WormMine: AnatomyTerm WBbt:0005784

• Definition: cell line which early in development becomes differentiated from the remaining somatic cell line, and alone has the potential to undergo meiosis and form gametes.
• Name: germ line
• Primary Identifier: WBbt:0005784
• Synonym: germline

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59 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
Germline ablation	Genes that showed differential expression in the comparision of germline-ablated animals fed on E. coli OP50 versus un-ablated animals fed E. coli OP50.	Differential expression was calculated by empirical Bayes method using the eBayes function, and control of FDR was employed as the multiple testing correction. Authors used cutoff of absolute log2 fold change greater than or equal to 1.5 AND p_value less than or equal to 0.05 to call differentially expressed genes.	WBPaper00041466:PP_germline-ablation_regulated
	Genes that showed increased expression in wdr-5(ok1417) comparing with in N2.	Statistical analysis for misexpression was performed using a moderated t test from the package limma. All genes with a false discovery rate (FDR) of <= 5% (p <= 0.05) were selected as differentially regulated.	WBPaper00045861:wdr-5(ok1417)_upregulated
	Transcripts that showed significantly decreased expression in dissected female germline comparing to in dissected male germline.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:female_vs_male_downregulated
	Transcripts that showed significantly increased expression in oocyte germline cells comparing to in mitosis germline cells.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:oocyte_vs_mitosis_upregulated
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
	Genes that showed increased expression after germline ablation comparing to un-ablated animals.	The differential expression between germline-ablated versus gonad-ablated animals was computed via the functions makeContrasts and contrasts.fit in the limma package in R/Bioconductor.	WBPaper00045571:germline-ablation_upregulated
	Genes that showed decreased expression in wdr-5(ok1417) comparing with in N2.	Statistical analysis for misexpression was performed using a moderated t test from the package limma. All genes with a false discovery rate (FDR) of <= 5% (p <= 0.05) were selected as differentially regulated.	WBPaper00045861:wdr-5(ok1417)_downregulated
	Transcripts enriched in germline by comparing dissected germline tissue with dissected intestine tissue, both injected with empty RNAi vector.	Genes were determined germline-enriched if the lowest expression value (log2(FPKM+1)) observed in the germline empty vector samples was at least 2-fold higher than the highest expression value observed in the intestine empty vector samples.	WBPaper00051039:germline_enriched
	Transcripts that showed significantly decreased expression in mitosis germline cells comparing to in meiosis germline cells.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:mitosis_vs_meiosis_downregulated
	Transcripts that showed significantly decreased expression in oocyte germline cells comparing to in mitosis germline cells.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:oocyte_vs_mitosis_downregulated
	Transcripts expressed in germline, according to RNA tomography.	RNA tomography	WBPaper00055648:germline_expressed
	Genes that showed decreased expression after germline ablation comparing to un-ablated animals.	The differential expression between germline-ablated versus gonad-ablated animals was computed via the functions makeContrasts and contrasts.fit in the limma package in R/Bioconductor.	WBPaper00045571:germline-ablation_downregulated
	Transcripts that showed significantly decreased expression in the germline of iff-1(RNAi) animals comparing to the germine of N2 animals applied with control vector at 15C.	Statistical comparisons were made by two-tailed t-test, n=3 (each replicate contains 150 extruded germ lines from N2 wild-type worms), P < 0.01 was considered significant.	WBPaper00057288:iff-1(RNAi)_downregulated_transcript
	Transcripts activated by glp-1(ar202), a gain-of-function allele of glp-1, in the gld-2(q497) gld-1(q485) background at young adult stage, comparing to glp-1(q175) null allele.	edgeR fold change >= 2, FDR <= 0.05.	WBPaper00059440:GLP-1_activated
	Transcripts activated by lag-1(oz536oz537), in the gld-2(q497)gld-1(q485); glp-1(ar202) background at young adult stage after 48 hours of 1mM auxin treatment.	edgeR fold change >= 2, FDR <= 0.05.	WBPaper00059440:LAG-1_activated_48hr-auxin
	Genes that showed increased expression in set-2(ok952) comparing with in N2.	Statistical analysis for misexpression was performed using a moderated t test from the package limma. All genes with a false discovery rate (FDR) of <= 5% (p <= 0.05) were selected as differentially regulated.	WBPaper00045861:set-2(ok952)_upregulated
	Genes that were enriched in spermatogenic fem-3(q96gf) gonads comparing to in oogenic fog-2(q71), according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Spermatogenic
	Transcripts that showed significantly increased expression in dissected female germline comparing to in dissected male germline.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:female_vs_male_upregulated
	Single-cell RNA-Seq cell group 1_0 with unidentified tissue expression pattern.	scVI 0.6.0	WBPaper00065841:1_0
	Transcripts that showed significantly increased expression in mes-4(bn73) comparing to in control animals in early germ cells (EGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mes-4(bn73)_upregulated_EGCs
Temperature shift: 15C vs 20 C.	Transcripts that showed significantly decreased expression in N2 animals treated with empty RNAi vector at 15C comparing to N2 animals treated with empty RNAi vector at 20C.	Statistical comparisons were made by two-tailed t-test, n=3 (each replicate contains 150 extruded germ lines from N2 wild-type worms), P < 0.01 was considered significant.	WBPaper00057288:Cold_downregulated_transcript
	Single-cell RNA-Seq cell group 3_0 expressed in germline.	scVI 0.6.0	WBPaper00065841:3_0
	Transcripts that showed significantly increased expression in the germline of iff-1(RNAi) animals comparing to the germine of N2 animals applied with control vector at 15C.	Statistical comparisons were made by two-tailed t-test, n=3 (each replicate contains 150 extruded germ lines from N2 wild-type worms), P < 0.01 was considered significant.	WBPaper00057288:iff-1(RNAi)_upregulated_transcript
	Transcripts that showed significantly decreased expression in jmjd-5(zr1234) germine comparing to in N2 germline at 25 centigrade. Positive log2FC designates downregualted genes and vice versa.	DESeq2, adjusted p value < 0.01 and absolute log2FC > = 1.	WBPaper00062156:jmjd-5(zr1234)_downregulated_germline
	Abundant spermatogenesis enriched proteins copurified with chromatin.	N.A.	WBPaper00028451:Abundant_spermatogenesis_enriched
	Genes that were enriched in oogenic fog-2(q71) gonads comparing to in spermatogenic fem-3(q96gf), according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Oogenic
	Transcripts that showed significantly decreased expression in mes-4(bn73) comparing to in control animals in early germ cells (EGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mes-4(bn73)_downregulated_EGCs
Temperature shift: 15C vs 20 C.	Transcripts that showed significantly increased expression in N2 animals treated with empty RNAi vector at 15C comparing to N2 animals treated with empty RNAi vector at 20C.	Statistical comparisons were made by two-tailed t-test, n=3 (each replicate contains 150 extruded germ lines from N2 wild-type worms), P < 0.01 was considered significant.	WBPaper00057288:Cold_upregulated_transcript
	Low abundant spermatogenesis enriched proteins copurified with chromatin.	N.A.	WBPaper00028451:Low_abundance_spermatogenesis_enriched
	Single-cell RNA-Seq cell group 57_1 expressed in germline.	scVI 0.6.0	WBPaper00065841:57_1

706 Expression Patterns

• Primary Identifier: Expr16078
• Pattern: In adult hermaphrodites, CBR-CSR-1 was enriched in both germline and somatic nuclei. We observed CBR-CSR-1 in association with oocyte nuclei and enriched on chromosomes in oocytes. Again, we did not reliably observe CSR-1 localization to perinuclear and cytoplasmic granules, which would be indicative of P granules. CBR-CSR-1 was also enriched in somatic gut nuclei, further supporting a nuclear role for this Argonaute.

• Primary Identifier: Expr4839
• Remark: Picture: Figure 4A.
• Pattern: When the adult glp-4(bn2ts) mutants were cultured at 25 centigrades, the rog-1 mRNA was undetectable. In contrast, the mRNA expression of a ubiquitously expressed gene, act-1, was decreased but detectable at the non-permissive temperature in the mutant worms. These results indicate that the rog-1 gene is preferentially expressed in the germ cells, implying a role in these cells.

• Primary Identifier: Expr4795
• Remark: The subcellular patterns observed in experiments using anti-HAF-6 antibody were similar to the patterns of GFP expression observed in transgenic animals expressing the HAF-6::GFP fusion protein.
• Pattern: HAF-6 was predominantly expressed in intestinal and germline tissue.
• Subcellular Localization: In double-labeling experiments, the anti-HAF-6 antibody did not decorate the same cellular compartment as a mitochondrial antibody (anti-Complex IV). Authors did observe co-compartmentalization using anti-HAF-6 and anti-Calreticulin antibodies, indicating that HAF-6 likely resides in the endoplasmic reticulum and not in mitochondria. HAF-6 localization extended to perinuclear regions in germline tissue, which is consistent with an endoplasmic reticulum (ER) localization. However, localization of HAF-6 to the nuclear periphery was not prominent in intestinal tissue.

• Primary Identifier: Expr4912
• Remark: Picture: Fig. 3a.
• Pattern: An abundant band of ~3.5 kb corresponding to the predicted vbh-1 mRNA(s) was highly expressed in animals with feminized gonads (fem-1). vbh-1 was also detected at lower levels in wild type (N2) and masculinized (fem-3) animals. The vbh-1 transcript was reduced significantly in glp-4(bn2) adult hermaphrodites, in which the germline is underproliferated showing that vbh-1 mRNA is germline enriched and is expressed during both spermatogenesis and oogenesis.

• Primary Identifier: Expr4913
• Remark: Picture: Fig. 3b,c.
• Pattern: Western blot analysis using glp-4(bn2) mutant protein extracts (that possess virtually no germ line) showed that VBH-1 expression is germline-specific. In contrast, VBH-1 was abundant in fem-1(hc17) and fem-3(q20gf) animals that produce only oocytes or only sperm, respectively. Accumulation of any specific VBH-1 isoforms, in whole animal extracts from L4 hermaphrodites, feminized animals, masculinized animals or males, was not observed. These experiments suggest that the VBH-1 protein is germline-specific, and is expressed during both spermatogenesis and oogenesis.

• Primary Identifier: Expr4368
• Pattern: Exclusively localized in germ cells. No significant signals were detected when sense probes were used.

• Primary Identifier: Expr4369
• Pattern: Exclusively localized in germ cells. No significant signals were detected when sense probes were used.

• Primary Identifier: Expr4364
• Pattern: CPB-3 was barely detected in an extract of glp-4(bn2) adult animals cultured at the restrictive temperature, which lacked germ cells, suggesting that CPB-3 was enriched in the germline at the adult stage.

• Primary Identifier: Expr4365
• Remark: No detailed description on cellular expression pattern in other tissues.
• Pattern: In gonads of either L4 or young adult wild-type hermaphrodites, CPB-3 was barely detectable at the most distal end, was gradually expressed in the mitotic region, and reached high levels in the transition zone and the pachytene region. Its expression was then gradually decreased in the proximal pachytene region, and no staining was observed in mature sperm and oocytes.
• Subcellular Localization: Staining of dissected gonads with anti-CPB-3 antibodies appeared specific because no substantial signal was detected in the cpb-3(tm1746) mutant. CPB-3 was stained predominantly in the cytoplasm.

• Primary Identifier: Expr4243
• Pattern: In wild-type animals, cki-2 mRNA is normally present in the hermaphrodite germ line but is excluded from the distal mitotic zone.

• Primary Identifier: Expr4226
• Pattern: LAG-2/Venus protein was found in DTC and also weakly in germ cells, suggesting that the fusion protein is secreted by DTC to proximal gonadal cells.

• Primary Identifier: Expr4206
• Pattern: In situ expression data obtained from the Nematode Expression Pattern Database (http://nematode.lab.nig.ac.jp/): a low level of ego-1 mRNA was detected in the L4 and adult germline. A very low level of mRNA, which is presumably maternal, was also visible in young embryos.

• Primary Identifier: Expr4579
• Remark: scrm-1 in this paper refers to T22H2.5, the official name is plsc-2 according to WS174.
• Subcellular Localization: Wild-type C. elegans embryos stained with anti-SCRM-1 antibodies displayed a plasma-membrane staining pattern that was observed in all cells throughout embryogenesis, whereas no specific staining was observed in scrm-1(tm805) mutant embryos. Similar plasma-membrane localization of SCRM-1 was observed in germ cells of wild-type animals, but not in those of scrm-1(tm805) animals.

• Primary Identifier: Expr4653
• Remark: No detailed description expression patterns in other life stages.
• Pattern: In L4 germ lines, authors also examined SP56, the earliest known marker of sperm differentiation: SP56 antibodies recognize a minor sperm protein in primary, secondary, and mature spermatocytes. SP56 was first seen approximately 6 hr after the molt from L3 to L4 (3 hr, n = 17; 6 hr, n = 14; 10 hr, n = 19), where staining was limited to the proximal-most germ cells. As animals matured through the L4 stage, the SP56 domain expanded distally to include an increasing number of cells. Importantly, FOG-1 and SP56 were not present in the same cells at the same time. Instead, FOG-1 staining preceded SP56 staining in both time and space. For example, the proximal-most germ cells expressed FOG-1 in late L3 and early L4 ; those same cells expressed SP56 in mid-L4 (6 hr), when the FOG-1 domain had moved distally. Authors conclude that in wild-type larvae, FOG-1 is expressed transiently in germ cells destined for spermatogenesis. In wild-type larvae, FOG-1 became easily detectable in the second half of L2. In early L3 larvae, FOG-1 levels increased in the proximal region of most germ lines, and by late L3, FOG-1 staining was strong in that proximal region of all germ lines. FOG-1 remained abundant for approximately the first half of the L4 stage, although its location moved distally within the germ line.

• Primary Identifier: Expr4496
• Pattern: The spatio-temporal mRNA expression of asb-1 in postembryonic development matches the characteristic pattern of germline-specific genes; asb-1 mRNA was expressed specifically in the germ line since the early L1 stage, when germ line consists of two primordial germ cells, Z2 and Z3.

• Primary Identifier: Expr4544
• Remark: PUF-5 expression during late embryonic and larval development has not been investigated.
• Pattern: PUF-5 expression was first detected near the gonad bend, where germ cell nuclei were in late stages of pachytene, and increased as germ nuclei exited pachytene and moved into the proximal arm, with highest expression in developing oocytes in the distal portion of the proximal gonad. Remarkably, PUF-5 staining abruptly disappeared in the proximal-most one to three oocytes and was very low in early stage embryos (n > 50).
• Subcellular Localization: PUF-5 staining in oocytes was mostly cytoplasmic, but some PUF-5 was detected in perinuclear and cytoplasmic P granules as judged by co-localization with PGL-1.

• Primary Identifier: Expr4504
• Pattern: MRG-1 is highly enriched in nuclei and concentrated on chromatin. In early embryos, MRG-1 is present in the nuclei of all blastomeres. In late embryos and young larvae, MRG-1 staining is higher in the nuclei of the two primordial germ cells, Z2 and Z3, than in somatic blastomeres. In larvae and adults, MRG-1 staining is seen primarily in the nuclei of germ cells, although it is also faintly visible in the nuclei of several somatic cell types, including intestinal cells. In the adult germ line, all germ nuclei in the mitotic and meiotic regions are stained. These results demonstrate that MRG-1 is present in the germ line at all stages of development and is maternally loaded into embryos. In addition, zygotically expressed MRG-1 is produced in all cells by at least the 100-cell stage; it accumulates to higher levels in the primordial germ cells than in somatic tissues.
• Subcellular Localization: Expressed in nuclei.

• Primary Identifier: Expr4093
• Remark: Curated by authors based on online in-situ hybridization database (Y. Kohara, personal communication; http://nematode.lab.nig.ac.jp).
• Pattern: Expressed in germline(faint)/embryo.

• Primary Identifier: Expr14361

• Primary Identifier: Expr4160
• Remark: Curated by authors based on online in-situ hybridization database (Y. Kohara, personal communication; http://nematode.lab.nig.ac.jp).
• Pattern: Expressed in proximal germline.

• Primary Identifier: Expr14372

• Primary Identifier: Expr11005
• Pattern: RGA-4 is expressed in the germ line and in the early embryo. Expression seems to cease around the 100- to 200-cell stage.

• Primary Identifier: Expr14374

• Primary Identifier: Expr2372
• Pattern: hip-1::CFP expression was restricted to the germline, gonad, pharynx, and several neurons that extend axons along the dorsal and ventral nerve cords.

• Primary Identifier: Expr12194
• Subcellular Localization: In the germline, RDE-8 localizes to P-Granule-Associated mutator foci.

• Primary Identifier: Expr14760
• Pattern: We observed cytosolic tagged GCK-2 throughout vulval development (VPCs). We observed the expression of GCK-2 in all tissues, including the germline and embryos in the adult hermaphrodite.

• Primary Identifier: Expr13971
• Subcellular Localization: Immunofluorescence confirmed that MORC- 1::3xFLAG is expressed in the nuclei of germline and somatic cells.

• Primary Identifier: Expr13972
• Subcellular Localization: Co-immunofluorescence revealed that MORC-1::3xFLAG localizes adjacent to, but not overlapping with, H3K9me3 in the distal germline. Furthermore, in pachytene nuclei, which have highly condensed chromosomes that can be visualized with DAPI staining, we observed MORC-1::3xFLAG at the nuclear periphery and adjacent to, but not overlapping with, the condensed chromosomes, seemingly as a barrier around condensed chromatin.

• Primary Identifier: Expr1200067
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr4062
• Remark: Curated by authors based on online in-situ hybridization database (Y. Kohara, personal communication; http://nematode.lab.nig.ac.jp).
• Pattern: Expressed in distal germline.

0 Life Stages

2 Parents

Definition	Name	Synonym	Primary Identifier
	reproductive system		WBbt:0005747
Association of cells with a common embryological origin or pathway and similar structure and function. Usually, cells of a tissue are contiguous at cell membranes and may be of one or more types. Tissues aggregate to form organs.	Tissue		WBbt:0005729