WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Anatomy Term :

Definition  member of a set of two cells that generate exclusively sperm and ovum. Name  germline precursor cell
Primary Identifier  WBbt:0006849 Synonym  PGC

3 Children

Definition Name Synonym Primary Identifier
Germ line precursor cell Z2 lineage name: P4.p WBbt:0004576
Germ line precursor cell Z3 lineage name: P4.a WBbt:0004575
a cell, of either sex, directly concerned in the production of a new organism. germ cell   WBbt:0006796

31 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly increased expression in mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage. DESeq2(v1.32.0), FDR < 0.05. WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs
  Genes that showed expression levels higher than the corresponding reference sample (embryonic 0hr reference). A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. WBPaper00037950:germline-precursors_blastula-embryo_expressed
  Transcripts that showed significantly decreased expression in mes-3(bn199) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage. DESeq2(v1.32.0), FDR < 0.05. WBPaper00064315:mes-3(bn199)_downregulated_PGCs
  Transcripts that showed significantly decreased expression in mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage. DESeq2(v1.32.0), FDR < 0.05. WBPaper00064315:mrg-1(qa6200)_downregulated_PGCs
  Transcripts that showed significantly increased expression in mes-3(bn199) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage. DESeq2(v1.32.0), FDR < 0.05. WBPaper00064315:mes-3(bn199)_upregulated_PGCs
  Transcripts that were depleted in embryonic primordial germ cells (PGCs) comparing to in whole embryo, according to NuGen RNAseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:PGCs_depleted_NuGen
  Transcripts that showed significantly decreased expression in L1 larva comparing to in embryo, in primordial germ cells (PGCs) of N2 animals fed with control bacteria, according to SMARTseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:embryo-to-L1_downregulated_WT_SMARTseq
  Transcripts that showed significantly decreased expression in starved nos-1(gv5)nos-2(RNAi);lin-15B(RNAi) comparing to in starved nos-1(gv5)nos-2(RNAi), in primordial germ cells (PGCs) at L1 larva, according to Truseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:lin-15B(RNAi)_downregulated_starved-L1_Truseq
  Transcripts that showed significantly increased expression in fed nos-1(gv5)nos-2(RNAi) comparing to in starved wild type, in primordial germ cells (PGCs) at L1 larva, according to Truseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:nos-1(gv5)nos-2(RNAi)_upregulated_fed-L1_Truseq
  Transcripts that showed significantly increased expression in nos-1(gv5)nos-2(RNAi) comparing to in wild type, in primordial germ cells (PGCs) at L1 larva, according to SMARTseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:nos-1(gv5)nos-2(RNAi)_upregulated_L1_SMARTseq
  Transcripts that showed significantly increased expression in starved nos-1(gv5)nos-2(RNAi) comparing to in starved wild type, in primordial germ cells (PGCs) at L1 larva, according to Truseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:nos-1(gv5)nos-2(RNAi)_upregulated_starved-L1_Truseq
  Genes significantly enriched (> 2x, FDR < 5%) in a particular cell-type versus a reference sample of all cells at the same stage. A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. WBPaper00037950:germline-precursors_embryo_enriched
  Genes that show selective expression in a subset of cell types vs broadly expressed in many cell types. Correspond to 20% - 57% of enriched_genes for a given cell type. A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. WBPaper00037950:germline-precursors_embryo_SelectivelyEnriched
  Transcripts that showed significantly decreased expression in nos-1(gv5)nos-2(RNAi) comparing to in wild type, in primordial germ cells (PGCs) at L1 larva, according to SMARTseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:nos-1(gv5)nos-2(RNAi)_downregulated_L1_SMARTseq
  Transcripts that were enriched in embryonic primordial germ cells (PGCs) comparing to in whole embryo, according to NuGen RNAseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:PGCs_enriched_NuGen
  Transcripts that showed significantly increased expression in fed mes-2(RNAi) comparing to in starved wild type, in primordial germ cells (PGCs) at L1 larva, according to Truseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:mes-2(RNAi)_upregulated_fed-L1_Truseq
  Transcripts that showed significantly increased expression in fed mes-4(RNAi) comparing to in starved wild type, in primordial germ cells (PGCs) at L1 larva, according to Truseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:mes-4(RNAi)_upregulated_fed-L1_Truseq
  Transcripts that showed significantly increased expression in L1 larva comparing to in embryo, in primordial germ cells (PGCs) of nos-1(gv5)nos-2(RNAi) animals, according to SMARTseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:embryo-to-L1_upregulated_nos-1(gv5)nos-2(RNAi)_SMARTseq
  Transcripts that showed significantly decreased expression in fed mes-4(RNAi) comparing to in starved wild type, in primordial germ cells (PGCs) at L1 larva, according to Truseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:mes-4(RNAi)_downregulated_fed-L1_Truseq
  Transcripts that showed significantly decreased expression in L1 larva comparing to in embryo, in primordial germ cells (PGCs) of nos-1(gv5)nos-2(RNAi) animals, according to SMARTseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:embryo-to-L1_downregulated_nos-1(gv5)nos-2(RNAi)_SMARTseq
  Transcripts that showed significantly decreased expression in mes-4(bn73) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage. DESeq2(v1.32.0), FDR < 0.05. WBPaper00064315:mes-4(bn73)_downregulated_PGCs
  Transcripts that showed significantly increased expression in nos-1(gv5)nos-2(RNAi) comparing to in wild type, in primordial germ cells (PGCs) at embryo stage, according to SMARTseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:nos-1(gv5)nos-2(RNAi)_upregulated_embryo_SMARTseq
  Transcripts that showed significantly increased expression in L1 larva comparing to in embryo, in primordial germ cells (PGCs) of N2 animals fed with control bacteria, according to SMARTseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:embryo-to-L1_upregulated_WT_SMARTseq
  Transcripts that showed significantly increased expression in starved nos-1(gv5)nos-2(RNAi);lin-15B(RNAi) comparing to in starved nos-1(gv5)nos-2(RNAi), in primordial germ cells (PGCs) at L1 larva, according to Truseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:lin-15B(RNAi)_upregulated_starved-L1_Truseq
  Transcripts that showed significantly decreased expression in fed nos-1(gv5)nos-2(RNAi) comparing to in starved wild type, in primordial germ cells (PGCs) at L1 larva, according to Truseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:nos-1(gv5)nos-2(RNAi)_downregulated_fed-L1_Truseq
  Transcripts that showed significantly decreased expression in starved nos-1(gv5)nos-2(RNAi) comparing to in starved wild type, in primordial germ cells (PGCs) at L1 larva, according to Truseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:nos-1(gv5)nos-2(RNAi)_downregulated_starved-L1_Truseq
  Transcripts that showed significantly increased expression in mes-4(bn73) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage. DESeq2(v1.32.0), FDR < 0.05. WBPaper00064315:mes-4(bn73)_upregulated_PGCs
  Transcripts that showed significantly decreased expression in fed mes-2(RNAi) comparing to in starved wild type, in primordial germ cells (PGCs) at L1 larva, according to Truseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:mes-2(RNAi)_downregulated_fed-L1_Truseq
  Transcripts that showed significantly decreased expression in met-1(bn200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage. DESeq2(v1.32.0), FDR < 0.05. WBPaper00064315:met-1(bn200)_downregulated_PGCs
  Transcripts that showed significantly decreased expression in nos-1(gv5)nos-2(RNAi) comparing to in wild type, in primordial germ cells (PGCs) at embryo stage, according to SMARTseq. For differential gene expression analysis, sets of independent mutant and control mapped reads (e.g biological replicates) were used in cuffdiff analysis. The cutoff of FDR(q value)=0.05 was used as a significance cutoff for all the analyses. WBPaper00053321:nos-1(gv5)nos-2(RNAi)_downregulated_embryo_SMARTseq

9 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr14697 We confirmed that endogenous XPC-1 was indeed expressed in the PGCs in L1 larva.  
    Expr15173   In early embryogenesis, ERM-1::GFP localized to the entire plasma membrane as well as the cytoplasm. As morphogenesis initiates, ERM-1::GFP was primarily detected at the apical surface of epithelial tissues and in primordial germ cells (PGCs). In larval stages, we observed apical localization of ERM-1::GFP in epithelial tissues including the intestine, seam cells, and excretory canals. In the syncytial germline, ERM-1 was associated with the entire plasma membrane but enriched at the apical domain.
Temporal description   Expr10101   Every germline nucleus displays a single large DAO-5-positive nucleolus. In the 2-cell stage embryo, the DAO-5 signal consists of 15-25 small dots of varying intensity distributed throughout each nucleus. Nucleolus-like structures were never observed at this early stage. The first appearance of a nucleolar structure occurs at the 6- to 8-cell stage, when larger spherical bodies (~0.5 mm in diameter) are immunodetected amidst the dot-like signals. Shortly after, the number of small dot-like signals that are detected decreases drastically (but some persist until later stages) and, except for the germline cell, all embryonic nuclei then harbor one or, in the vast majority, two distinct DAO- 5 or FIB-1 signals of equal size and intensity. This pattern remains broadly similar throughout embryogenesis, with the notable exception that intestinal nuclei often contain a single large DAO-5/FIB-1 positive nucleolus at later stages. It should be noted that at all embryonic stages examined, a substantial pool of diffuse nucleoplasmic DAO-5 was also detected. In the adult, the localization of DAO-5 was examined in more detail in the polyploid intestinal nuclei, which contain a large centrally-located nucleolus. In these nucleoli, the DAO-5 signal describes a hollow sphere that surrounds a DNA-poor core. In addition to being present in this portion of the nucleolus, DAO-5 is found in numerous small punctate structures throughout the nucleoplasm of intestinal nuclei. The DAO-5/FIB-1 positive nucleoplasmic foci that we observe in early C. elegans embryos are reminiscent of the prenucleolar bodies that are detected in the last stages of mitosis and that coalesce on rDNA in early G1.
    Expr15138 Strikingly, analysis of the previously uncharacterized H3.3 homologs revealed that his-70 and his-74 show germ line-restricted expression patterns. His-74 expression is restricted to the germ line at all stages of development in both males and hermaphrodites. HIS-74::GFP is only faintly visible in early embryos, and robustly reappears in the primordial germ cells (PGCs; the germ line precursor cells that will give rise to the entire germ line of the worm) and faintly in some cells surrounding the PGCs.  
    Expr13419 Transgenic lines containing stably integrated transgenes expressing an N-terminus fusion of 3FLAG::GFP to XND-1 showed identical expression patterns to that of immunostaining [Expr13418]; GFP was discernible only in the PGCs during embryonic development, expression persisted exclusively in the germline nuclei throughout larval development, and adult expression was observed in the mitotic zone through the late pachytene region with an autosomal bias (Wagner et al., 2010). XND-1 protein abruptly disappears from the late pachytene region and remains absent in mature oocytes and sperm. No somatic expression was observed with the transgenes or by immunostaining, confirming our prior conclusion from genetic studies that xnd-1 function appears limited to the germ line (Wagner et al., 2010).  
    Expr10149 HMR-1 is expressed in both primordial germ cells and endoderm.  
    Expr16011 MOG-7::degron::GFP expression was detected in germline nuclei throughout development, commencing in the primordial germ cells of L1 larvae through to oocytes and sperm in adults. Somatic expression of MOG-7::degron::GFP was detected in embryos from the 2-cell stage and throughout worm development in most, if not all, cells.  
    Expr11022 In WT worms, PGL-1, a key component of PGL granules, was exclusively expressed in the two germline precursor cells.  
    Expr13923    

0 Life Stages

1 Parents

Definition Name Synonym Primary Identifier
a cellular object that consists of subcellular components, expresses genes or functions. Cell Cell type WBbt:0004017