WormMine: AnatomyTerm WBbt:0008378

• Definition: Nucleated cell which has a diploid set of chromosomes.
• Name: somatic cell
• Primary Identifier: WBbt:0008378
• Synonym: FMA:72300

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0 Expression Clusters

106 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: Expr10747
• Pattern: TCER-1::GFP was present in all germ cell nuclei, starting from the mitotic cells at the distal end to the oocytes at the proximal end of the gonad. TCER-1::mCherry showed an identical expression pattern (data not shown). Both of these transgenes were expressed in somatic nuclei as well (data not shown). TCER-1 reporter fusions were present at the inner periphery of the nucleus, often in a crescent-shaped fashion. However, we did not detect any fluorescence signal corresponding to either of the TCER-1 reporter fusions in the cytoplasm.
• Subcellular Localization: TCER-1 reporter fusions were present at the inner periphery of the nucleus.

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

• Primary Identifier: Expr15209
• Pattern: Using a novel manf-1 reporter allele, we confirmed that the MANF protein is expressed throughout development and is expressed in most somatic cells in L1 larvae, which is the developmental stage that we focused on in the current study.

• Primary Identifier: Expr16332
• Pattern: We observed GFP expression in somatic cells in six candidates (his-61p, his-64p, hil-4p, rla-0p, rpl-7Ap, and Y37E3.8p) in addition to the germline. Expression in the soma from his-61p, his-64p, and hil-4p was limited compared to the broad expression found using rla-0p, rpl-7Ap, and Y37E3.8p.

• Primary Identifier: Expr16246
• Pattern: At larval stage, GFP::SET-21 was expressed in soma but GFP::SET-32 was expressed in germline.
• Subcellular Localization: GFP::SET-21 exclusively located in the nucleus but GFP::SET-32 located in both the nucleus and cytoplasm in embryos.

• Primary Identifier: Expr7990
• Remark: Picture: Fig. 3B.
• Pattern: At the nonpermissive temperature, glp-4(bn2ts) mutants produce a somatic gonad that is largely devoid of germ cells, fem-2(e2105ts) mutants make oocytes but no sperm, and fem-3(q20sd) mutants make sperm but no oocytes. gla-3 expression was detected in all three mutant backgrounds, demonstrating that gla-3 is expressed in both germline and soma.

• Primary Identifier: Expr9995
• Pattern: vha-12 is broadly expressed in most, if not all, somatic cell-types in larvae and adults. Robust GFP expression is observed in the H-shaped excretory cell, the excretory pore, intestine, and hypodermal cells. GFP reporter expression is observed at low levels in muscle. Consistent with the uncoordinated phenotype, expression is observed in all neurons.

• Primary Identifier: Expr10555
• Pattern: In WT animals, SID-5 was detected by immunohistochemistry in somatic cell types including intestine, muscle, neurons, somatic gonad, and embryos, but not in the germline. Transcriptional and translational sid-5 GFP reporters were expressed in most, if not all, somatic tissues. The translational fusion protein appeared to associate with membranes in the cytoplasm of intestinal cells.
• Subcellular Localization: SID-5 associates, at least partially, with late endosomes.

• Primary Identifier: Expr14944
• Pattern: We performed smFISH for endogenous car-1 mRNAs and observed widespread expression in somatic cells including touch receptor neurons (TRNs) and other neurons besides the germline.

• Primary Identifier: Expr11575
• Remark: Temporal description
• Pattern: Transcription was detected as early as 100 min into development in all cells except the germline. Later in embryogenesis, expression was restricted to neurons, epidermal cells, and cells of the pharynx. In adults, expression was found in head and tail neurons and in neurons along the body, in addition to strong expression in the pharynx and spermatheca.
• Subcellular Localization: A translational fusion protein had the following subcellular localization. In embryos, SRGP-1::GFP localized specifically to sites of contact between cells. When first detected, approximately 150 min after first cleavage, SRGP-1::GFP appeared along most cell-cell contacts. After epidermal differentiation, SRGP-1 appeared uniformly along all apical junctions, where it colocalized with cadherin complex components. SRGP-1 did not colocalize appreciably with DLG-1/discs large and AJM-1, but appeared to reside predominantly apical to the DLG-1-AJM-1 complex. Immunostaining of endogenous SRGP-1 with a polyclonal antibody validated the observations made with the GFP-tagged protein.

• Primary Identifier: Expr9980
• Pattern: PAN-1 is a P granule component that co-localizes with GLH-1 in the germline from the first larval stage throughout germline development; it is present in P granules surrounding the germ cell nuclei throughout oogenesis, until oocytes mature and P granules disperse in the oocyte cytoplasm, and throughout spermatogenesis, except in mature sperm. In addition, PAN-1 is found in the pharynx and intestine, the somatic tissues associated with molting.
• Subcellular Localization: At the L1 stage, PAN-1 is seen in the pharynx and on the membranes of intestinal cells; PAN-1 also localizes to punctate granules that surround the nuclei of Z2 and Z3, the two germline precursor cells. This perinuclear localization to the germline precursor cells is characteristic of P granules and PAN-1 persists at this location as the wild type larvae mature. As wild type larvae mature, PAN-1 remains localized around the developing germ cell nuclei. Immuno-reactivity of older larvae to PAN-1 antibody revealed a strong, uniform cytoplasmic distribution in somatic tissue, as well as a distinct peri-nuclear pattern for PAN-1 around the germ cell nuclei, confirmed as localizing with P granules by confocal images that show the co-localization of PAN-1 with the P-granule proteins GLH-1 and PGL-1 as also seen for PGL-1 in the L3 larva. During embryogenesis, PAN-1 protein is uniformly distributed throughout the cytoplasm of the germline and somatic blastomeres, as seen for pan-1 mRNA, with no obvious concentration of PAN-1 in the P granules. PAN-1 was not seen in P granules at any stage of embryogenesis. In the adult worm PAN-1 is most obvious in the germline P granules shown here in a single gonad arm of an adult hermaphrodite. In confocal images, PAN-1 co-localizes with GLH-1 and PGL-1 throughout the germline, beginning with the distal mitotic region through to the proximal region, which contains maturing oocytes. After oocyte maturation, the nuclear membrane breaks down and PAN-1, as is the case for other P-granule proteins, disperses into the cytoplasm. The perinuclear localization of PAN-1 is most obvious in the meiotic, pachytene region of the germline, as also seen with PGL-1. In the adult male testis, PAN-1 is also present in P granules co-localizing with GLH-1 throughout spermatogenesis. However, PAN-1 is not present in mature sperm. Along with its germline location, PAN-1 is also concentrated in the somatic tissue of the pharynx in adult hermaphrodites, males, and larvae, a presence that is less obvious in the L1 stage and is very obvious in the adult, while PAN-1 reacts at decreased levels in the adult gut. PAN-1 protein was detected throughout the cytoplasm of both somatic and germline tissues in adult hermaphrodite worms, while the pre-immune sera were negative.

• Primary Identifier: Expr12807
• Pattern: The H19N07.3 protein is expressed in all somatic cell nuclei.

• Primary Identifier: Expr16307
• Pattern: chd-1 gene is broadly expressed in the worm. We observed broad expression throughout worms including in the germ line and somatic tissues. Interestingly, while sfGFP was evenly diffuse in somatic cells and the distal germ line, it concentrated strongly in the nuclei of oocytes and early embryonic cells.

• Primary Identifier: Expr16308
• Pattern: We imaged CHD-1::sfGFP (bs125) worms and found that CHD-1::sfGFP was enriched in nuclei throughout the worm. This included all germ-line nuclei and many somatic cells such as the intestinal cells and cells of the pharynx and somatic gonad. At a subcellular level, the only structure in which we detected CHD-1 enrichment was the nucleus. Importantly, we did not detect localization to centrosomes. While CHD-1::sfGFP expression was detected in oocyte nuclei, the levels were lower than other germ-line nuclei.

• Primary Identifier: Expr12358
• Pattern: The GFP::RDE-12 protein appeared to localize in discrete cytoplasmic foci in both the soma and germline. Wild-type RDE-12 colocalized with PGL-1 in perinuclear P granules in the germline.

• Primary Identifier: Expr12359
• Subcellular Localization: GFP::RDE-12 localized throughout the cytoplasm and in perinuclear foci in somatic cells and colocalized prominently with P granules in the germline. Confocal microscopy revealed that perinuclear GFP::RDE- 12 foci in somatic cells sometimes overlap with nuclear pores stained with a nucleoporin-specific antibody.

• Primary Identifier: Expr15445
• Pattern: The endogenous C-terminal TOP-2::GFP is expressed in nuclei throughout the worm soma, germ line, and in developing embryos. In the germ line, TOP-2 is expressed from the mitotic zone at the distal tip to the most proximal oocyte, which is preparing for fertilization.

• Primary Identifier: Expr14527
• Pattern: In animals raised under normoxia, the nhr- 57::gfp reporter was weakly expressed in several somatic cells including the intestinal cells, but not in the VPCs before VI. After the first round of VPC divisions in mid-L3 larvae, nhr-57::gfp expression became visible in the descendants of the uninduced distal VPCs but remained undetectable in the descendants of the induced proximal VPCs until they had completed their last round of division and terminally differentiated.

• Primary Identifier: Expr13667
• Pattern: LIN-15B expression was first detected in the germline in the L4 stage in nuclei near the end of the pachytene region where germ cells initiate oogenesis. Nuclear LIN-15B was present in all oocytes and inherited by all embryonic blastomeres, including the germline P blastomeres. LIN-15B remained present at high levels in all somatic nuclei throughout embryogenesis. In contrast, in the germ lineage, LIN- 15B levels decreased sharply during the division of the germline founder cell P4 that generates the two PGCs. LIN-15B expression remained at background levels in PGCs throughout embryogenesis.

• Primary Identifier: Expr15978
• Pattern: Live imaging of worms expressing wrmScarlet::TDPT-1 showed that TDPT-1 is expressed in both the soma and germ line. TDPT-1 was found within nuclei throughout the germ line and within the spermatheca, somatic cell nuclei, and in the nuclei of developing embryos in hermaphrodites at 20°C.

• Primary Identifier: Expr11044
• Pattern: The cerEx01 transgene showed widespread expression of rsr-2 in somatic lineages but a restricted pattern in the germline in which the GFP signal was low or absent in the most distal part where mitosis takes place. In addition, we corroborated the exclusion of rsr-2 expression from the distal end of the germline at mRNA level by in situ hybridization.

• Primary Identifier: Expr13515
• Pattern: SID-3 was detected in somatic cells with stronger expression observed in the intestinal cells. SID-3 colocalizes with VIRO-2 to the apical side of the intestine.

• Primary Identifier: Expr13516
• Pattern: VIRO-2 was detected in somatic cells with stronger expression observed in the intestinal cells. VIRO-2 colocalizes with SID-3 to the apical side of the intestine.

• Primary Identifier: Expr10101
• Remark: Temporal description
• Subcellular Localization: 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.

• Primary Identifier: Expr12747
• Pattern: Animals carrying this CEBP-2::GFP transgene express GFP broadly in somatic tissues including the intestine, with strong nuclear localization.

• Primary Identifier: Expr13852
• Pattern: HMG-4 is expressed predominantly in the soma with high intensity in the intestine and has only weak expression in the germline.

• Primary Identifier: Expr14645
• Pattern: TRA-2B:HA was detected exclusively in the nuclei of dissected tissues of larvae and adults, including those of the intestine and somatic gonad (sheath and distal tip cells). Nuclear localization of TRA-2B in somatic cells is consistent with previous studies using antibodies (Shimada et al., 2006) and reporter transgenes (Lum et al., 2000; Mapes et al., 2010)

• Primary Identifier: Expr15940
• Pattern: In early embryos, CSR-1 localizes to both the germline and somatic blastomeres. CSR-1 in the somatic blastomeres is mainly cytoplasmic and persists for several cell divisions.

• Primary Identifier: Expr11851
• Pattern: the Pvbh-1::GFP::vbh-1::vbh-1 reporter showed high expression in both soma and germline. GFP::VBH-1 expression from line xmSi06 was observed in the cytoplasm of intestinal cells, with a clear enrichment in the apical pole in control animals. Although xmSi06 animals show somatic vbh-1 expression the authors cannot discard that this is an artifact of this transgene.
• Subcellular Localization: Extruded gonads and embryos from xmSi05 adults (soma and germline expression) were placed on a slide and observed under an epifluorescence microscope to analyze the location of the transgene. The authors have previously reported that VBH-1 is expressed in cytoplasmic foci, perinuclear germ granules termed P granules in germ cells, and diffusely expressed throughout the cytoplasm of all blastomeres [WBPaper00031012]. The GFP transgene showed the same expression as the endogenous VBH-1 in germline cells and embryos suggesting that the expression of the transgene was similar to endogenous VBH-1.

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1 Parents

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