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
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
50630,SRR8182162,SRX5002129,SRS4036792,SRP168473,PRJNA505329,Retention of paternal epigenetic memory in the developing teleost germline [RNA Seq],GSE122480,Transcriptome Analysis,Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However  it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory  in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: Using low input RNA seq we have profiled transcriptomes of zebrafish primordial germ cells PGCs and age matched somatic cells at 4 blastula  7 gastrula  24 pharyngula prim 5 and 36 pharyngula prim 25 hpf,parent bioproject:PRJNA506076,pubmed:31296860,,PGC 4hpf RNA seq rep2,GSM3467112,,tissue:PGCs 4hpf RNA seq replicate 2|cell type:primordial germ cells|developmental stage:4hpf,PGC 4hpf RNA seq rep2,Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al  2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al  2011  BMC Bioinformatics Differential gene expression analysis was performed using edgeR Robinson et al  2010; Bioinformatics; McCarthy et al  2012; Nucleic Acids Research Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 4 developmental stages in replicates.,PGCs 4hpf RNA seq replicate 2,,PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp,,cell type:primordial germ cells|developmental stage:4hpf,GSM3467112,GSM3467112: PGC 4hpf RNA seq rep2; Danio rerio; RNA Seq,GSM3467112,,1,PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp,GEO Accession:GSM3467112,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP168473,,,PGC_4h_rep2_R1.fastq.gz PGC_4h_rep2_R2.fastq.gz,fastq fastq,10301586506.0,50997953.0,GSM3467112 r1,0:101 1:101,A:1809758627;C:3331670429;G:3356297455;T:1803226655;N:633340,101,101,,,1809758627,3331670429,3356297455,1803226655,633340,SRX5002129,SRS4036792,SRA808716,GEO,"Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute",2,0.98374,0.98401,0.24104,0.21912,0.87247,0.87411,0.79911,0.9123,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Australia,2018-11-13,Blastula,Embryo,Gonad,Reproductive System
50631,SRR8182161,SRX5002128,SRS4036791,SRP168473,PRJNA505329,Retention of paternal epigenetic memory in the developing teleost germline [RNA Seq],GSE122480,Transcriptome Analysis,Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However  it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory  in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: Using low input RNA seq we have profiled transcriptomes of zebrafish primordial germ cells PGCs and age matched somatic cells at 4 blastula  7 gastrula  24 pharyngula prim 5 and 36 pharyngula prim 25 hpf,parent bioproject:PRJNA506076,pubmed:31296860,,PGC 4hpf RNA seq rep1,GSM3467111,,tissue:PGCs 4hpf RNA seq replicate 1|cell type:primordial germ cells|developmental stage:4hpf,PGC 4hpf RNA seq rep1,Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al  2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al  2011  BMC Bioinformatics Differential gene expression analysis was performed using edgeR Robinson et al  2010; Bioinformatics; McCarthy et al  2012; Nucleic Acids Research Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 4 developmental stages in replicates.,PGCs 4hpf RNA seq replicate 1,,PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp,,cell type:primordial germ cells|developmental stage:4hpf,GSM3467111,GSM3467111: PGC 4hpf RNA seq rep1; Danio rerio; RNA Seq,GSM3467111,,1,PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp,GEO Accession:GSM3467111,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP168473,,,PGC_4h_rep1_R2.fastq.gz PGC_4h_rep1_R1.fastq.gz,fastq fastq,9574792728.0,47399964.0,GSM3467111 r1,0:101 1:101,A:1692891419;C:3093672509;G:3106183795;T:1681454876;N:590129,101,101,,,1692891419,3093672509,3106183795,1681454876,590129,SRX5002128,SRS4036791,SRA808716,GEO,"Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute",2,0.98299,0.98415,0.21038,0.18779,0.87326,0.87393,0.89723,0.88342,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,Australia,2018-11-13,Blastula,Embryo,Gonad,Reproductive System