rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
40635,SRR3231318,SRX1637096,SRS1342907,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate5.1,GSM2090862,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090862,GSM2090862: 3.5hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090862,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090862,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate5.1_R1_001.fastq.gz 3.5hpf_wt_Plate5.1_R2_001.fastq.gz,fastq fastq,465283988.0,3083951.0,GSM2090862 r1,0:75.46 1:75.41,A:131913263;C:74557873;G:91090052;T:167720369;N:2431,75,75,,,131913263,74557873,91090052,167720369,2431,SRX1637096,SRS1342907,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00196,0.01756,0.00174,0.00396,0.99981,0.97512,0.4375,0.58617,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40636,SRR3231319,SRX1637096,SRS1342907,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate5.1,GSM2090862,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090862,GSM2090862: 3.5hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090862,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090862,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate5.2_R1_001.fastq.gz 3.5hpf_wt_Plate5.2_R2_001.fastq.gz,fastq fastq,492787533.0,3266133.0,GSM2090862 r2,0:75.46 1:75.41,A:138920634;C:79266412;G:96252502;T:178340643;N:7342,75,75,,,138920634,79266412,96252502,178340643,7342,SRX1637096,SRS1342907,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00175,0.01711,0.00149,0.00417,0.99965,0.9754,0.28571,0.59079,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40637,SRR3231320,SRX1637096,SRS1342907,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate5.1,GSM2090862,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090862,GSM2090862: 3.5hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090862,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090862,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate5.3_R1_001.fastq.gz 3.5hpf_wt_Plate5.3_R2_001.fastq.gz,fastq fastq,478302056.0,3170122.0,GSM2090862 r3,0:75.46 1:75.41,A:134552769;C:76719834;G:94014994;T:173009599;N:4860,75,75,,,134552769,76719834,94014994,173009599,4860,SRX1637096,SRS1342907,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0018,0.01735,0.00154,0.00386,0.99967,0.97429,0.23809,0.55019,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40638,SRR3231321,SRX1637096,SRS1342907,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate5.1,GSM2090862,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090862,GSM2090862: 3.5hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090862,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090862,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate5_R1_001.fastq.gz 3.5hpf_wt_Plate5_R2_001.fastq.gz,fastq fastq,487978460.0,3234287.0,GSM2090862 r4,0:75.46 1:75.41,A:138127249;C:78568068;G:95022582;T:176256804;N:3757,75,75,,,138127249,78568068,95022582,176256804,3757,SRX1637096,SRS1342907,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00178,0.01711,0.00155,0.00374,0.99975,0.97457,0.38888,0.54467,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40639,SRR3231314,SRX1637095,SRS1342908,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate4.1,GSM2090861,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090861,GSM2090861: 3.5hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090861,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090861,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate4.1_R1_001.fastq.gz 3.5hpf_wt_Plate4.1_R2_001.fastq.gz,fastq fastq,1165572863.0,7724698.0,GSM2090861 r1,0:75.47 1:75.42,A:341597187;C:187300441;G:218487967;T:418181251;N:6017,75,75,,,341597187,187300441,218487967,418181251,6017,SRX1637095,SRS1342908,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0024,0.05972,0.00175,0.01107,0.99894,0.93363,0.46268,0.54466,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40640,SRR3231315,SRX1637095,SRS1342908,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate4.1,GSM2090861,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090861,GSM2090861: 3.5hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090861,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090861,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate4.2_R1_001.fastq.gz 3.5hpf_wt_Plate4.2_R2_001.fastq.gz,fastq fastq,1231311328.0,8160147.0,GSM2090861 r2,0:75.48 1:75.42,A:359044176;C:198664662;G:229959438;T:443624264;N:18788,75,75,,,359044176,198664662,229959438,443624264,18788,SRX1637095,SRS1342908,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0022,0.06116,0.00155,0.01128,0.99888,0.93229,0.40298,0.54742,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40641,SRR3231316,SRX1637095,SRS1342908,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate4.1,GSM2090861,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090861,GSM2090861: 3.5hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090861,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090861,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate4.3_R1_001.fastq.gz 3.5hpf_wt_Plate4.3_R2_001.fastq.gz,fastq fastq,1197590912.0,7936665.0,GSM2090861 r3,0:75.48 1:75.42,A:348626376;C:192686213;G:225139549;T:431126048;N:12726,75,75,,,348626376,192686213,225139549,431126048,12726,SRX1637095,SRS1342908,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00247,0.06111,0.00168,0.01107,0.9987,0.9318,0.41176,0.55782,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40642,SRR3231317,SRX1637095,SRS1342908,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate4.1,GSM2090861,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090861,GSM2090861: 3.5hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090861,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090861,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate4_R1_001.fastq.gz 3.5hpf_wt_Plate4_R2_001.fastq.gz,fastq fastq,1224213980.0,8113208.0,GSM2090861 r4,0:75.48 1:75.42,A:358299358;C:197501927;G:228122097;T:440281285;N:9313,75,75,,,358299358,197501927,228122097,440281285,9313,SRX1637095,SRS1342908,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00255,0.06199,0.00181,0.0116,0.9989,0.93326,0.48684,0.54385,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40643,SRR3231310,SRX1637094,SRS1342909,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate3.1,GSM2090860,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090860,GSM2090860: 3.5hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090860,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090860,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate3.1_R1_001.fastq.gz 3.5hpf_wt_Plate3.1_R2_001.fastq.gz,fastq fastq,626596035.0,4155091.0,GSM2090860 r1,0:75.44 1:75.37,A:192353640;C:87072147;G:109704935;T:237462123;N:3190,75,75,,,192353640,87072147,109704935,237462123,3190,SRX1637094,SRS1342909,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00677,0.07893,0.00548,0.01598,0.99898,0.92987,0.43902,0.58089,73,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40644,SRR3231311,SRX1637094,SRS1342909,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate3.1,GSM2090860,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090860,GSM2090860: 3.5hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090860,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090860,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate3.2_R1_001.fastq.gz 3.5hpf_wt_Plate3.2_R2_001.fastq.gz,fastq fastq,662952483.0,4396049.0,GSM2090860 r2,0:75.44 1:75.37,A:202110673;C:92410890;G:116053839;T:252366901;N:10180,75,75,,,202110673,92410890,116053839,252366901,10180,SRX1637094,SRS1342909,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00616,0.08027,0.00497,0.01696,0.99896,0.9277,0.50649,0.58134,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40645,SRR3231312,SRX1637094,SRS1342909,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate3.1,GSM2090860,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090860,GSM2090860: 3.5hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090860,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090860,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate3.3_R1_001.fastq.gz 3.5hpf_wt_Plate3.3_R2_001.fastq.gz,fastq fastq,647301548.0,4292251.0,GSM2090860 r3,0:75.44 1:75.37,A:197180599;C:89984465;G:113867175;T:246262732;N:6577,75,75,,,197180599,89984465,113867175,246262732,6577,SRX1637094,SRS1342909,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00689,0.08136,0.00549,0.01688,0.99876,0.92654,0.54347,0.58937,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40646,SRR3231313,SRX1637094,SRS1342909,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate3.1,GSM2090860,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090860,GSM2090860: 3.5hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090860,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090860,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate3_R1_001.fastq.gz 3.5hpf_wt_Plate3_R2_001.fastq.gz,fastq fastq,656915830.0,4356034.0,GSM2090860 r4,0:75.44 1:75.37,A:201028065;C:91591416;G:114616914;T:249674244;N:5191,75,75,,,201028065,91591416,114616914,249674244,5191,SRX1637094,SRS1342909,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00611,0.08116,0.0049,0.01729,0.99892,0.92661,0.37662,0.45981,75,74,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40647,SRR3231306,SRX1637093,SRS1342910,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate2.1,GSM2090859,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090859,GSM2090859: 3.5hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090859,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090859,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate2.1_R1_001.fastq.gz 3.5hpf_wt_Plate2.1_R2_001.fastq.gz,fastq fastq,885364409.0,5869953.0,GSM2090859 r1,0:75.43 1:75.40,A:267732586;C:139479978;G:161193259;T:316954042;N:4544,75,75,,,267732586,139479978,161193259,316954042,4544,SRX1637093,SRS1342910,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0027,0.09073,0.00136,0.01929,0.99801,0.92275,0.52678,0.59397,75,74,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40648,SRR3231307,SRX1637093,SRS1342910,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate2.1,GSM2090859,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090859,GSM2090859: 3.5hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090859,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090859,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate2.2_R1_001.fastq.gz 3.5hpf_wt_Plate2.2_R2_001.fastq.gz,fastq fastq,935453664.0,6201750.0,GSM2090859 r2,0:75.44 1:75.40,A:280574811;C:147981655;G:170370395;T:336513026;N:13777,75,75,,,280574811,147981655,170370395,336513026,13777,SRX1637093,SRS1342910,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00297,0.09176,0.00155,0.01869,0.99809,0.91946,0.46666,0.59074,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40649,SRR3231308,SRX1637093,SRS1342910,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate2.1,GSM2090859,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090859,GSM2090859: 3.5hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090859,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090859,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate2.3_R1_001.fastq.gz 3.5hpf_wt_Plate2.3_R2_001.fastq.gz,fastq fastq,912201099.0,6047636.0,GSM2090859 r3,0:75.44 1:75.40,A:273615357;C:143852122;G:166864092;T:327859891;N:9637,75,75,,,273615357,143852122,166864092,327859891,9637,SRX1637093,SRS1342910,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00346,0.0931,0.00171,0.01934,0.99728,0.91975,0.64238,0.59662,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40650,SRR3231309,SRX1637093,SRS1342910,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate2.1,GSM2090859,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090859,GSM2090859: 3.5hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090859,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090859,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate2_R1_001.fastq.gz 3.5hpf_wt_Plate2_R2_001.fastq.gz,fastq fastq,926760672.0,6144176.0,GSM2090859 r4,0:75.44 1:75.40,A:278868658;C:146660825;G:168550011;T:332674041;N:7137,75,75,,,278868658,146660825,168550011,332674041,7137,SRX1637093,SRS1342910,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00323,0.09308,0.00182,0.01911,0.99786,0.91999,0.52892,0.59305,76,73,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40651,SRR3231304,SRX1637092,SRS1342911,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate1.1,GSM2090858,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090858,GSM2090858: 3.5hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090858,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090858,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate1.1_R1_001.fastq.gz 3.5hpf_wt_Plate1.1_R2_001.fastq.gz,fastq fastq,1401396768.0,13739184.0,GSM2090858 r1,0:51 1:51,A:347756042;C:255264101;G:254249668;T:529161525;N:14965432,51,51,,,347756042,255264101,254249668,529161525,14965432,SRX1637092,SRS1342911,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00267,0.00682,0.00252,0.0043,0.99975,0.99407,0.5909,0.36136,51,51,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40652,SRR3231305,SRX1637092,SRS1342911,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate1.1,GSM2090858,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090858,GSM2090858: 3.5hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090858,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090858,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate1_R1_001.fastq.gz 3.5hpf_wt_Plate1_R2_001.fastq.gz,fastq fastq,1363312518.0,13365809.0,GSM2090858 r2,0:51 1:51,A:338101381;C:247778705;G:246079568;T:516046779;N:15306085,51,51,,,338101381,247778705,246079568,516046779,15306085,SRX1637092,SRS1342911,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00301,0.00726,0.0028,0.00467,0.99963,0.99387,0.53125,0.39461,51,51,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40653,SRR3231300,SRX1637091,SRS1342912,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf Tdrd6a :  Plate5.1,GSM2090857,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090857,GSM2090857: 3.5hpf Tdrd6a :  Plate5.1; Danio rerio; RNA Seq,GSM2090857,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090857,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate5.1_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate5.1_R2_001.fastq.gz,fastq fastq,530054811.0,3515786.0,GSM2090857 r1,0:75.42 1:75.34,A:170905056;C:77131049;G:91888905;T:190127099;N:2702,75,75,,,170905056,77131049,91888905,190127099,2702,SRX1637091,SRS1342912,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.02617,0.05634,0.01838,0.01758,0.99754,0.95448,0.23693,0.5735,76,74,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40654,SRR3231301,SRX1637091,SRS1342912,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf Tdrd6a :  Plate5.1,GSM2090857,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090857,GSM2090857: 3.5hpf Tdrd6a :  Plate5.1; Danio rerio; RNA Seq,GSM2090857,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090857,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate5.2_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate5.2_R2_001.fastq.gz,fastq fastq,557894343.0,3700294.0,GSM2090857 r2,0:75.43 1:75.35,A:178074028;C:81692578;G:96833862;T:201285418;N:8457,75,75,,,178074028,81692578,96833862,201285418,8457,SRX1637091,SRS1342912,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.02111,0.05616,0.01461,0.01725,0.99738,0.95172,0.26252,0.56747,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40655,SRR3231302,SRX1637091,SRS1342912,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf Tdrd6a :  Plate5.1,GSM2090857,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090857,GSM2090857: 3.5hpf Tdrd6a :  Plate5.1; Danio rerio; RNA Seq,GSM2090857,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090857,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate5.3_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate5.3_R2_001.fastq.gz,fastq fastq,542585088.0,3598766.0,GSM2090857 r3,0:75.42 1:75.35,A:173334337;C:79046469;G:94586129;T:195612312;N:5841,75,75,,,173334337,79046469,94586129,195612312,5841,SRX1637091,SRS1342912,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.02344,0.05621,0.01663,0.01767,0.9974,0.95327,0.24376,0.57321,76,74,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40656,SRR3231303,SRX1637091,SRS1342912,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf Tdrd6a :  Plate5.1,GSM2090857,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090857,GSM2090857: 3.5hpf Tdrd6a :  Plate5.1; Danio rerio; RNA Seq,GSM2090857,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090857,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate5_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate5_R2_001.fastq.gz,fastq fastq,553684137.0,3672462.0,GSM2090857 r4,0:75.42 1:75.34,A:177515943;C:81065494;G:95795614;T:199302825;N:4261,75,75,,,177515943,81065494,95795614,199302825,4261,SRX1637091,SRS1342912,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.02234,0.05529,0.01558,0.01742,0.99758,0.95377,0.24158,0.56936,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40657,SRR3231296,SRX1637090,SRS1342913,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf Tdrd6a :  Plate4.1,GSM2090856,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090856,GSM2090856: 3.5hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090856,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090856,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate4.1_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate4.1_R2_001.fastq.gz,fastq fastq,758489825.0,5027396.0,GSM2090856 r1,0:75.47 1:75.41,A:223477381;C:119338529;G:141593308;T:274076559;N:4048,75,75,,,223477381,119338529,141593308,274076559,4048,SRX1637090,SRS1342913,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00426,0.0881,0.00214,0.01568,0.99703,0.92527,0.49494,0.60675,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40658,SRR3231297,SRX1637090,SRS1342913,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf Tdrd6a :  Plate4.1,GSM2090856,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090856,GSM2090856: 3.5hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090856,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090856,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate4.2_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate4.2_R2_001.fastq.gz,fastq fastq,802062750.0,5316073.0,GSM2090856 r2,0:75.47 1:75.41,A:234800617;C:126749965;G:149363757;T:291136187;N:12224,75,75,,,234800617,126749965,149363757,291136187,12224,SRX1637090,SRS1342913,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00408,0.09004,0.00226,0.01667,0.99742,0.92216,0.5337,0.60822,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40659,SRR3231298,SRX1637090,SRS1342913,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf Tdrd6a :  Plate4.1,GSM2090856,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090856,GSM2090856: 3.5hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090856,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090856,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate4.3_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate4.3_R2_001.fastq.gz,fastq fastq,781265465.0,5178193.0,GSM2090856 r3,0:75.47 1:75.41,A:228400304;C:123116486;G:146409916;T:283330556;N:8203,75,75,,,228400304,123116486,146409916,283330556,8203,SRX1637090,SRS1342913,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00418,0.09132,0.00184,0.01663,0.99683,0.92285,0.5066,0.5994,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40660,SRR3231299,SRX1637090,SRS1342913,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf Tdrd6a :  Plate4.1,GSM2090856,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090856,GSM2090856: 3.5hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090856,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090856,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate4_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate4_R2_001.fastq.gz,fastq fastq,796243663.0,5277519.0,GSM2090856 r4,0:75.47 1:75.41,A:233877044;C:125841514;G:147929074;T:288590102;N:5929,75,75,,,233877044,125841514,147929074,288590102,5929,SRX1637090,SRS1342913,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00412,0.09175,0.00213,0.01649,0.99722,0.92243,0.47916,0.60143,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40661,SRR3231294,SRX1637089,SRS1342914,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf Tdrd6a :  Plate3.1,GSM2090855,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090855,GSM2090855: 3.5hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090855,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090855,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate3.1_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate3.1_R2_001.fastq.gz,fastq fastq,1252913022.0,12283461.0,GSM2090855 r1,0:51 1:51,A:323874510;C:195258080;G:204580544;T:514382561;N:14817327,51,51,,,323874510,195258080,204580544,514382561,14817327,SRX1637089,SRS1342914,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00518,0.04289,0.00473,0.01518,0.99926,0.95412,0.41935,0.41704,51,51,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40662,SRR3231295,SRX1637089,SRS1342914,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf Tdrd6a :  Plate3.1,GSM2090855,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090855,GSM2090855: 3.5hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090855,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090855,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate3_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate3_R2_001.fastq.gz,fastq fastq,1241394468.0,12170534.0,GSM2090855 r2,0:51 1:51,A:320378911;C:193092040;G:202025341;T:508939554;N:16958622,51,51,,,320378911,193092040,202025341,508939554,16958622,SRX1637089,SRS1342914,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00484,0.04293,0.00447,0.01494,0.99951,0.95452,0.42,0.41403,51,51,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40663,SRR3231292,SRX1637088,SRS1342915,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf Tdrd6a :  Plate2.1,GSM2090854,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090854,GSM2090854: 3.5hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090854,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090854,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate2.1_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate2.1_R2_001.fastq.gz,fastq fastq,978116046.0,9589373.0,GSM2090854 r1,0:51 1:51,A:235926359;C:165980181;G:173164459;T:392643478;N:10401569,51,51,,,235926359,165980181,173164459,392643478,10401569,SRX1637088,SRS1342915,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00854,0.17952,0.00744,0.06281,0.99855,0.90017,0.4892,0.66386,51,51,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40664,SRR3231293,SRX1637088,SRS1342915,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf Tdrd6a :  Plate2.1,GSM2090854,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090854,GSM2090854: 3.5hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090854,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090854,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate2_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate2_R2_001.fastq.gz,fastq fastq,957502560.0,9387280.0,GSM2090854 r2,0:51 1:51,A:230320241;C:162167341;G:169171883;T:384426371;N:11416724,51,51,,,230320241,162167341,169171883,384426371,11416724,SRX1637088,SRS1342915,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00896,0.17968,0.008,0.06282,0.9987,0.89899,0.55645,0.65931,51,51,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40665,SRR3231290,SRX1637087,SRS1342916,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf Tdrd6a :  Plate1.1,GSM2090853,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090853,GSM2090853: 3.5hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090853,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090853,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate1.1_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate1.1_R2_001.fastq.gz,fastq fastq,1086532458.0,10652279.0,GSM2090853 r1,0:51 1:51,A:251396959;C:181408258;G:195341853;T:446862283;N:11523105,51,51,,,251396959,181408258,195341853,446862283,11523105,SRX1637087,SRS1342916,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0136,0.1857,0.01211,0.06822,0.99829,0.90585,0.59239,0.72278,51,51,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40666,SRR3231291,SRX1637087,SRS1342916,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf Tdrd6a :  Plate1.1,GSM2090853,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf Tdrd6a :  Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090853,GSM2090853: 3.5hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090853,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090853,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_Tdrd6a-:-_Plate1_R1_001.fastq.gz 3.5hpf_Tdrd6a-:-_Plate1_R2_001.fastq.gz,fastq fastq,1066918470.0,10459985.0,GSM2090853 r2,0:51 1:51,A:246360010;C:177989653;G:191393960;T:438501621;N:12673226,51,51,,,246360010,177989653,191393960,438501621,12673226,SRX1637087,SRS1342916,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.01365,0.18567,0.01228,0.06729,0.99831,0.90347,0.55029,0.35593,51,51,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
60053,SRR12125394,SRX8646713,SRS6930256,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb6 4.25hpf,GSM4648242,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb6 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648242,GSM4648242: TL emb6 4.25hpf; Danio rerio; RNA Seq,GSM4648242,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648242,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb6_4_25hpf.fastq,fastq,648226908.0,10289316.0,GSM4648242 r1,0:63,A:186626188;C:108596134;G:148654113;T:204221173;N:129300,63,,,,186626188,108596134,148654113,204221173,129300,SRX8646713,SRS6930256,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84314,,0.06862,,0.77398,,0.56825,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60054,SRR12125393,SRX8646712,SRS6930255,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb5 4.25hpf,GSM4648241,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb5 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648241,GSM4648241: TL emb5 4.25hpf; Danio rerio; RNA Seq,GSM4648241,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648241,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb5_4_25hpf.fastq,fastq,734406057.0,11657239.0,GSM4648241 r1,0:63,A:210803716;C:130159870;G:171759422;T:221537069;N:145980,63,,,,210803716,130159870,171759422,221537069,145980,SRX8646712,SRS6930255,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85492,,0.06162,,0.78212,,0.38833,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60055,SRR12125392,SRX8646711,SRS6930254,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb4 4.25hpf,GSM4648240,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb4 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648240,GSM4648240: TL emb4 4.25hpf; Danio rerio; RNA Seq,GSM4648240,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648240,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb4_4_25hpf.fastq,fastq,848080548.0,13461596.0,GSM4648240 r1,0:63,A:244171248;C:146950905;G:197166889;T:259622371;N:169135,63,,,,244171248,146950905,197166889,259622371,169135,SRX8646711,SRS6930254,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85266,,0.06536,,0.78356,,0.61672,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60056,SRR12125391,SRX8646710,SRS6930253,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb6 4.25hpf,GSM4648239,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb6 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648239,GSM4648239: AB emb6 4.25hpf; Danio rerio; RNA Seq,GSM4648239,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648239,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb6_4_25hpf.fastq,fastq,801023769.0,12714663.0,GSM4648239 r1,0:63,A:229516390;C:133164924;G:183459290;T:254724395;N:158770,63,,,,229516390,133164924,183459290,254724395,158770,SRX8646710,SRS6930253,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84498,,0.08229,,0.76516,,0.54649,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60057,SRR12125390,SRX8646709,SRS6930252,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb5 4.25hpf,GSM4648238,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb5 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648238,GSM4648238: AB emb5 4.25hpf; Danio rerio; RNA Seq,GSM4648238,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648238,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb5_4_25hpf.fastq,fastq,916020630.0,14540010.0,GSM4648238 r1,0:63,A:265921679;C:156404174;G:214021996;T:279489346;N:183435,63,,,,265921679,156404174,214021996,279489346,183435,SRX8646709,SRS6930252,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86891,,0.06574,,0.78332,,0.64733,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60058,SRR12125389,SRX8646708,SRS6930251,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb4 4.25hpf,GSM4648237,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb4 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648237,GSM4648237: AB emb4 4.25hpf; Danio rerio; RNA Seq,GSM4648237,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648237,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb4_4_25hpf.fastq,fastq,648949077.0,10300779.0,GSM4648237 r1,0:63,A:189284026;C:107954215;G:152710596;T:198865842;N:134398,63,,,,189284026,107954215,152710596,198865842,134398,SRX8646708,SRS6930251,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86363,,0.07026,,0.77701,,0.64544,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60059,SRR12125388,SRX8646707,SRS6930250,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb3 4.25hpf,GSM4648236,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb3 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648236,GSM4648236: TL emb3 4.25hpf; Danio rerio; RNA Seq,GSM4648236,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648236,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb3_4_25hpf.fastq,fastq,516466016.0,7708448.0,GSM4648236 r1,0:67,A:159159432;C:88645898;G:115271897;T:153289294;N:99495,67,,,,159159432,88645898,115271897,153289294,99495,SRX8646707,SRS6930250,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83753,,0.06603,,0.78255,,0.63318,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60060,SRR12125387,SRX8646706,SRS6930249,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb2 4.25hpf,GSM4648235,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb2 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648235,GSM4648235: TL emb2 4.25hpf; Danio rerio; RNA Seq,GSM4648235,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648235,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb2_4_25hpf.fastq,fastq,733560086.0,10948658.0,GSM4648235 r1,0:67,A:223892555;C:125768367;G:165649772;T:218113018;N:136374,67,,,,223892555,125768367,165649772,218113018,136374,SRX8646706,SRS6930249,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83779,,0.067,,0.77987,,0.63741,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60061,SRR12125386,SRX8646705,SRS6930248,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb1 4.25hpf,GSM4648234,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb1 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648234,GSM4648234: TL emb1 4.25hpf; Danio rerio; RNA Seq,GSM4648234,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648234,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb1_4_25hpf.fastq,fastq,996559273.0,14874019.0,GSM4648234 r1,0:67,A:306056021;C:172219093;G:225165148;T:292935389;N:183622,67,,,,306056021,172219093,225165148,292935389,183622,SRX8646705,SRS6930248,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83661,,0.06598,,0.78042,,0.64801,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60062,SRR12125385,SRX8646704,SRS6930247,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb3 4.25hpf,GSM4648233,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb3 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648233,GSM4648233: AB emb3 4.25hpf; Danio rerio; RNA Seq,GSM4648233,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648233,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb3_4_25hpf.fastq,fastq,995183629.0,14853487.0,GSM4648233 r1,0:67,A:306982973;C:172407171;G:224381340;T:291223894;N:188251,67,,,,306982973,172407171,224381340,291223894,188251,SRX8646704,SRS6930247,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83741,,0.07596,,0.77484,,0.64838,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60063,SRR12125384,SRX8646703,SRS6930246,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb2 4.25hpf,GSM4648232,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb2 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648232,GSM4648232: AB emb2 4.25hpf; Danio rerio; RNA Seq,GSM4648232,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648232,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb2_4_25hpf.fastq,fastq,816027371.0,12179513.0,GSM4648232 r1,0:67,A:254674603;C:143689351;G:189951309;T:227560983;N:151125,67,,,,254674603,143689351,189951309,227560983,151125,SRX8646703,SRS6930246,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.87586,,0.0588,,0.79683,,0.77034,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60064,SRR12125383,SRX8646702,SRS6930245,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb1 4.25hpf,GSM4648231,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb1 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648231,GSM4648231: AB emb1 4.25hpf; Danio rerio; RNA Seq,GSM4648231,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648231,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb1_4_25hpf.fastq,fastq,908152237.0,13554511.0,GSM4648231 r1,0:67,A:285792221;C:161035180;G:211856601;T:249299580;N:168655,67,,,,285792221,161035180,211856601,249299580,168655,SRX8646702,SRS6930245,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.87466,,0.05237,,0.80671,,0.80003,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60065,SRR12125382,SRX8646701,SRS6930244,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb6 3.25hpf,GSM4648230,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb6 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648230,GSM4648230: TL emb6 3.25hpf; Danio rerio; RNA Seq,GSM4648230,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648230,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb6_3_25hpf.fastq,fastq,406690011.0,6455397.0,GSM4648230 r1,0:63,A:120677773;C:70454448;G:91897989;T:123574695;N:85106,63,,,,120677773,70454448,91897989,123574695,85106,SRX8646701,SRS6930244,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84562,,0.05274,,0.78709,,0.6243,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60066,SRR12125381,SRX8646700,SRS6930243,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb5 3.25hpf,GSM4648229,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb5 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648229,GSM4648229: TL emb5 3.25hpf; Danio rerio; RNA Seq,GSM4648229,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648229,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb5_3_25hpf.fastq,fastq,1342709172.0,21312844.0,GSM4648229 r1,0:63,A:393268889;C:230336007;G:306128117;T:412697568;N:278591,63,,,,393268889,230336007,306128117,412697568,278591,SRX8646700,SRS6930243,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84679,,0.05277,,0.78376,,0.61146,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60067,SRR12125380,SRX8646699,SRS6930241,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb4 3.25hpf,GSM4648228,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb4 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648228,GSM4648228: TL emb4 3.25hpf; Danio rerio; RNA Seq,GSM4648228,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648228,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb4_3_25hpf.fastq,fastq,679340970.0,10783190.0,GSM4648228 r1,0:63,A:202043678;C:117431893;G:154094046;T:205633514;N:137839,63,,,,202043678,117431893,154094046,205633514,137839,SRX8646699,SRS6930241,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84563,,0.05116,,0.78691,,0.63857,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60068,SRR12125379,SRX8646698,SRS6930240,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb6 3.25hpf,GSM4648227,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb6 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648227,GSM4648227: AB emb6 3.25hpf; Danio rerio; RNA Seq,GSM4648227,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648227,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb6_3_25hpf.fastq,fastq,1053160038.0,16716826.0,GSM4648227 r1,0:63,A:309310336;C:174248829;G:236443053;T:332944871;N:212949,63,,,,309310336,174248829,236443053,332944871,212949,SRX8646698,SRS6930240,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84084,,0.0644,,0.77297,,0.55261,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60069,SRR12125378,SRX8646697,SRS6930242,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb5 3.25hpf,GSM4648226,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb5 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648226,GSM4648226: AB emb5 3.25hpf; Danio rerio; RNA Seq,GSM4648226,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648226,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb5_3_25hpf.fastq,fastq,767622366.0,12184482.0,GSM4648226 r1,0:63,A:230696545;C:135055273;G:178818369;T:222896193;N:155986,63,,,,230696545,135055273,178818369,222896193,155986,SRX8646697,SRS6930242,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.87843,,0.04331,,0.79555,,0.72222,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60070,SRR12125377,SRX8646696,SRS6930239,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb4 3.25hpf,GSM4648225,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb4 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648225,GSM4648225: AB emb4 3.25hpf; Danio rerio; RNA Seq,GSM4648225,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648225,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb4_3_25hpf.fastq,fastq,579009312.0,9190624.0,GSM4648225 r1,0:63,A:175049727;C:97082374;G:133102260;T:173656136;N:118815,63,,,,175049727,97082374,133102260,173656136,118815,SRX8646696,SRS6930239,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86011,,0.05008,,0.78492,,0.67432,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60071,SRR12125376,SRX8646695,SRS6930238,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb3 3.25hpf,GSM4648224,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb3 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648224,GSM4648224: TL emb3 3.25hpf; Danio rerio; RNA Seq,GSM4648224,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648224,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb3_3_25hpf.fastq,fastq,718330718.0,10721354.0,GSM4648224 r1,0:67,A:219495085;C:119739206;G:164136215;T:214827087;N:133125,67,,,,219495085,119739206,164136215,214827087,133125,SRX8646695,SRS6930238,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82675,,0.05622,,0.7864,,0.61084,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60072,SRR12125423,SRX8646694,SRS6930237,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb2 3.25hpf,GSM4648223,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb2 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648223,GSM4648223: TL emb2 3.25hpf; Danio rerio; RNA Seq,GSM4648223,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648223,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb2_3_25hpf.fastq,fastq,846806836.0,12638908.0,GSM4648223 r1,0:67,A:258192271;C:142127876;G:194759995;T:251567003;N:159691,67,,,,258192271,142127876,194759995,251567003,159691,SRX8646694,SRS6930237,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82715,,0.05329,,0.7891,,0.63308,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60073,SRR12125422,SRX8646693,SRS6930236,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb1 3.25hpf,GSM4648222,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb1 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648222,GSM4648222: TL emb1 3.25hpf; Danio rerio; RNA Seq,GSM4648222,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648222,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb1_3_25hpf.fastq,fastq,967198332.0,14435796.0,GSM4648222 r1,0:67,A:295354111;C:161347921;G:222828106;T:287484566;N:183628,67,,,,295354111,161347921,222828106,287484566,183628,SRX8646693,SRS6930236,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82551,,0.05319,,0.78474,,0.63465,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60074,SRR12125421,SRX8646692,SRS6930235,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb3 3.25hpf,GSM4648221,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb3 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648221,GSM4648221: AB emb3 3.25hpf; Danio rerio; RNA Seq,GSM4648221,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648221,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb3_3_25hpf.fastq,fastq,1097446667.0,16379801.0,GSM4648221 r1,0:67,A:335650326;C:184923523;G:253014446;T:323651876;N:206496,67,,,,335650326,184923523,253014446,323651876,206496,SRX8646692,SRS6930235,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83064,,0.05743,,0.78236,,0.62817,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60075,SRR12125420,SRX8646691,SRS6930234,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb2 3.25hpf,GSM4648220,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb2 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648220,GSM4648220: AB emb2 3.25hpf; Danio rerio; RNA Seq,GSM4648220,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648220,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb2_3_25hpf.fastq,fastq,1052234397.0,15704991.0,GSM4648220 r1,0:67,A:323684738;C:185585498;G:254328718;T:288441126;N:194317,67,,,,323684738,185585498,254328718,288441126,194317,SRX8646691,SRS6930234,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.87949,,0.03749,,0.80779,,0.79902,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60076,SRR12125419,SRX8646690,SRS6930233,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb1 3.25hpf,GSM4648219,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb1 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648219,GSM4648219: AB emb1 3.25hpf; Danio rerio; RNA Seq,GSM4648219,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648219,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb1_3_25hpf.fastq,fastq,1673968267.0,24984601.0,GSM4648219 r1,0:67,A:518959586;C:292464694;G:402352389;T:459881035;N:310563,67,,,,518959586,292464694,402352389,459881035,310563,SRX8646690,SRS6930233,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86486,,0.03996,,0.80647,,0.78106,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60077,SRR12125418,SRX8646689,SRS6930232,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb6 2.25hpf,GSM4648218,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb6 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648218,GSM4648218: TL emb6 2.25hpf; Danio rerio; RNA Seq,GSM4648218,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648218,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb6_2_25hpf.fastq,fastq,653742054.0,10376858.0,GSM4648218 r1,0:63,A:191909466;C:110924763;G:150375764;T:200399289;N:132772,63,,,,191909466,110924763,150375764,200399289,132772,SRX8646689,SRS6930232,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83788,,0.05116,,0.78354,,0.60585,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60078,SRR12125417,SRX8646688,SRS6930230,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb5 2.25hpf,GSM4648217,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb5 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648217,GSM4648217: TL emb5 2.25hpf; Danio rerio; RNA Seq,GSM4648217,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648217,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb5_2_25hpf.fastq,fastq,781357626.0,12402502.0,GSM4648217 r1,0:63,A:228115778;C:132378621;G:181704836;T:238999917;N:158474,63,,,,228115778,132378621,181704836,238999917,158474,SRX8646688,SRS6930230,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84083,,0.05244,,0.78226,,0.60881,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60079,SRR12125416,SRX8646687,SRS6930229,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb4 2.25hpf,GSM4648216,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb4 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648216,GSM4648216: TL emb4 2.25hpf; Danio rerio; RNA Seq,GSM4648216,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648216,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb4_2_25hpf.fastq,fastq,421965369.0,6697863.0,GSM4648216 r1,0:63,A:124392499;C:67934245;G:96491307;T:133060705;N:86613,63,,,,124392499,67934245,96491307,133060705,86613,SRX8646687,SRS6930229,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83068,,0.05472,,0.78311,,0.5438,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60080,SRR12125415,SRX8646686,SRS6930228,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb6 2.25hpf,GSM4648215,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb6 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648215,GSM4648215: AB emb6 2.25hpf; Danio rerio; RNA Seq,GSM4648215,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648215,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb6_2_25hpf.fastq,fastq,628644744.0,9978488.0,GSM4648215 r1,0:63,A:184633079;C:102913810;G:143484876;T:197486280;N:126699,63,,,,184633079,102913810,143484876,197486280,126699,SRX8646686,SRS6930228,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83277,,0.06148,,0.77617,,0.55775,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60081,SRR12125414,SRX8646685,SRS6930231,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb5 2.25hpf,GSM4648214,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb5 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648214,GSM4648214: AB emb5 2.25hpf; Danio rerio; RNA Seq,GSM4648214,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648214,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb5_2_25hpf.fastq,fastq,814541301.0,12929227.0,GSM4648214 r1,0:63,A:242788318;C:140374211;G:193168440;T:238045602;N:164730,63,,,,242788318,140374211,193168440,238045602,164730,SRX8646685,SRS6930231,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86463,,0.04609,,0.78914,,0.69402,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60082,SRR12125413,SRX8646684,SRS6930227,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb4 2.25hpf,GSM4648213,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb4 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648213,GSM4648213: AB emb4 2.25hpf; Danio rerio; RNA Seq,GSM4648213,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648213,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb4_2_25hpf.fastq,fastq,616851396.0,9791292.0,GSM4648213 r1,0:63,A:184681235;C:102359437;G:145006560;T:184679393;N:124771,63,,,,184681235,102359437,145006560,184679393,124771,SRX8646684,SRS6930227,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85058,,0.04957,,0.79017,,0.66075,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60083,SRR12125412,SRX8646683,SRS6930226,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb3 2.25hpf,GSM4648212,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb3 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648212,GSM4648212: TL emb3 2.25hpf; Danio rerio; RNA Seq,GSM4648212,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648212,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb3_2_25hpf.fastq,fastq,1186700114.0,17711942.0,GSM4648212 r1,0:67,A:370074693;C:200098953;G:261433673;T:354868674;N:224121,67,,,,370074693,200098953,261433673,354868674,224121,SRX8646683,SRS6930226,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82908,,0.0523,,0.7837,,0.61246,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60084,SRR12125411,SRX8646682,SRS6930225,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb2 2.25hpf,GSM4648211,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb2 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648211,GSM4648211: TL emb2 2.25hpf; Danio rerio; RNA Seq,GSM4648211,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648211,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb2_2_25hpf.fastq,fastq,952230197.0,14212391.0,GSM4648211 r1,0:67,A:293613397;C:158998327;G:211896479;T:287542246;N:179748,67,,,,293613397,158998327,211896479,287542246,179748,SRX8646682,SRS6930225,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82682,,0.05463,,0.78581,,0.60992,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60085,SRR12125410,SRX8646681,SRS6930224,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb1 2.25hpf,GSM4648210,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb1 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648210,GSM4648210: TL emb1 2.25hpf; Danio rerio; RNA Seq,GSM4648210,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648210,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb1_2_25hpf.fastq,fastq,889434246.0,13275138.0,GSM4648210 r1,0:67,A:284892995;C:151063100;G:198507402;T:254807861;N:162888,67,,,,284892995,151063100,198507402,254807861,162888,SRX8646681,SRS6930224,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.81409,,0.04129,,0.79819,,0.67976,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60086,SRR12125409,SRX8646680,SRS6930223,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb3 2.25hpf,GSM4648209,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb3 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648209,GSM4648209: AB emb3 2.25hpf; Danio rerio; RNA Seq,GSM4648209,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648209,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb3_2_25hpf.fastq,fastq,1018630279.0,15203437.0,GSM4648209 r1,0:67,A:317428176;C:175810114;G:228314923;T:296891187;N:185879,67,,,,317428176,175810114,228314923,296891187,185879,SRX8646680,SRS6930223,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83444,,0.04892,,0.78577,,0.65007,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60087,SRR12125408,SRX8646679,SRS6930222,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb2 2.25hpf,GSM4648208,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb2 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648208,GSM4648208: AB emb2 2.25hpf; Danio rerio; RNA Seq,GSM4648208,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648208,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb2_2_25hpf.fastq,fastq,1455828193.0,21728779.0,GSM4648208 r1,0:67,A:456676551;C:251609741;G:334731434;T:412538456;N:272011,67,,,,456676551,251609741,334731434,412538456,272011,SRX8646679,SRS6930222,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85982,,0.04242,,0.79399,,0.72904,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60088,SRR12125407,SRX8646678,SRS6930221,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb1 2.25hpf,GSM4648207,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb1 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648207,GSM4648207: AB emb1 2.25hpf; Danio rerio; RNA Seq,GSM4648207,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648207,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb1_2_25hpf.fastq,fastq,1156150325.0,17255975.0,GSM4648207 r1,0:67,A:367116449;C:201866700;G:266919704;T:320031593;N:215879,67,,,,367116449,201866700,266919704,320031593,215879,SRX8646678,SRS6930221,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85881,,0.03651,,0.80346,,0.76662,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures