,4593127.0,GSM2090849 r1,0:75.47 1:75.35,A:200412235;C:124307113;G:146191995;T:221774807;N:67596,75,75,,,200412235,124307113,146191995,221774807,67596,SRX1637083,SRS1342919,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00405,0.02858,0.00276,0.00696,0.99752,0.9722,0.64935,0.55705,76,74,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40678,SRR3231277,SRX1637083,SRS1342919,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate3.1,GSM2090849,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090849,GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090849,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090849,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate3.2_R1_001.fastq.gz 24hpf_wt_Plate3.2_R2_001.fastq.gz,fastq fastq,701569969.0,4651611.0,GSM2090849 r2,0:75.47 1:75.35,A:203675895;C:126097325;G:146891489;T:224837147;N:68113,75,75,,,203675895,126097325,146891489,224837147,68113,SRX1637083,SRS1342919,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00395,0.0305,0.0027,0.00699,0.9976,0.97088,0.4863,0.57133,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40679,SRR3231278,SRX1637083,SRS1342919,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate3.1,GSM2090849,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090849,GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090849,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090849,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate3.3_R1_001.fastq.gz 24hpf_wt_Plate3.3_R2_001.fastq.gz,fastq fastq,688668111.0,4566244.0,GSM2090849 r3,0:75.47 1:75.35,A:199652330;C:123454100;G:144848134;T:220657099;N:56448,75,75,,,199652330,123454100,144848134,220657099,56448,SRX1637083,SRS1342919,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00369,0.02792,0.00272,0.00658,0.99803,0.9727,0.50427,0.55885,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40680,SRR3231279,SRX1637083,SRS1342919,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate3.1,GSM2090849,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090849,GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090849,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090849,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate3_R1_001.fastq.gz 24hpf_wt_Plate3_R2_001.fastq.gz,fastq fastq,702507993.0,4657860.0,GSM2090849 r4,0:75.47 1:75.35,A:203715514;C:126718380;G:147182176;T:224817151;N:74772,75,75,,,203715514,126718380,147182176,224817151,74772,SRX1637083,SRS1342919,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00392,0.0275,0.00279,0.00707,0.99778,0.97297,0.46666,0.56022,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40681,SRR3231272,SRX1637082,SRS1342921,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate2.1,GSM2090848,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090848,GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090848,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090848,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate2.1_R1_001.fastq.gz 24hpf_wt_Plate2.1_R2_001.fastq.gz,fastq fastq,298994170.0,1982738.0,GSM2090848 r1,0:75.44 1:75.35,A:93083508;C:44907251;G:52817440;T:108158577;N:27394,75,75,,,93083508,44907251,52817440,108158577,27394,SRX1637082,SRS1342921,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01409,0.02745,0.01105,0.00689,0.99847,0.97512,0.14754,0.54124,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40682,SRR3231273,SRX1637082,SRS1342921,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate2.1,GSM2090848,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090848,GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090848,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090848,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate2.2_R1_001.fastq.gz 24hpf_wt_Plate2.2_R2_001.fastq.gz,fastq fastq,306815504.0,2034672.0,GSM2090848 r2,0:75.44 1:75.36,A:95967069;C:46066723;G:53601976;T:111150011;N:29725,75,75,,,95967069,46066723,53601976,111150011,29725,SRX1637082,SRS1342921,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01382,0.03079,0.01075,0.00723,0.99859,0.97344,0.14334,0.56436,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40683,SRR3231274,SRX1637082,SRS1342921,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate2.1,GSM2090848,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090848,GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090848,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090848,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate2.3_R1_001.fastq.gz 24hpf_wt_Plate2.3_R2_001.fastq.gz,fastq fastq,300764521.0,1994537.0,GSM2090848 r3,0:75.44 1:75.35,A:93852241;C:45007343;G:52938896;T:108939437;N:26604,75,75,,,93852241,45007343,52938896,108939437,26604,SRX1637082,SRS1342921,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0141,0.02918,0.01084,0.0072,0.99853,0.97437,0.12264,0.55403,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40684,SRR3231275,SRX1637082,SRS1342921,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate2.1,GSM2090848,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090848,GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090848,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090848,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate2_R1_001.fastq.gz 24hpf_wt_Plate2_R2_001.fastq.gz,fastq fastq,302297329.0,2004669.0,GSM2090848 r4,0:75.44 1:75.35,A:94284770;C:45616868;G:52928512;T:109434957;N:32222,75,75,,,94284770,45616868,52928512,109434957,32222,SRX1637082,SRS1342921,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01369,0.02852,0.01069,0.00705,0.99874,0.97526,0.10472,0.56414,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40685,SRR3231268,SRX1637081,SRS1342935,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate1.1,GSM2090847,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090847,GSM2090847: 24hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090847,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090847,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate1.1_R1_001.fastq.gz 24hpf_wt_Plate1.1_R2_001.fastq.gz,fastq fastq,836011252.0,5542746.0,GSM2090847 r1,0:75.49 1:75.34,A:254663944;C:151442656;G:167697929;T:262199779;N:6944,75,75,,,254663944,151442656,167697929,262199779,6944,SRX1637081,SRS1342935,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.03375,0.07314,0.02792,0.0396,0.98882,0.95753,0.54559,0.53265,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40686,SRR3231269,SRX1637081,SRS1342935,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate1.1,GSM2090847,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090847,GSM2090847: 24hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090847,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090847,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate1.2_R1_001.fastq.gz 24hpf_wt_Plate1.2_R2_001.fastq.gz,fastq fastq,830338169.0,5505101.0,GSM2090847 r2,0:75.49 1:75.34,A:254439239;C:150818963;G:164159782;T:260734365;N:185820,75,75,,,254439239,150818963,164159782,260734365,185820,SRX1637081,SRS1342935,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.03438,0.07482,0.02833,0.04098,0.98867,0.95868,0.55778,0.56233,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40687,SRR3231270,SRX1637081,SRS1342935,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate1.1,GSM2090847,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090847,GSM2090847: 24hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090847,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090847,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate1.3_R1_001.fastq.gz 24hpf_wt_Plate1.3_R2_001.fastq.gz,fastq fastq,832999933.0,5522579.0,GSM2090847 r3,0:75.49 1:75.34,A:252395960;C:151022816;G:167338952;T:262031054;N:211151,75,75,,,252395960,151022816,167338952,262031054,211151,SRX1637081,SRS1342935,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0331,0.07425,0.02697,0.04008,0.98817,0.95862,0.53915,0.54556,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40688,SRR3231271,SRX1637081,SRS1342935,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf wt Plate1.1,GSM2090847,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090847,GSM2090847: 24hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090847,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090847,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_wt_Plate1_R1_001.fastq.gz 24hpf_wt_Plate1_R2_001.fastq.gz,fastq fastq,838188458.0,5557389.0,GSM2090847 r4,0:75.48 1:75.34,A:257879266;C:152322486;G:165090591;T:262885421;N:10694,75,75,,,257879266,152322486,165090591,262885421,10694,SRX1637081,SRS1342935,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.03416,0.07497,0.0282,0.04152,0.98871,0.95927,0.49844,0.55123,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40689,SRR3231264,SRX1637080,SRS1342936,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf Tdrd6a :  Plate3.1,GSM2090846,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf Tdrd6a :  Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090846,GSM2090846: 24hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090846,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090846,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_Tdrd6a-:-_Plate3.1_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate3.1_R2_001.fastq.gz,fastq fastq,1371297393.0,9095769.0,GSM2090846 r1,0:75.42 1:75.35,A:425284978;C:236010283;G:260994358;T:448883843;N:123931,75,75,,,425284978,236010283,260994358,448883843,123931,SRX1637080,SRS1342936,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01833,0.04333,0.01582,0.01601,0.99594,0.96871,0.43243,0.56321,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40690,SRR3231265,SRX1637080,SRS1342936,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf Tdrd6a :  Plate3.1,GSM2090846,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf Tdrd6a :  Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090846,GSM2090846: 24hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090846,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090846,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_Tdrd6a-:-_Plate3.2_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate3.2_R2_001.fastq.gz,fastq fastq,1397660189.0,9270812.0,GSM2090846 r2,0:75.42 1:75.34,A:435127552;C:240183852;G:263594089;T:458617665;N:137031,75,75,,,435127552,240183852,263594089,458617665,137031,SRX1637080,SRS1342936,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01782,0.04718,0.01547,0.01691,0.9963,0.96737,0.46382,0.54605,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40691,SRR3231266,SRX1637080,SRS1342936,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf Tdrd6a :  Plate3.1,GSM2090846,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf Tdrd6a :  Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090846,GSM2090846: 24hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090846,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090846,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_Tdrd6a-:-_Plate3.3_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate3.3_R2_001.fastq.gz,fastq fastq,1369635087.0,9085243.0,GSM2090846 r3,0:75.41 1:75.34,A:425335498;C:234980221;G:259843705;T:449365378;N:110285,75,75,,,425335498,234980221,259843705,449365378,110285,SRX1637080,SRS1342936,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01833,0.04405,0.01594,0.01596,0.99636,0.9694,0.49166,0.56044,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40692,SRR3231267,SRX1637080,SRS1342936,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf Tdrd6a :  Plate3.1,GSM2090846,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf Tdrd6a :  Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090846,GSM2090846: 24hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090846,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090846,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_Tdrd6a-:-_Plate3_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate3_R2_001.fastq.gz,fastq fastq,1410682920.0,9356966.0,GSM2090846 r4,0:75.42 1:75.34,A:436822225;C:244639009;G:267991531;T:461073192;N:156963,75,75,,,436822225,244639009,267991531,461073192,156963,SRX1637080,SRS1342936,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01761,0.04359,0.01513,0.01603,0.99584,0.96871,0.46718,0.55856,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40693,SRR3231260,SRX1637079,SRS1342937,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf Tdrd6a :  Plate2.1,GSM2090845,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf Tdrd6a :  Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090845,GSM2090845: 24hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090845,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090845,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_Tdrd6a-:-_Plate2.1_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate2.1_R2_001.fastq.gz,fastq fastq,908747232.0,6024927.0,GSM2090845 r1,0:75.47 1:75.36,A:280168278;C:154557506;G:169723057;T:304291004;N:7387,75,75,,,280168278,154557506,169723057,304291004,7387,SRX1637079,SRS1342937,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.18399,0.33806,0.16099,0.20721,0.95846,0.87878,0.49734,0.53532,76,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40694,SRR3231261,SRX1637079,SRS1342937,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf Tdrd6a :  Plate2.1,GSM2090845,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf Tdrd6a :  Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090845,GSM2090845: 24hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090845,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090845,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_Tdrd6a-:-_Plate2.2_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate2.2_R2_001.fastq.gz,fastq fastq,899928650.0,5966433.0,GSM2090845 r2,0:75.47 1:75.36,A:279603733;C:153512612;G:165252396;T:301355799;N:204110,75,75,,,279603733,153512612,165252396,301355799,204110,SRX1637079,SRS1342937,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.18665,0.33654,0.16315,0.20612,0.95812,0.87641,0.48791,0.53087,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40695,SRR3231262,SRX1637079,SRS1342937,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf Tdrd6a :  Plate2.1,GSM2090845,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf Tdrd6a :  Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090845,GSM2090845: 24hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090845,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090845,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_Tdrd6a-:-_Plate2.3_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate2.3_R2_001.fastq.gz,fastq fastq,910589284.0,6036899.0,GSM2090845 r3,0:75.47 1:75.36,A:279344268;C:154985581;G:170329370;T:305702456;N:227609,75,75,,,279344268,154985581,170329370,305702456,227609,SRX1637079,SRS1342937,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.1847,0.33529,0.16159,0.20809,0.95806,0.88101,0.48203,0.53309,76,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40696,SRR3231263,SRX1637079,SRS1342937,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf Tdrd6a :  Plate2.1,GSM2090845,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf Tdrd6a :  Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090845,GSM2090845: 24hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090845,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090845,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_Tdrd6a-:-_Plate2_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate2_R2_001.fastq.gz,fastq fastq,911364231.0,6042507.0,GSM2090845 r4,0:75.46 1:75.36,A:284483499;C:155490114;G:166537185;T:304841630;N:11803,75,75,,,284483499,155490114,166537185,304841630,11803,SRX1637079,SRS1342937,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.1873,0.33611,0.16336,0.20573,0.95812,0.87554,0.48685,0.52933,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40697,SRR3231256,SRX1637078,SRS1342938,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf Tdrd6a :  Plate1.1,GSM2090844,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf Tdrd6a :  Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090844,GSM2090844: 24hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090844,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090844,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_Tdrd6a-:-_Plate1.1_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate1.1_R2_001.fastq.gz,fastq fastq,604973130.0,4010320.0,GSM2090844 r1,0:75.46 1:75.39,A:187609294;C:95230616;G:105121464;T:217006596;N:5160,75,75,,,187609294,95230616,105121464,217006596,5160,SRX1637078,SRS1342938,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.24179,0.45155,0.21128,0.26362,0.95475,0.84183,0.54132,0.53298,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40698,SRR3231257,SRX1637078,SRS1342938,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,24hpf Tdrd6a :  Plate1.1,GSM2090844,,tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,24hpf Tdrd6a :  Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:24hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090844,GSM2090844: 24hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090844,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090844,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,24hpf_Tdrd6a-:-_Plate1.2_R1_001.fastq.gz 24hpf_Tdrd6a-:-_Plate1.2_R2_001.fastq.gz,fastq fastq,597266507.0,3959286.0,GSM2090844 r2,0:75.46 1:75.39,A:186751324;C:94261867;G:101806474;T:214309214;N:137628,75,75,,,186751324,94261867,101806474,214309214,137628,SRX1637078,SRS1342938,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.24002,0.44945,0.20966,0.26222,0.95595,0.84313,0.53005,0.52366,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System