{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Embryo\" and tissue_curation = \"Gonad\"", "rows": [[24594, "SRR25462243", "SRX21195038", "SRS18453964", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PV M3", "GSM7669033", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing", "PV M3", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ", "GSM7669033", "GSM7669033: PV M3; Danio rerio; RNA Seq", "GSM7669033 r1", "GSM7669033", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_M3_R1.fastq.gz PV_M3_R2.fastq.gz", "fastq fastq", 4644457090.0, 23465750.0, "GSM7669033 r1", "0:98.98 1:98.94", "A:1196567358;C:1114203322;G:1109379777;T:1223156356;N:1150277", 98, 98, null, null, 1196567358, 1114203322, 1109379777, 1223156356, 1150277, "SRX21195038", "SRS18453964", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94849, 0.95248, 0.02727, 0.02708, 0.73602, 0.73718, 0.48396, 0.4855, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24595, "SRR25462244", "SRX21195037", "SRS18453963", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PV M2", "GSM7669032", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing", "PV M2", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ", "GSM7669032", "GSM7669032: PV M2; Danio rerio; RNA Seq", "GSM7669032 r1", "GSM7669032", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_M2_R1.fastq.gz PV_M2_R2.fastq.gz", "fastq fastq", 2464506276.0, 12449948.0, "GSM7669032 r1", "0:98.99 1:98.96", "A:632587002;C:593372099;G:591579950;T:646214108;N:753117", 98, 98, null, null, 632587002, 593372099, 591579950, 646214108, 753117, "SRX21195037", "SRS18453963", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94889, 0.9522, 0.02585, 0.02585, 0.73669, 0.73841, 0.48398, 0.48486, 100, 99, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24596, "SRR25462245", "SRX21195036", "SRS18453962", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PV M1", "GSM7669031", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / |geo loc name:missing|collection date:missing", "PV M1", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:MT ybx1 / ", "GSM7669031", "GSM7669031: PV M1; Danio rerio; RNA Seq", "GSM7669031 r1", "GSM7669031", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_M1_R1.fastq.gz PV_M1_R2.fastq.gz", "fastq fastq", 3634173229.0, 18461903.0, "GSM7669031 r1", "0:98.44 1:98.41", "A:930322973;C:875929476;G:875710056;T:948595199;N:3615525", 98, 98, null, null, 930322973, 875929476, 875710056, 948595199, 3615525, "SRX21195036", "SRS18453962", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94787, 0.95134, 0.02457, 0.02445, 0.73762, 0.73843, 0.48244, 0.48069, 100, 98, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24597, "SRR25462246", "SRX21195035", "SRS18453961", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PV WT3", "GSM7669030", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing", "PV WT3", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+", "GSM7669030", "GSM7669030: PV WT3; Danio rerio; RNA Seq", "GSM7669030 r1", "GSM7669030", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_WT3_R2.fastq PV_WT3_R1.fastq", "fastq fastq", 2965772270.0, 14976621.0, "GSM7669030 r1", "0:99.03 1:98.99", "A:759343389;C:716154246;G:713466520;T:775995980;N:812135", 99, 98, null, null, 759343389, 716154246, 713466520, 775995980, 812135, "SRX21195035", "SRS18453961", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.95027, 0.95485, 0.02356, 0.02292, 0.74422, 0.74554, 0.47974, 0.48267, 100, 98, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24598, "SRR25462247", "SRX21195034", "SRS18453960", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PV WT2", "GSM7669029", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing", "PV WT2", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+", "GSM7669029", "GSM7669029: PV WT2; Danio rerio; RNA Seq", "GSM7669029 r1", "GSM7669029", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_WT2_R2.fastq PV_WT2_R1.fastq", "fastq fastq", 2021387268.0, 10195384.0, "GSM7669029 r1", "0:99.15 1:99.12", "A:517788644;C:487363563;G:485168383;T:530550229;N:516449", 99, 99, null, null, 517788644, 487363563, 485168383, 530550229, 516449, "SRX21195034", "SRS18453960", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.95113, 0.9544, 0.02394, 0.02364, 0.74168, 0.74363, 0.47881, 0.47499, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [24599, "SRR25462248", "SRX21195033", "SRS18453959", "SRP452269", "PRJNA1000446", "Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish", "GSE239623", "Transcriptome Analysis", "Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.", null, null, null, "PV WT1", "GSM7669028", null, "source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing", "PV WT1", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file", "follicle", null, "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+", "GSM7669028", "GSM7669028: PV WT1; Danio rerio; RNA Seq", "GSM7669028 r1", "GSM7669028", "1", "TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452269", null, null, "PV_WT1_R1.fastq PV_WT1_R2.fastq", "fastq fastq", 3244660111.0, 16481925.0, "GSM7669028 r1", "0:98.44 1:98.42", "A:831426044;C:781489498;G:779991004;T:848549246;N:3204319", 98, 98, null, null, 831426044, 781489498, 779991004, 848549246, 3204319, "SRX21195033", "SRS18453959", null, null, "Karp 12006A, Biology of Vascular Program, Boston Children's Hospital", 2, 0.94779, 0.95185, 0.02328, 0.02298, 0.74294, 0.74391, 0.48052, 0.47966, 95, 95, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2023-07-31", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [37997, "SRR1265760", "SRX529154", "SRS598851", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Testis Replicate 3 sRNAseq", "GSM1376643", null, "source name:Testis|gender:male|tissue:Testis|genetic background:Wild type Singapore strain", "Testis Replicate 3 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Testis", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Testis|genetic background:Wild type Singapore strain", "GSM1376643", "GSM1376643: Testis Replicate 3 sRNAseq; Danio rerio; miRNA Seq", "GSM1376643", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376643", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZT004_GCCAAT_L004_R1.fastq.gz", "fastq", 1096387628.0, 14426153.0, "GSM1376643 r1", "0:76", "A:268706118;C:286539627;G:262643519;T:278353167;N:145197", 76, null, null, null, 268706118, 286539627, 262643519, 278353167, 145197, "SRX529154", "SRS598851", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00659, null, 0.00333, null, 0.99845, null, 0.7331, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [37998, "SRR1265759", "SRX529153", "SRS598850", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Testis Replicate 2 sRNAseq", "GSM1376642", null, "source name:Testis|gender:male|tissue:Testis|genetic background:Wild type Singapore strain", "Testis Replicate 2 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Testis", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Testis|genetic background:Wild type Singapore strain", "GSM1376642", "GSM1376642: Testis Replicate 2 sRNAseq; Danio rerio; miRNA Seq", "GSM1376642", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376642", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZT003_ACAGTG_L004_R1.fastq.gz", "fastq", 1562745896.0, 20562446.0, "GSM1376642 r1", "0:76", "A:381752411;C:387452090;G:395892335;T:397438930;N:210130", 76, null, null, null, 381752411, 387452090, 395892335, 397438930, 210130, "SRX529153", "SRS598850", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.01222, null, 0.00651, null, 0.99788, null, 0.69591, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [37999, "SRR1265758", "SRX529152", "SRS598849", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Testis Replicate 1 sRNAseq", "GSM1376641", null, "source name:Testis|gender:male|tissue:Testis|genetic background:Wild type Singapore strain", "Testis Replicate 1 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Testis", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Testis|genetic background:Wild type Singapore strain", "GSM1376641", "GSM1376641: Testis Replicate 1 sRNAseq; Danio rerio; miRNA Seq", "GSM1376641", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376641", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZT001_TGACCA_L004_R1.fastq.gz", "fastq", 1368892316.0, 18011741.0, "GSM1376641 r1", "0:76", "A:335715713;C:358829703;G:326742789;T:347419137;N:184974", 76, null, null, null, 335715713, 358829703, 326742789, 347419137, 184974, "SRX529152", "SRS598849", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00032, null, 3e-05, null, 0.99943, null, 0.69387, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [38000, "SRR1265757", "SRX529151", "SRS598848", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Ovary Replicate 3 sRNAseq", "GSM1376640", null, "source name:Ovary|gender:female|tissue:Ovary|genetic background:Wild type Singapore strain", "Ovary Replicate 3 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Ovary", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Ovary|genetic background:Wild type Singapore strain", "GSM1376640", "GSM1376640: Ovary Replicate 3 sRNAseq; Danio rerio; miRNA Seq", "GSM1376640", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376640", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZO006_GATCAG_L008_R1.fastq.gz", "fastq", 1411005984.0, 27666784.0, "GSM1376640 r1", "0:51", "A:326542153;C:314421825;G:411019622;T:358847379;N:175005", 51, null, null, null, 326542153, 314421825, 411019622, 358847379, 175005, "SRX529151", "SRS598848", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00638, null, 0.00068, null, 0.99513, null, 0.75483, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [38001, "SRR1265756", "SRX529150", "SRS598847", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Ovary Replicate 2 sRNAseq", "GSM1376639", null, "source name:Ovary|gender:female|tissue:Ovary|genetic background:Wild type Singapore strain", "Ovary Replicate 2 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Ovary", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Ovary|genetic background:Wild type Singapore strain", "GSM1376639", "GSM1376639: Ovary Replicate 2 sRNAseq; Danio rerio; miRNA Seq", "GSM1376639", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376639", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZO005_ACTTGA_L008_R1.fastq.gz", "fastq", 765419424.0, 15008224.0, "GSM1376639 r1", "0:51", "A:179455664;C:170237021;G:221342071;T:194287721;N:96947", 51, null, null, null, 179455664, 170237021, 221342071, 194287721, 96947, "SRX529150", "SRS598847", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.02512, null, 0.00355, null, 0.98212, null, 0.67744, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [38002, "SRR1265755", "SRX529149", "SRS598846", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Ovary Replicate 1 sRNAseq", "GSM1376638", null, "source name:Ovary|gender:female|tissue:Ovary|genetic background:Wild type Singapore strain", "Ovary Replicate 1 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Ovary", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Ovary|genetic background:Wild type Singapore strain", "GSM1376638", "GSM1376638: Ovary Replicate 1 sRNAseq; Danio rerio; miRNA Seq", "GSM1376638", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376638", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZO004_CAGATC_L008_R1.fastq.gz", "fastq", 487558674.0, 9559974.0, "GSM1376638 r1", "0:51", "A:114833813;C:108951811;G:140408702;T:123302557;N:61791", 51, null, null, null, 114833813, 108951811, 140408702, 123302557, 61791, "SRX529149", "SRS598846", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00298, null, 0.0004, null, 0.99644, null, 0.84584, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [39861, "SRR2177451", "SRX1161443", "SRS1042406", "SRP062686", "PRJNA293487", "Danio rerio Digital Gene Expression Sequencing", "PRJNA293487", "Other", "Differential expression between WT and CD82a from Morpholino treated embyro of Danio rerio", null, null, "Differential expression between WT and CD82a Morpholino treated embyro of Danio rerio", null, "control", null, "isolate:Danio rerio embyro|dev stage:embyro|sex:missing|tissue:ovary|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Digital Gene Expression Sequencing", "control", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "SRP062686", null, null, "control_R1.fastq.gz control_R2.fastq.gz", "fastq fastq", 1381289200.0, 6906446.0, "control", "0:100 1:100", "A:362182510;C:331106787;G:327770778;T:360198909;N:30216", 100, 100, null, null, 362182510, 331106787, 327770778, 360198909, 30216, "SRX1161443", "SRS1042406", "SRA290388", "Shanghai Ocean University|Department of Biology and Biotechnology", "Shanghai Ocean University", 2, 0.95634, 0.95016, 0.06922, 0.06922, 0.7013, 0.70368, 0.46985, 0.47013, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2016-08-21", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [39862, "SRR2177447", "SRX1161442", "SRS1042404", "SRP062686", "PRJNA293487", "Danio rerio Digital Gene Expression Sequencing", "PRJNA293487", "Other", "Differential expression between WT and CD82a from Morpholino treated embyro of Danio rerio", null, null, "Differential expression between WT and CD82a Morpholino treated embyro of Danio rerio", null, "ATG", null, "isolate:Danio rerio embyro|dev stage:embyro|sex:missing|tissue:ovary|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Digital Gene Expression Sequencing", "ATG", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "SRP062686", null, null, "ATG_R1.fastq.gz ATG_R2.fastq.gz", "fastq fastq", 1278088000.0, 6390440.0, "ATG", "0:100 1:100", "A:335532626;C:305947212;G:302508524;T:334072046;N:27592", 100, 100, null, null, 335532626, 305947212, 302508524, 334072046, 27592, "SRX1161442", "SRS1042404", "SRA290388", "Shanghai Ocean University|Department of Biology and Biotechnology", "Shanghai Ocean University", 2, 0.95535, 0.94653, 0.07264, 0.07271, 0.70402, 0.7082, 0.46712, 0.46962, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2016-08-21", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [40599, "SRR3231354", "SRX1637105", "SRS1342922", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate4.1", "GSM2090871", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate4.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090871", "GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq", "GSM2090871", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090871", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate4.1_R1_001.fastq.gz 8hpf_wt_Plate4.1_R2_001.fastq.gz", "fastq fastq", 2340114249.0, 31038332.0, "GSM2090871 r1", "0:75.50 1:75.29", "A:719873895;C:416010081;G:472221417;T:731461092;N:547764", 75, 75, null, null, 719873895, 416010081, 472221417, 731461092, 547764, "SRX1637105", "SRS1342922", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 1, 0.00529, null, 0.00355, null, 0.99655, null, 0.52173, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40600, "SRR3231355", "SRX1637105", "SRS1342922", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate4.1", "GSM2090871", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate4.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090871", "GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq", "GSM2090871", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090871", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate4.2_R1_001.fastq.gz 8hpf_wt_Plate4.2_R2_001.fastq.gz", "fastq fastq", 2340187687.0, 31038332.0, "GSM2090871 r2", "0:75.50 1:75.29", "A:718375391;C:414519064;G:478873036;T:728401149;N:19047", 75, 75, null, null, 718375391, 414519064, 478873036, 728401149, 19047, "SRX1637105", "SRS1342922", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 1, 0.00524, null, 0.00333, null, 0.99634, null, 0.47321, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40601, "SRR3231356", "SRX1637105", "SRS1342922", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate4.1", "GSM2090871", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate4.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090871", "GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq", "GSM2090871", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090871", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate4.3_R1_001.fastq.gz 8hpf_wt_Plate4.3_R2_001.fastq.gz", "fastq fastq", 2331948832.0, 15464230.0, "GSM2090871 r3", "0:75.51 1:75.29", "A:710801790;C:413559417;G:478178818;T:728790143;N:618664", 75, 75, null, null, 710801790, 413559417, 478178818, 728790143, 618664, "SRX1637105", "SRS1342922", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00263, 0.00843, 0.0023, 0.00555, 0.99955, 0.99437, 0.37837, 0.52459, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40602, "SRR3231357", "SRX1637105", "SRS1342922", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate4.1", "GSM2090871", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate4.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090871", "GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq", "GSM2090871", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090871", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate4_R1_001.fastq.gz 8hpf_wt_Plate4_R2_001.fastq.gz", "fastq fastq", 2346532249.0, 15562065.0, "GSM2090871 r4", "0:75.50 1:75.29", "A:726362504;C:417435976;G:471522192;T:731180603;N:30974", 75, 75, null, null, 726362504, 417435976, 471522192, 731180603, 30974, "SRX1637105", "SRS1342922", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.0024, 0.00837, 0.00209, 0.00548, 0.99975, 0.99409, 0.2, 0.53439, 75, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40603, "SRR3231350", "SRX1637104", "SRS1342923", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate3.1", "GSM2090870", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate3.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090870", "GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq", "GSM2090870", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090870", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate3.1_R2_001.fastq.gz 8hpf_wt_Plate3.1_R1_001.fastq.gz", "fastq fastq", 1401297283.0, 9290433.0, "GSM2090870 r1", "0:75.49 1:75.34", "A:419635887;C:271951633;G:296507210;T:413191086;N:11467", 75, 75, null, null, 419635887, 271951633, 296507210, 413191086, 11467, "SRX1637104", "SRS1342923", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00163, 0.00616, 0.00116, 0.00341, 0.99951, 0.99425, 0.125, 0.59722, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40604, "SRR3231351", "SRX1637104", "SRS1342923", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate3.1", "GSM2090870", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate3.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090870", "GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq", "GSM2090870", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090870", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate3.2_R1_001.fastq.gz 8hpf_wt_Plate3.2_R2_001.fastq.gz", "fastq fastq", 1401701707.0, 9293054.0, "GSM2090870 r2", "0:75.50 1:75.34", "A:422173594;C:272799681;G:292195265;T:414209404;N:323763", 75, 75, null, null, 422173594, 272799681, 292195265, 414209404, 323763, "SRX1637104", "SRS1342923", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00183, 0.0057, 0.00134, 0.00307, 0.99959, 0.9948, 0.18965, 0.59402, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40605, "SRR3231352", "SRX1637104", "SRS1342923", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate3.1", "GSM2090870", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate3.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090870", "GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq", "GSM2090870", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090870", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate3.3_R1_001.fastq.gz 8hpf_wt_Plate3.3_R2_001.fastq.gz", "fastq fastq", 1395747908.0, 9253276.0, "GSM2090870 r3", "0:75.50 1:75.34", "A:416176386;C:270989429;G:295563056;T:412655214;N:363823", 75, 75, null, null, 416176386, 270989429, 295563056, 412655214, 363823, "SRX1637104", "SRS1342923", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00148, 0.0058, 0.00112, 0.00312, 0.99969, 0.99476, 0.16279, 0.54093, 75, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40606, "SRR3231353", "SRX1637104", "SRS1342923", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate3.1", "GSM2090870", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate3.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090870", "GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq", "GSM2090870", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090870", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate3_R1_001.fastq.gz 8hpf_wt_Plate3_R2_001.fastq.gz", "fastq fastq", 1407551761.0, 9332199.0, "GSM2090870 r4", "0:75.49 1:75.34", "A:425795996;C:274090898;G:292401737;T:415244521;N:18609", 75, 75, null, null, 425795996, 274090898, 292401737, 415244521, 18609, "SRX1637104", "SRS1342923", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00196, 0.00615, 0.00142, 0.00325, 0.99926, 0.99403, 0.39682, 0.57712, 74, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40607, "SRR3231346", "SRX1637103", "SRS1342924", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate2.1", "GSM2090869", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate2.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090869", "GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq", "GSM2090869", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090869", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate2.1_R1_001.fastq.gz 8hpf_wt_Plate2.1_R2_001.fastq.gz", "fastq fastq", 952595024.0, 6315631.0, "GSM2090869 r1", "0:75.47 1:75.36", "A:302137554;C:151875219;G:168962721;T:329611160;N:8370", 75, 75, null, null, 302137554, 151875219, 168962721, 329611160, 8370, "SRX1637103", "SRS1342924", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00829, 0.04086, 0.00683, 0.01381, 0.99898, 0.97133, 0.21481, 0.68244, 75, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40608, "SRR3231347", "SRX1637103", "SRS1342924", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate2.1", "GSM2090869", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate2.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090869", "GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq", "GSM2090869", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090869", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate2.2_R1_001.fastq.gz 8hpf_wt_Plate2.2_R2_001.fastq.gz", "fastq fastq", 946451815.0, 6274940.0, "GSM2090869 r2", "0:75.47 1:75.36", "A:302374789;C:151074230;G:165028305;T:327758585;N:215906", 75, 75, null, null, 302374789, 151074230, 165028305, 327758585, 215906, "SRX1637103", "SRS1342924", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00869, 0.03997, 0.00704, 0.01272, 0.99888, 0.97183, 0.24342, 0.68028, 75, 74, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40609, "SRR3231348", "SRX1637103", "SRS1342924", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate2.1", "GSM2090869", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate2.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090869", "GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq", "GSM2090869", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090869", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate2.3_R2_001.fastq.gz 8hpf_wt_Plate2.3_R1_001.fastq.gz", "fastq fastq", 947126047.0, 6279272.0, "GSM2090869 r3", "0:75.48 1:75.36", "A:299035197;C:150983123;G:168162807;T:328697140;N:247780", 75, 75, null, null, 299035197, 150983123, 168162807, 328697140, 247780, "SRX1637103", "SRS1342924", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00868, 0.03867, 0.00717, 0.01319, 0.99864, 0.97356, 0.29285, 0.66677, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40610, "SRR3231349", "SRX1637103", "SRS1342924", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate2.1", "GSM2090869", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate2.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090869", "GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq", "GSM2090869", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090869", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate2_R1_001.fastq.gz 8hpf_wt_Plate2_R2_001.fastq.gz", "fastq fastq", 948028451.0, 6285580.0, "GSM2090869 r4", "0:75.47 1:75.36", "A:304286797;C:151414365;G:164490323;T:327824187;N:12779", 75, 75, null, null, 304286797, 151414365, 164490323, 327824187, 12779, "SRX1637103", "SRS1342924", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.0086, 0.04012, 0.00712, 0.01343, 0.99888, 0.97177, 0.29411, 0.66575, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40611, "SRR3231342", "SRX1637102", "SRS1342925", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate1.1", "GSM2090868", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate1.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090868", "GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq", "GSM2090868", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090868", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate1.1_R1_001.fastq.gz 8hpf_wt_Plate1.1_R2_001.fastq.gz", "fastq fastq", 1189452130.0, 7888435.0, "GSM2090868 r1", "0:75.47 1:75.32", "A:375847699;C:199289576;G:245818831;T:368358068;N:137956", 75, 75, null, null, 375847699, 199289576, 245818831, 368358068, 137956, "SRX1637102", "SRS1342925", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00377, 0.02162, 0.00304, 0.01018, 0.99931, 0.9848, 0.29032, 0.61771, 75, 73, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40612, "SRR3231343", "SRX1637102", "SRS1342925", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate1.1", "GSM2090868", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate1.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090868", "GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq", "GSM2090868", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090868", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate1.2_R1_001.fastq.gz 8hpf_wt_Plate1.2_R2_001.fastq.gz", "fastq fastq", 1238856894.0, 8215764.0, "GSM2090868 r2", "0:75.47 1:75.32", "A:389215255;C:208182440;G:256176425;T:385173832;N:108942", 75, 75, null, null, 389215255, 208182440, 256176425, 385173832, 108942, "SRX1637102", "SRS1342925", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00375, 0.02269, 0.00298, 0.01135, 0.99928, 0.98423, 0.40579, 0.61686, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40613, "SRR3231344", "SRX1637102", "SRS1342925", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate1.1", "GSM2090868", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate1.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090868", "GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq", "GSM2090868", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090868", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate1.3_R1_001.fastq.gz 8hpf_wt_Plate1.3_R2_001.fastq.gz", "fastq fastq", 1240573542.0, 8227185.0, "GSM2090868 r3", "0:75.47 1:75.32", "A:389703162;C:207657187;G:257329681;T:385780094;N:103418", 75, 75, null, null, 389703162, 207657187, 257329681, 385780094, 103418, "SRX1637102", "SRS1342925", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00354, 0.02325, 0.00287, 0.01111, 0.99922, 0.98309, 0.47368, 0.60449, 75, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40614, "SRR3231345", "SRX1637102", "SRS1342925", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf wt Plate1.1", "GSM2090868", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf wt Plate1.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090868", "GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq", "GSM2090868", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090868", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_wt_Plate1_R1_001.fastq.gz 8hpf_wt_Plate1_R2_001.fastq.gz", "fastq fastq", 1215460175.0, 8061085.0, "GSM2090868 r4", "0:75.46 1:75.32", "A:382475416;C:204057930;G:251490776;T:377293780;N:142273", 75, 75, null, null, 382475416, 204057930, 251490776, 377293780, 142273, "SRX1637102", "SRS1342925", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00394, 0.02131, 0.00309, 0.0101, 0.99928, 0.98472, 0.34285, 0.61368, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40615, "SRR3231338", "SRX1637101", "SRS1342933", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate4.1", "GSM2090867", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate4.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090867", "GSM2090867: 8hpf Tdrd6a : Plate4.1; Danio rerio; RNA Seq", "GSM2090867", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090867", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate4.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4.1_R2_001.fastq.gz", "fastq fastq", 660308475.0, 4377096.0, "GSM2090867 r1", "0:75.49 1:75.36", "A:203051507;C:115872485;G:122313924;T:219064434;N:6125", 75, 75, null, null, 203051507, 115872485, 122313924, 219064434, 6125, "SRX1637101", "SRS1342933", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00239, 0.00751, 0.00191, 0.00364, 0.99941, 0.99385, 0.5625, 0.71067, 75, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40616, "SRR3231339", "SRX1637101", "SRS1342933", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate4.1", "GSM2090867", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate4.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090867", "GSM2090867: 8hpf Tdrd6a : Plate4.1; Danio rerio; RNA Seq", "GSM2090867", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090867", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate4.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4.2_R2_001.fastq.gz", "fastq fastq", 659386859.0, 4370960.0, "GSM2090867 r2", "0:75.50 1:75.36", "A:204037715;C:116060649;G:120151402;T:218981853;N:155240", 75, 75, null, null, 204037715, 116060649, 120151402, 218981853, 155240, "SRX1637101", "SRS1342933", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00303, 0.00736, 0.00246, 0.00371, 0.99941, 0.99429, 0.45614, 0.65738, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40617, "SRR3231340", "SRX1637101", "SRS1342933", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate4.1", "GSM2090867", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate4.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090867", "GSM2090867: 8hpf Tdrd6a : Plate4.1; Danio rerio; RNA Seq", "GSM2090867", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090867", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate4.3_R2_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4.3_R1_001.fastq.gz", "fastq fastq", 656929514.0, 4354565.0, "GSM2090867 r3", "0:75.50 1:75.36", "A:200970859;C:115371071;G:121921931;T:218498053;N:167600", 75, 75, null, null, 200970859, 115371071, 121921931, 218498053, 167600, "SRX1637101", "SRS1342933", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00267, 0.00746, 0.00211, 0.00354, 0.99926, 0.99371, 0.58181, 0.66467, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40618, "SRR3231341", "SRX1637101", "SRS1342933", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate4.1", "GSM2090867", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate4.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090867", "GSM2090867: 8hpf Tdrd6a : Plate4.1; Danio rerio; RNA Seq", "GSM2090867", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090867", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate4_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4_R2_001.fastq.gz", "fastq fastq", 659750831.0, 4373567.0, "GSM2090867 r4", "0:75.49 1:75.36", "A:205228191;C:116070031;G:119659384;T:218783801;N:9424", 75, 75, null, null, 205228191, 116070031, 119659384, 218783801, 9424, "SRX1637101", "SRS1342933", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00286, 0.00728, 0.00232, 0.00355, 0.99945, 0.99439, 0.47169, 0.69696, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40619, "SRR3231334", "SRX1637100", "SRS1342932", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate3.1", "GSM2090866", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate3.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090866", "GSM2090866: 8hpf Tdrd6a : Plate3.1; Danio rerio; RNA Seq", "GSM2090866", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090866", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate3.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3.1_R2_001.fastq.gz", "fastq fastq", 991807830.0, 6574461.0, "GSM2090866 r1", "0:75.50 1:75.35", "A:306057776;C:164673747;G:183621348;T:337443425;N:11534", 75, 75, null, null, 306057776, 164673747, 183621348, 337443425, 11534, "SRX1637100", "SRS1342932", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00573, 0.01848, 0.00474, 0.0066, 0.99918, 0.98362, 0.36274, 0.59804, 75, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40620, "SRR3231335", "SRX1637100", "SRS1342932", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate3.1", "GSM2090866", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate3.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090866", "GSM2090866: 8hpf Tdrd6a : Plate3.1; Danio rerio; RNA Seq", "GSM2090866", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090866", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate3.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3.2_R2_001.fastq.gz", "fastq fastq", 985873592.0, 6535185.0, "GSM2090866 r2", "0:75.50 1:75.35", "A:306272693;C:164036011;G:179508984;T:335829272;N:226632", 75, 75, null, null, 306272693, 164036011, 179508984, 335829272, 226632, "SRX1637100", "SRS1342932", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00561, 0.0179, 0.00465, 0.00654, 0.99918, 0.98437, 0.31, 0.63328, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40621, "SRR3231336", "SRX1637100", "SRS1342932", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate3.1", "GSM2090866", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate3.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090866", "GSM2090866: 8hpf Tdrd6a : Plate3.1; Danio rerio; RNA Seq", "GSM2090866", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090866", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate3.3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3.3_R2_001.fastq.gz", "fastq fastq", 985261576.0, 6530964.0, "GSM2090866 r3", "0:75.51 1:75.35", "A:302874779;C:163594572;G:182423657;T:336116219;N:252349", 75, 75, null, null, 302874779, 163594572, 182423657, 336116219, 252349, "SRX1637100", "SRS1342932", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.0057, 0.01777, 0.00484, 0.00661, 0.99926, 0.98482, 0.3146, 0.64967, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40622, "SRR3231337", "SRX1637100", "SRS1342932", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate3.1", "GSM2090866", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate3.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090866", "GSM2090866: 8hpf Tdrd6a : Plate3.1; Danio rerio; RNA Seq", "GSM2090866", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090866", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3_R2_001.fastq.gz", "fastq fastq", 988364061.0, 6551921.0, "GSM2090866 r4", "0:75.50 1:75.35", "A:308483971;C:164508093;G:179109944;T:336245723;N:16330", 75, 75, null, null, 308483971, 164508093, 179109944, 336245723, 16330, "SRX1637100", "SRS1342932", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00558, 0.0188, 0.00462, 0.00684, 0.99912, 0.98354, 0.38775, 0.62734, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40623, "SRR3231330", "SRX1637099", "SRS1342934", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate2.1", "GSM2090865", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate2.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090865", "GSM2090865: 8hpf Tdrd6a : Plate2.1; Danio rerio; RNA Seq", "GSM2090865", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090865", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate2.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2.1_R2_001.fastq.gz", "fastq fastq", 1347558297.0, 8935001.0, "GSM2090865 r1", "0:75.49 1:75.32", "A:428692990;C:233467157;G:260154804;T:425229674;N:13672", 75, 75, null, null, 428692990, 233467157, 260154804, 425229674, 13672, "SRX1637099", "SRS1342934", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00717, 0.02482, 0.00583, 0.01367, 0.9977, 0.98301, 0.54347, 0.62642, 74, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40624, "SRR3231331", "SRX1637099", "SRS1342934", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate2.1", "GSM2090865", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate2.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090865", "GSM2090865: 8hpf Tdrd6a : Plate2.1; Danio rerio; RNA Seq", "GSM2090865", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090865", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate2.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2.2_R2_001.fastq.gz", "fastq fastq", 1347477358.0, 8934352.0, "GSM2090865 r2", "0:75.50 1:75.32", "A:431085993;C:234267083;G:255942417;T:425873702;N:308163", 75, 75, null, null, 431085993, 234267083, 255942417, 425873702, 308163, "SRX1637099", "SRS1342934", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00723, 0.02422, 0.00571, 0.01316, 0.99748, 0.9825, 0.4935, 0.61373, 75, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40625, "SRR3231332", "SRX1637099", "SRS1342934", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate2.1", "GSM2090865", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate2.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090865", "GSM2090865: 8hpf Tdrd6a : Plate2.1; Danio rerio; RNA Seq", "GSM2090865", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090865", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate2.3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2.3_R2_001.fastq.gz", "fastq fastq", 1342511024.0, 8901101.0, "GSM2090865 r3", "0:75.50 1:75.32", "A:424536537;C:232976344;G:259737347;T:424897714;N:363082", 75, 75, null, null, 424536537, 232976344, 259737347, 424897714, 363082, "SRX1637099", "SRS1342934", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00707, 0.02424, 0.00579, 0.01341, 0.99788, 0.98277, 0.3897, 0.60237, 75, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40626, "SRR3231333", "SRX1637099", "SRS1342934", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate2.1", "GSM2090865", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate2.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090865", "GSM2090865: 8hpf Tdrd6a : Plate2.1; Danio rerio; RNA Seq", "GSM2090865", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090865", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2_R2_001.fastq.gz", "fastq fastq", 1349985043.0, 8951395.0, "GSM2090865 r4", "0:75.49 1:75.32", "A:433870230;C:234813106;G:255398294;T:425882927;N:20486", 75, 75, null, null, 433870230, 234813106, 255398294, 425882927, 20486, "SRX1637099", "SRS1342934", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00663, 0.02406, 0.00536, 0.01336, 0.99772, 0.98281, 0.48872, 0.63184, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40627, "SRR3231326", "SRX1637098", "SRS1342905", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate1.1", "GSM2090864", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate1.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090864", "GSM2090864: 8hpf Tdrd6a : Plate1.1; Danio rerio; RNA Seq", "GSM2090864", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090864", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate1.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1.1_R2_001.fastq.gz", "fastq fastq", 2529086421.0, 16774294.0, "GSM2090864 r1", "0:75.43 1:75.34", "A:796779684;C:413533280;G:487547543;T:830919763;N:306151", 75, 75, null, null, 796779684, 413533280, 487547543, 830919763, 306151, "SRX1637098", "SRS1342905", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.05805, 0.15018, 0.04986, 0.07872, 0.98729, 0.92443, 0.5, 0.46925, 76, 76, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40628, "SRR3231327", "SRX1637098", "SRS1342905", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate1.1", "GSM2090864", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate1.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090864", "GSM2090864: 8hpf Tdrd6a : Plate1.1; Danio rerio; RNA Seq", "GSM2090864", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090864", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate1.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1.2_R2_001.fastq.gz", "fastq fastq", 2629569381.0, 17440212.0, "GSM2090864 r2", "0:75.43 1:75.34", "A:823719446;C:431439564;G:506909577;T:867265650;N:235144", 75, 75, null, null, 823719446, 431439564, 506909577, 867265650, 235144, "SRX1637098", "SRS1342905", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.0575, 0.1556, 0.04944, 0.08069, 0.98648, 0.92245, 0.5, 0.58664, 76, 76, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40629, "SRR3231328", "SRX1637098", "SRS1342905", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate1.1", "GSM2090864", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate1.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090864", "GSM2090864: 8hpf Tdrd6a : Plate1.1; Danio rerio; RNA Seq", "GSM2090864", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090864", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate1.3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1.3_R2_001.fastq.gz", "fastq fastq", 2626839769.0, 17422028.0, "GSM2090864 r3", "0:75.43 1:75.35", "A:822264952;C:429448970;G:507899334;T:867005630;N:220883", 75, 75, null, null, 822264952, 429448970, 507899334, 867005630, 220883, "SRX1637098", "SRS1342905", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.05904, 0.1574, 0.05085, 0.08206, 0.98685, 0.92133, 0.50407, 0.58481, 75, 75, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40630, "SRR3231329", "SRX1637098", "SRS1342905", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8hpf Tdrd6a : Plate1.1", "GSM2090864", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "8hpf Tdrd6a : Plate1.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090864", "GSM2090864: 8hpf Tdrd6a : Plate1.1; Danio rerio; RNA Seq", "GSM2090864", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090864", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8hpf_Tdrd6a-:-_Plate1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1_R2_001.fastq.gz", "fastq fastq", 2592347629.0, 17194377.0, "GSM2090864 r4", "0:75.43 1:75.34", "A:813940505;C:424856630;G:499860954;T:853378694;N:310846", 75, 75, null, null, 813940505, 424856630, 499860954, 853378694, 310846, "SRX1637098", "SRS1342905", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.0589, 0.14612, 0.05081, 0.07706, 0.98756, 0.92829, 0.52503, 0.46498, 75, 75, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [40631, "SRR3231322", "SRX1637097", "SRS1342906", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8and24hpf wt Plate1.1", "GSM2090863", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8and24hpf wt Plate1.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090863", "GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq", "GSM2090863", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090863", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8and24hpf_wt_Plate1.1_R1_001.fastq.gz 8and24hpf_wt_Plate1.1_R2_001.fastq.gz", "fastq fastq", 354951269.0, 2354572.0, "GSM2090863 r1", "0:75.37 1:75.38", "A:109255676;C:46649925;G:56800706;T:142212324;N:32638", 75, 75, null, null, 109255676, 46649925, 56800706, 142212324, 32638, "SRX1637097", "SRS1342906", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.08814, 0.58586, 0.05414, 0.12777, 0.98236, 0.8253, 0.52224, 0.5333, 75, 55, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40632, "SRR3231323", "SRX1637097", "SRS1342906", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8and24hpf wt Plate1.1", "GSM2090863", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8and24hpf wt Plate1.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090863", "GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq", "GSM2090863", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090863", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8and24hpf_wt_Plate1.2_R1_001.fastq.gz 8and24hpf_wt_Plate1.2_R2_001.fastq.gz", "fastq fastq", 373175186.0, 2475371.0, "GSM2090863 r2", "0:75.37 1:75.38", "A:114080796;C:49251081;G:59964869;T:149836843;N:41597", 75, 75, null, null, 114080796, 49251081, 59964869, 149836843, 41597, "SRX1637097", "SRS1342906", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.0895, 0.59282, 0.05309, 0.12622, 0.9811, 0.82185, 0.51449, 0.52518, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40633, "SRR3231324", "SRX1637097", "SRS1342906", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8and24hpf wt Plate1.1", "GSM2090863", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8and24hpf wt Plate1.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090863", "GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq", "GSM2090863", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090863", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8and24hpf_wt_Plate1.3_R1_001.fastq.gz 8and24hpf_wt_Plate1.3_R2_001.fastq.gz", "fastq fastq", 376796544.0, 2499144.0, "GSM2090863 r3", "0:75.38 1:75.39", "A:114262594;C:49685044;G:61341084;T:151464220;N:43602", 75, 75, null, null, 114262594, 49685044, 61341084, 151464220, 43602, "SRX1637097", "SRS1342906", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.08885, 0.60874, 0.05444, 0.12569, 0.98177, 0.81233, 0.51071, 0.53112, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40634, "SRR3231325", "SRX1637097", "SRS1342906", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "8and24hpf wt Plate1.1", "GSM2090863", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "8and24hpf wt Plate1.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090863", "GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq", "GSM2090863", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090863", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "8and24hpf_wt_Plate1_R1_001.fastq.gz 8and24hpf_wt_Plate1_R2_001.fastq.gz", "fastq fastq", 370852802.0, 2459988.0, "GSM2090863 r4", "0:75.37 1:75.38", "A:113706258;C:48924259;G:59523739;T:148663433;N:35113", 75, 75, null, null, 113706258, 48924259, 59523739, 148663433, 35113, "SRX1637097", "SRS1342906", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.08962, 0.59214, 0.05376, 0.12667, 0.98226, 0.82142, 0.53851, 0.52744, 75, 32, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40635, "SRR3231318", "SRX1637096", "SRS1342907", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "3.5hpf wt Plate5.1", "GSM2090862", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate5.1", "GSM2090862", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate5.1", "GSM2090862", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate5.1", "GSM2090862", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate4.1", "GSM2090861", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate4.1", "GSM2090861", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate4.1", "GSM2090861", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate4.1", "GSM2090861", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate3.1", "GSM2090860", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate3.1", "GSM2090860", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate3.1", "GSM2090860", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate3.1", "GSM2090860", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate2.1", "GSM2090859", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate2.1", "GSM2090859", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate2.1", "GSM2090859", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate2.1", "GSM2090859", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate1.1", "GSM2090858", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf wt Plate1.1", "GSM2090858", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf Tdrd6a : Plate5.1", "GSM2090857", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf Tdrd6a : Plate5.1", "GSM2090857", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf Tdrd6a : Plate5.1", "GSM2090857", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf Tdrd6a : Plate5.1", "GSM2090857", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf Tdrd6a : Plate4.1", "GSM2090856", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf Tdrd6a : Plate4.1", "GSM2090856", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf Tdrd6a : Plate4.1", "GSM2090856", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf Tdrd6a : Plate4.1", "GSM2090856", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf Tdrd6a : Plate3.1", "GSM2090855", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf Tdrd6a : Plate3.1", "GSM2090855", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf Tdrd6a : Plate2.1", "GSM2090854", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf Tdrd6a : Plate2.1", "GSM2090854", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf Tdrd6a : Plate1.1", "GSM2090853", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "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", null, "3.5hpf Tdrd6a : Plate1.1", "GSM2090853", null, "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\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA 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", null, "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", null, "SRP071848", null, null, "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, null, null, 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", null, "Germany", "2016-03-16", "Blastula", "Embryo", "Gonad", "Reproductive System"], [40669, "SRR3231284", "SRX1637085", "SRS1342918", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate5.1", "GSM2090851", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate5.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090851", "GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq", "GSM2090851", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090851", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate5.1_R1_001.fastq.gz 24hpf_wt_Plate5.1_R2_001.fastq.gz", "fastq fastq", 558605417.0, 3704499.0, "GSM2090851 r1", "0:75.45 1:75.34", "A:170059730;C:87004627;G:101477517;T:200008732;N:54811", 75, 75, null, null, 170059730, 87004627, 101477517, 200008732, 54811, "SRX1637085", "SRS1342918", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.01541, 0.18137, 0.00841, 0.03816, 0.99206, 0.90047, 0.55425, 0.56591, 76, 32, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40670, "SRR3231285", "SRX1637085", "SRS1342918", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate5.1", "GSM2090851", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate5.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090851", "GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq", "GSM2090851", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090851", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate5.2_R1_001.fastq.gz 24hpf_wt_Plate5.2_R2_001.fastq.gz", "fastq fastq", 581533785.0, 3856402.0, "GSM2090851 r2", "0:75.45 1:75.34", "A:176436951;C:90826765;G:105424561;T:208785606;N:59902", 75, 75, null, null, 176436951, 90826765, 105424561, 208785606, 59902, "SRX1637085", "SRS1342918", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.01519, 0.18239, 0.0089, 0.03729, 0.99306, 0.89917, 0.59594, 0.573, 74, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40671, "SRR3231286", "SRX1637085", "SRS1342918", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate5.1", "GSM2090851", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate5.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090851", "GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq", "GSM2090851", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090851", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate5.3_R1_001.fastq.gz 24hpf_wt_Plate5.3_R2_001.fastq.gz", "fastq fastq", 581069691.0, 3853089.0, "GSM2090851 r3", "0:75.45 1:75.35", "A:175088129;C:90460041;G:106640639;T:208812858;N:68024", 75, 75, null, null, 175088129, 90460041, 106640639, 208812858, 68024, "SRX1637085", "SRS1342918", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.01551, 0.19274, 0.00932, 0.0399, 0.99289, 0.89319, 0.57195, 0.56478, 74, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40672, "SRR3231287", "SRX1637085", "SRS1342918", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate5.1", "GSM2090851", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate5.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090851", "GSM2090851: 24hpf wt Plate5.1; Danio rerio; RNA Seq", "GSM2090851", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090851", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate5_R1_001.fastq.gz 24hpf_wt_Plate5_R2_001.fastq.gz", "fastq fastq", 576677563.0, 3824304.0, "GSM2090851 r4", "0:75.45 1:75.34", "A:175248120;C:90164865;G:104482050;T:206728496;N:54032", 75, 75, null, null, 175248120, 90164865, 104482050, 206728496, 54032, "SRX1637085", "SRS1342918", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.01561, 0.18528, 0.00921, 0.03947, 0.99302, 0.8981, 0.60185, 0.58278, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40673, "SRR3231280", "SRX1637084", "SRS1342920", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate4.1", "GSM2090850", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate4.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090850", "GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq", "GSM2090850", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090850", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate4.1_R1_001.fastq.gz 24hpf_wt_Plate4.1_R2_001.fastq.gz", "fastq fastq", 739151929.0, 4905477.0, "GSM2090850 r1", "0:75.40 1:75.28", "A:237453179;C:120215450;G:139806121;T:241606048;N:71131", 75, 75, null, null, 237453179, 120215450, 139806121, 241606048, 71131, "SRX1637084", "SRS1342920", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.01446, 0.18296, 0.00907, 0.03633, 0.99442, 0.91147, 0.57858, 0.55259, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40674, "SRR3231281", "SRX1637084", "SRS1342920", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate4.1", "GSM2090850", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate4.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090850", "GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq", "GSM2090850", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090850", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate4.2_R1_001.fastq.gz 24hpf_wt_Plate4.2_R2_001.fastq.gz", "fastq fastq", 769081502.0, 5103797.0, "GSM2090850 r2", "0:75.40 1:75.29", "A:245920087;C:125753713;G:145142187;T:252183239;N:82276", 75, 75, null, null, 245920087, 125753713, 145142187, 252183239, 82276, "SRX1637084", "SRS1342920", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.01429, 0.18495, 0.00907, 0.0378, 0.99435, 0.91181, 0.60136, 0.5509, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40675, "SRR3231282", "SRX1637084", "SRS1342920", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate4.1", "GSM2090850", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate4.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090850", "GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq", "GSM2090850", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090850", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate4.3_R1_001.fastq.gz 24hpf_wt_Plate4.3_R2_001.fastq.gz", "fastq fastq", 763478256.0, 5066455.0, "GSM2090850 r3", "0:75.40 1:75.29", "A:242520066;C:123970168;G:146100841;T:250803049;N:84132", 75, 75, null, null, 242520066, 123970168, 146100841, 250803049, 84132, "SRX1637084", "SRS1342920", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.01481, 0.1935, 0.0093, 0.03777, 0.99448, 0.90526, 0.5546, 0.56044, 74, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40676, "SRR3231283", "SRX1637084", "SRS1342920", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate4.1", "GSM2090850", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate4.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090850", "GSM2090850: 24hpf wt Plate4.1; Danio rerio; RNA Seq", "GSM2090850", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090850", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate4_R1_001.fastq.gz 24hpf_wt_Plate4_R2_001.fastq.gz", "fastq fastq", 762348830.0, 5059335.0, "GSM2090850 r4", "0:75.40 1:75.28", "A:244240563;C:124701855;G:143859660;T:249474441;N:72311", 75, 75, null, null, 244240563, 124701855, 143859660, 249474441, 72311, "SRX1637084", "SRS1342920", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.01537, 0.18668, 0.00965, 0.03681, 0.99407, 0.91066, 0.54926, 0.55097, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40677, "SRR3231276", "SRX1637083", "SRS1342919", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate3.1", "GSM2090849", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate3.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090849", "GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq", "GSM2090849", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090849", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate3.1_R1_001.fastq.gz 24hpf_wt_Plate3.1_R2_001.fastq.gz", "fastq fastq", 692753746.0, 4593127.0, "GSM2090849 r1", "0:75.47 1:75.35", "A:200412235;C:124307113;G:146191995;T:221774807;N:67596", 75, 75, null, null, 200412235, 124307113, 146191995, 221774807, 67596, "SRX1637083", "SRS1342919", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00405, 0.02858, 0.00276, 0.00696, 0.99752, 0.9722, 0.64935, 0.55705, 76, 74, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40678, "SRR3231277", "SRX1637083", "SRS1342919", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate3.1", "GSM2090849", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate3.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090849", "GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq", "GSM2090849", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090849", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate3.2_R1_001.fastq.gz 24hpf_wt_Plate3.2_R2_001.fastq.gz", "fastq fastq", 701569969.0, 4651611.0, "GSM2090849 r2", "0:75.47 1:75.35", "A:203675895;C:126097325;G:146891489;T:224837147;N:68113", 75, 75, null, null, 203675895, 126097325, 146891489, 224837147, 68113, "SRX1637083", "SRS1342919", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00395, 0.0305, 0.0027, 0.00699, 0.9976, 0.97088, 0.4863, 0.57133, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40679, "SRR3231278", "SRX1637083", "SRS1342919", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate3.1", "GSM2090849", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate3.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090849", "GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq", "GSM2090849", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090849", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate3.3_R1_001.fastq.gz 24hpf_wt_Plate3.3_R2_001.fastq.gz", "fastq fastq", 688668111.0, 4566244.0, "GSM2090849 r3", "0:75.47 1:75.35", "A:199652330;C:123454100;G:144848134;T:220657099;N:56448", 75, 75, null, null, 199652330, 123454100, 144848134, 220657099, 56448, "SRX1637083", "SRS1342919", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00369, 0.02792, 0.00272, 0.00658, 0.99803, 0.9727, 0.50427, 0.55885, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40680, "SRR3231279", "SRX1637083", "SRS1342919", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate3.1", "GSM2090849", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate3.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090849", "GSM2090849: 24hpf wt Plate3.1; Danio rerio; RNA Seq", "GSM2090849", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090849", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate3_R1_001.fastq.gz 24hpf_wt_Plate3_R2_001.fastq.gz", "fastq fastq", 702507993.0, 4657860.0, "GSM2090849 r4", "0:75.47 1:75.35", "A:203715514;C:126718380;G:147182176;T:224817151;N:74772", 75, 75, null, null, 203715514, 126718380, 147182176, 224817151, 74772, "SRX1637083", "SRS1342919", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.00392, 0.0275, 0.00279, 0.00707, 0.99778, 0.97297, 0.46666, 0.56022, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40681, "SRR3231272", "SRX1637082", "SRS1342921", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate2.1", "GSM2090848", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate2.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090848", "GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq", "GSM2090848", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090848", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate2.1_R1_001.fastq.gz 24hpf_wt_Plate2.1_R2_001.fastq.gz", "fastq fastq", 298994170.0, 1982738.0, "GSM2090848 r1", "0:75.44 1:75.35", "A:93083508;C:44907251;G:52817440;T:108158577;N:27394", 75, 75, null, null, 93083508, 44907251, 52817440, 108158577, 27394, "SRX1637082", "SRS1342921", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.01409, 0.02745, 0.01105, 0.00689, 0.99847, 0.97512, 0.14754, 0.54124, 75, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40682, "SRR3231273", "SRX1637082", "SRS1342921", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate2.1", "GSM2090848", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate2.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090848", "GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq", "GSM2090848", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090848", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate2.2_R1_001.fastq.gz 24hpf_wt_Plate2.2_R2_001.fastq.gz", "fastq fastq", 306815504.0, 2034672.0, "GSM2090848 r2", "0:75.44 1:75.36", "A:95967069;C:46066723;G:53601976;T:111150011;N:29725", 75, 75, null, null, 95967069, 46066723, 53601976, 111150011, 29725, "SRX1637082", "SRS1342921", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.01382, 0.03079, 0.01075, 0.00723, 0.99859, 0.97344, 0.14334, 0.56436, 75, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40683, "SRR3231274", "SRX1637082", "SRS1342921", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate2.1", "GSM2090848", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate2.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090848", "GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq", "GSM2090848", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090848", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate2.3_R1_001.fastq.gz 24hpf_wt_Plate2.3_R2_001.fastq.gz", "fastq fastq", 300764521.0, 1994537.0, "GSM2090848 r3", "0:75.44 1:75.35", "A:93852241;C:45007343;G:52938896;T:108939437;N:26604", 75, 75, null, null, 93852241, 45007343, 52938896, 108939437, 26604, "SRX1637082", "SRS1342921", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.0141, 0.02918, 0.01084, 0.0072, 0.99853, 0.97437, 0.12264, 0.55403, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40684, "SRR3231275", "SRX1637082", "SRS1342921", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate2.1", "GSM2090848", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate2.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090848", "GSM2090848: 24hpf wt Plate2.1; Danio rerio; RNA Seq", "GSM2090848", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090848", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate2_R1_001.fastq.gz 24hpf_wt_Plate2_R2_001.fastq.gz", "fastq fastq", 302297329.0, 2004669.0, "GSM2090848 r4", "0:75.44 1:75.35", "A:94284770;C:45616868;G:52928512;T:109434957;N:32222", 75, 75, null, null, 94284770, 45616868, 52928512, 109434957, 32222, "SRX1637082", "SRS1342921", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.01369, 0.02852, 0.01069, 0.00705, 0.99874, 0.97526, 0.10472, 0.56414, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40685, "SRR3231268", "SRX1637081", "SRS1342935", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate1.1", "GSM2090847", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate1.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090847", "GSM2090847: 24hpf wt Plate1.1; Danio rerio; RNA Seq", "GSM2090847", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090847", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate1.1_R1_001.fastq.gz 24hpf_wt_Plate1.1_R2_001.fastq.gz", "fastq fastq", 836011252.0, 5542746.0, "GSM2090847 r1", "0:75.49 1:75.34", "A:254663944;C:151442656;G:167697929;T:262199779;N:6944", 75, 75, null, null, 254663944, 151442656, 167697929, 262199779, 6944, "SRX1637081", "SRS1342935", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.03375, 0.07314, 0.02792, 0.0396, 0.98882, 0.95753, 0.54559, 0.53265, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [40686, "SRR3231269", "SRX1637081", "SRS1342935", "SRP071848", "PRJNA315399", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq]", "GSE79283", "Transcriptome Analysis", "Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a / mother and wt mother carrying a kop::egfp f nos1 three primeUTR transgene. Therepost single cell trizol extractio was performed followed by RT IVT and RNA seq library prep.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "24hpf wt Plate1.1", "GSM2090847", null, "tissue:Germ cells|cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "24hpf wt Plate1.1", "post sequencing read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al. 2013 Junker et al 2015 using bwa Li and Durbin 2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3\u2019 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", null, "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "Zebrafish were maintained under standard conditions.", "cell line:Primary cells|developmental stage:24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al. Cell reports 2012", "GSM2090847", "GSM2090847: 24hpf wt Plate1.1; Danio rerio; RNA Seq", "GSM2090847", null, "1", "mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al. 2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.", "GEO Accession:GSM2090847", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP071848", null, null, "24hpf_wt_Plate1.2_R1_001.fastq.gz 24hpf_wt_Plate1.2_R2_001.fastq.gz", "fastq fastq", 830338169.0, 5505101.0, "GSM2090847 r2", "0:75.49 1:75.34", "A:254439239;C:150818963;G:164159782;T:260734365;N:185820", 75, 75, null, null, 254439239, 150818963, 164159782, 260734365, 185820, "SRX1637081", "SRS1342935", "SRA385812", "GEO", "Rene Ketting, RNA silencing, IMB", 2, 0.03438, 0.07482, 0.02833, 0.04098, 0.98867, 0.95868, 0.55778, 0.56233, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2016-03-16", "Pharyngula", "Embryo", "Gonad", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 157, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"devstage_curation_coarse\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "Embryo", "p1": "Gonad"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 145, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&experiment.library_strategy=miRNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 154, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad", "results": [{"value": "cDNA", "label": "cDNA", "count": 126, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&experiment.library_selection=cDNA", "selected": false}, {"value": "RANDOM PCR", "label": "RANDOM PCR", "count": 16, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&experiment.library_selection=RANDOM+PCR", "selected": false}, {"value": "size fractionation", "label": "size fractionation", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&experiment.library_selection=size+fractionation", "selected": false}, {"value": "RANDOM", "label": "RANDOM", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&experiment.library_selection=RANDOM", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 129, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 141, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&experiment.platform=ILLUMINA", "selected": false}, {"value": "PACBIO_SMRT", "label": "PACBIO_SMRT", "count": 16, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&experiment.platform=PACBIO_SMRT", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad", "results": [{"value": "Embryo", "label": "Embryo", "count": 157, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation=Gonad", "selected": true}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad", "results": [{"value": "Pharyngula", "label": "Pharyngula", "count": 46, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&devstage_curation=Pharyngula", "selected": false}, {"value": "Gastrula", "label": "Gastrula", "count": 38, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&devstage_curation=Gastrula", "selected": false}, {"value": "Blastula", "label": "Blastula", "count": 34, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&devstage_curation=Blastula", "selected": false}, {"value": "Zygote", "label": "Zygote", "count": 16, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&devstage_curation=Zygote", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 14, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&devstage_curation=Undetermined", "selected": false}, {"value": "Segmentation", "label": "Segmentation", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&devstage_curation=Segmentation", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&devstage_curation=Multi-stage", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad", "results": [{"value": "Reproductive System", "label": "Reproductive System", "count": 157, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&tissue_curation_coarse=Reproductive+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad", "results": [{"value": "Gonad", "label": "Gonad", "count": 157, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad", "results": [{"value": "celseq", "label": "celseq", "count": 100, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&technology=celseq", "selected": false}, {"value": "unknown", "label": "unknown", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&technology=unknown", "selected": false}, {"value": "bulk", "label": "bulk", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&technology=bulk", "selected": false}, {"value": "generic-scrnaseq-only", "label": "generic-scrnaseq-only", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&technology=generic-scrnaseq-only", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": "40686", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Gonad&_next=40686", "private": false, "allow_execute_sql": true, "query_ms": 107.75447099877056}