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34 rows where devstage_curation = "Blastula" and tissue_curation = "Gonad"

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technology 2

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tissue_curation 1

  • Gonad · 34 ✖

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experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

  • Blastula · 34 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;