WormMine: AnatomyTerm WBbt:0004579

• Definition: Embryonic head hypodermal cell
• Name: XXXR
• Primary Identifier: WBbt:0004579
• Synonym: lineage name: ABarpappaa

1 Children

Definition	Name	Synonym	Primary Identifier
nucleus of pedigree ABarpappaa	ABarpappaa nucleus		WBbt:0003258

2 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Top 300 transcripts enriched in XXXL, XXXR according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:XXX
	Transcripts enriched in XXX according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:XXX_enriched

29 Expression Patterns

• Primary Identifier: Expr4399
• Pattern: The sdf-9p::RFP fusion was expressed exclusively in two head cells with position and morphology consistent with their identification as the XXX cells. In both strains containing GFP and RFP reporter constructs, GFP and RFP colocalized, indicating that eak-4, sdf-9, and eak-6 are all expressed in XXXL/R.

• Primary Identifier: Expr4401
• Pattern: Expressed specifically in XXX, as was an SDF-9::GFP fusion protein. Also variably expressed in the intestine, a common site of artifactual GFP expression.
• Subcellular Localization: Localize to the plasma membrane of the XXX cells. Membrane localization was also apparent in intestinal cells.

• Primary Identifier: Expr4402
• Pattern: Expressed specifically in XXX, as was an SDF-9::GFP fusion protein. Also variably expressed in the intestine, a common site of artifactual GFP expression.
• Subcellular Localization: Localize to the plasma membrane of the XXX cells. Membrane localization was also apparent in intestinal cells.

• Primary Identifier: Expr4400
• Pattern: Expressed specifically in XXX, as was an SDF-9::GFP fusion protein. Also variably expressed in the intestine, a common site of artifactual GFP expression.
• Subcellular Localization: Localize to the plasma membrane of the XXX cells. Membrane localization was also apparent in intestinal cells.

• Primary Identifier: Expr7894
• Remark: Picture: Figure 4A.
• Pattern: These animals exhibited specific GFP expression in two cells in the head, the position and morphology of which suggested that they were the XXX cells . Colocalization of GFP and RFP in animals coexpressing eak-3::GFP and sdf-9::RFP, which marks the cytoplasm of the XXX cells, confirmed that the eak-3 promoter is specifically active in the XXX cells.

• Primary Identifier: Expr15909
• Pattern: Out of the 12 promoters, 8 drove expression in the XXX cells at various levels (asic-1, dhs-17, F14H8.2, C06A1.3, asp-9, B0034.5, F52E1.5, and nlp-15), one was impossible to score (T22E5.6) because it also drove high expression in the pharynx located very close to the XXX cells, and three did not show detectable expression in XXX cells (in adults; mab-9, twk-39, and lgc-36).

• Primary Identifier: Expr12798
• Pattern: tat-3 reporter signal first appears in embryos in the developing pharynx. In the fully formed alimentary system, very strong GFP fluorescence is observed in the muscle, marginal and buccal epithelial cells of the pharynx, the pharyngeal-intestinal valve and, with lesser intensity, the rectal epithelial cells. Seam cells display very strong fluorescence as soon as this lineage becomes established during embryonic development. In adults, moderate to weak fluorescence seems to arise from the XXX cells, some unidentified cells in the head and tail regions and the hypodermis. In the reproductive system, tat-3 reporter expression begins in the distal tip cells (DTC) in L1 and in the anchor cell (AC) in early L3. GFP signal is later visible in the dividing progeny of the vulval precursor cells (VPCs). In late L4, the anchor cell fuses with the uterine seam cell (utse), which does not express the reporter. The vulval cells continue exhibiting moderate fluorescence into the adulthood.

• Primary Identifier: Expr2880
• Pattern: Relatively strong expression in ganglia in the head and tail and in the anterior pharynx. GFP was not seen in ASI, ASJ, ADF or ASG (0 of 86 animals). Fluorescence in the anterior ganglion, where XXX is found, is at least an order of magnitude less than in the bright cells of the ganglia posterior to the nerve ring. The weakness of fluorescence has precluded identification of specific cells, but sometimes weak fluorescence was seen in the ventral, anterior part of the ganglion, where XXX resides (seven out of 53 animals). A small number of animals show weak expression in the hypodermis, muscles, intestine and distal tip cells.
• Subcellular Localization: DAF-5::GFP from the rescuing construct mostly localizes to nuclei, which is consistent with the idea that DAF-5 is a transcription factor and functions in the nucleus. The intensity of fluorescence and nuclear localization of DAF-5::GFP from the rescuing construct was examined in wild-type and in TGF pathway mutants, including dauers, and no obvious differences was seen.

• Primary Identifier: Expr16363
• Pattern: DAF-2::mNeonGreen was detected in neurons, XXX cells, vulval cells, germ cells, and oocytes. In the last three types of cells, DAF-2::mNeonGreen had clear plasma membrane (PM) localization as expected for a cell surface receptor. In the neurons and XXX cells, a pair of specialized hypodermal cells of neural endocrine function, strong DAF-2::mNeonGreen signals were seen in the cell bodies and along processes. The DAF-2::mNeonGreen-expressing neurons included all of the ciliated sensory neurons marked by the osm-6 promoter-driven mCherry protein.

• Primary Identifier: Expr3222
• Remark: Reporter gene fusion type not specified.
• Pattern: Epidermis: ncr-1Ap(l)::gfp was strongly expressed in the excretory cell and rectal epithelial cells from the early L1 larval stage and through all life stages. Seam cell expression was first observed in the late L1 stage, while expression in the lateral hypodermis increased during the L3 stage and peaked during the L4 stage. Seam cell and hypodermal expression gradually decreased in the adult stage and was hardly visible among older adults. ncr-1Ap(s)::gfp was not expressed in the hypodermis under normal growth conditions, though lateral hypodermal but not seam cell expression was dramatically upregulated in starved animals of all developmental stages. No increase in hypodermal expression was seen in starved ncr-1Ap(l)::gfp animals. Intestine: Both ncr-1Ap(s)::gfp and ncr-1Ap(l)::gfp were strongly expressed throughout the intestine, with posterior intestinal expression consistently stronger than anterior expression. Musculature: ncr-1Ap(l)::gfp was strongly expressed in pharyngeal muscles, but not in body wall muscles. Nervous system: ncr-1Ap(s)::gfp and ncr-1Ap(l)::gfp were expressed in the same set of head and tail neurons and a pair of neuron-like cells identified as the XXX cells. According to their location and cellular morphology, the head neurons were identified as the pharyngeal neuron I6, the inner labial sensory neurons IL2s and the amphid neurons ASE and ASG. The expression level in the amphid neurons was weaker than in the other head neurons. The tail neurons were identified as PHC, in which expression was first detected during the L2 stage, consistent with the time of birth of the neurons at the end of L1. In contrast to the widespread expression of ncr-1Ap::gfp, ncr-1Bp::gfp is expressed exclusively in 10-12 pairs of head and tail neurons. The tail neurons were identified as PHA, PHB and DVC. One pair of head neurons was identified as AWC. The other head neurons were very tentatively identified as RIC, RIM, FLP, ADA, ADE, RID and maybe AIY. We also occasionally observed expression in a pair of head cells anterior to the nerve ring. The position and morphology of these cells are similar to the XXX cells. With the exception of PHC neurons, expression in the tissues above was first observed during late embryogenesis and did not change during development. Somatic gonad: Both ncr-1Ap(s)::gfp and ncr-1Ap(l)::gfp were strongly expressed in the spermatheca and weakly in the gonadal sheath cells. The expression in the somatic gonad could be observed only in adults. Three reporter constructs, ncr-1Ap(s)::gfp, ncr-1Ap(l)::gfp and ncr-1Bp::gfp were made for ncr-1 because of its complex gene structure. The results indicate that ncr-1 expression is widespread and largely coincides with the reported distribution pattern of cholesterol in C. elegans, which includes the following tissues: intestine, pharynx, excretory gland cell, nerve ring, spermatheca and germ cells, including both oocytes and sperm.

• Primary Identifier: Expr15917
• Pattern: Out of the 12 promoters, 8 drove expression in the XXX cells at various levels (asic-1, dhs-17, F14H8.2, C06A1.3, asp-9, B0034.5, F52E1.5, and nlp-15), one was impossible to score (T22E5.6) because it also drove high expression in the pharynx located very close to the XXX cells, and three did not show detectable expression in XXX cells (in adults; mab-9, twk-39, and lgc-36).

• Primary Identifier: Expr16190
• Pattern: We examined the daf-9::GFP expression pattern in males and observed expression within the pharynx, gut, and hypodermis, as well as in the XXX cells, but did not observe expression in the male gonad.

• Primary Identifier: Expr9082
• Remark: Picture: Fig 5, Fig S6H.
• Pattern: At all stages of postembryonic development, transgenic animals exhibited fluorescence in the pharynx, nervous system, intestine, body wall muscle, hypodermis, vulva, and a group of cells near the anus. EAK-7::GFP is also expressed in the XXX cells.
• Subcellular Localization: EAK-7::GFP localized to the plasma membrane.

• Primary Identifier: Expr9089
• Remark: Picture: Figures 5D, Fig S6.
• Pattern: GFP was first expressed during embryogenesis. At all stages of postembryonic development, transgenic animals exhibited fluorescence in the pharynx, nervous system, intestine, body wall muscle, hypodermis, vulva, and a group of cells near the anus. EAK-7::GFP is also expressed in the XXX cells.
• Subcellular Localization: EAK-7::GFP localized to the plasma membrane.

• Primary Identifier: Expr8098
• Remark: Picture: Figure 1.
• Pattern: hsd-1 is exclusively expressed in the XXX(L/R) cells.

• Primary Identifier: Expr16364
• Pattern: This high-sensitivity daf-2 expression reporter was readily detectable in most C. elegans cells, including the ones that had been missed by the DAF-2::mNeonGreen fusion protein marker (Expr16363), that is, the intestine, hypodermis, gonadal sheath, and body wall muscles (BWM). With NuGFP, expression of daf-2 was observed starting in 2-cell embryos, and the expression continued throughout development and adulthood. Also expressed in head neurons, germ line, vulval cells, tail neurons, ciliated sensory neurons, XXX cells.

• Primary Identifier: Expr2915
• Remark: When this transgene was introduced into daf-2(e1370) and daf-7(e1372) mutant animals grown at the non-permissive temperature (25 centigrades), hypodermal expression of daf-9::GFP was absent in dauers, even though the daf-9::GFP expression in XXXL/R persisted. The lack of hypodermal daf-9::GFP expression was also noted in wild-type dauer animals derived from starvation. The daf-9::GFP transgene was unable to suppress dauer arrest of daf-2(e1370) and daf-7(e1372) animals (n>100) at the restrictive temperature (25 centigrades) and enhanced dauer arrest of these animals at the permissive temperature (15 centigrades).
• Pattern: daf-9::GFP is expressed in a pair of cells in the anterior ganglion in L1 larvae, which persists in all larval stages and in adults, in the hypodermis from the mid-L2 stage to the end of L4 stage, and in the spermatheca of adult hermaphrodites. The daf-9::GFP-expressing head cells have been identified as XXXL/R, which are thought to be embryonic hypodermal cells.

• Primary Identifier: Expr9913
• Pattern: In indirect immunofluorescence experiments, the purified antibodies revealed DAF-2 in the cell bodies and processes of neurons, most obviously in the nerve ring, the major neuropil of the animal. DAF-2 was also expressed in the cell bodies of a pair of cells anterior to the nerve ring that were identified as XXXL/R, based on their variable positions relative to the nerve ring from animal to animal. No such immunofluorescence was observed in the daf-2(m646) null mutant, indicating that the antibodies are specific to DAF-2. Whereas the highest level of DAF-2 was present in the nervous system, we also observed weak immunofluorescence in other tissues, such as the hypodermis. We observed DAF-2 in the nerve ring from the mid-L1 stage to adulthood.

• Primary Identifier: Expr10266
• Pattern: Inferred expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/

• Primary Identifier: Expr10378
• Pattern: Inferred expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/

• Primary Identifier: Expr10443
• Pattern: Inferred Expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/

• Primary Identifier: Expr3223
• Remark: Reporter gene fusion type not specified.
• Pattern: The expression of ncr-2p::gfp was restricted to the XXX cells and the somatic gonad. It was strongly expressed in the proximal gonadal sheath cells and weakly in the spermatheca. The XXX expression of ncr-2p::gfp was seen throughout development, while the gonadal expression was observed only in adults.

• Primary Identifier: Expr15910
• Pattern: Out of the 12 promoters, 8 drove expression in the XXX cells at various levels (asic-1, dhs-17, F14H8.2, C06A1.3, asp-9, B0034.5, F52E1.5, and nlp-15), one was impossible to score (T22E5.6) because it also drove high expression in the pharynx located very close to the XXX cells, and three did not show detectable expression in XXX cells (in adults; mab-9, twk-39, and lgc-36).

• Primary Identifier: Expr15911
• Pattern: Out of the 12 promoters, 8 drove expression in the XXX cells at various levels (asic-1, dhs-17, F14H8.2, C06A1.3, asp-9, B0034.5, F52E1.5, and nlp-15), one was impossible to score (T22E5.6) because it also drove high expression in the pharynx located very close to the XXX cells, and three did not show detectable expression in XXX cells (in adults; mab-9, twk-39, and lgc-36).

• Primary Identifier: Expr15912
• Pattern: Out of the 12 promoters, 8 drove expression in the XXX cells at various levels (asic-1, dhs-17, F14H8.2, C06A1.3, asp-9, B0034.5, F52E1.5, and nlp-15), one was impossible to score (T22E5.6) because it also drove high expression in the pharynx located very close to the XXX cells, and three did not show detectable expression in XXX cells (in adults; mab-9, twk-39, and lgc-36).

• Primary Identifier: Expr15913
• Pattern: Out of the 12 promoters, 8 drove expression in the XXX cells at various levels (asic-1, dhs-17, F14H8.2, C06A1.3, asp-9, B0034.5, F52E1.5, and nlp-15), one was impossible to score (T22E5.6) because it also drove high expression in the pharynx located very close to the XXX cells, and three did not show detectable expression in XXX cells (in adults; mab-9, twk-39, and lgc-36).

• Primary Identifier: Expr15914
• Pattern: Out of the 12 promoters, 8 drove expression in the XXX cells at various levels (asic-1, dhs-17, F14H8.2, C06A1.3, asp-9, B0034.5, F52E1.5, and nlp-15), one was impossible to score (T22E5.6) because it also drove high expression in the pharynx located very close to the XXX cells, and three did not show detectable expression in XXX cells (in adults; mab-9, twk-39, and lgc-36).

• Primary Identifier: Expr15915
• Pattern: Out of the 12 promoters, 8 drove expression in the XXX cells at various levels (asic-1, dhs-17, F14H8.2, C06A1.3, asp-9, B0034.5, F52E1.5, and nlp-15), one was impossible to score (T22E5.6) because it also drove high expression in the pharynx located very close to the XXX cells, and three did not show detectable expression in XXX cells (in adults; mab-9, twk-39, and lgc-36).

• Primary Identifier: Expr15916
• Pattern: Out of the 12 promoters, 8 drove expression in the XXX cells at various levels (asic-1, dhs-17, F14H8.2, C06A1.3, asp-9, B0034.5, F52E1.5, and nlp-15), one was impossible to score (T22E5.6) because it also drove high expression in the pharynx located very close to the XXX cells, and three did not show detectable expression in XXX cells (in adults; mab-9, twk-39, and lgc-36).

12 Life Stages

Remark	Definition	Other Name	Public Name	Primary Identifier
	The whole period of embryogenesis in the nematode Caenorhabditis elegans, from the formation of an egg until hatching.		embryo Ce	WBls:0000003
	The C. elegans life stage spanning 620-800min(hatch) after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. A stage after elongation is over. The last stage of embryogenesis. Also called pre-hatched embryo, late embryo or morphogenetic embryo.		fully-elongated embryo Ce	WBls:0000021
	The C. elegans life stage spanning 350-620min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The stage that embryo starts elongation until elongation is over.		elongating embryo Ce	WBls:0000015
	The C. elegans life stage spanning 290-350min after first cleavage at 20 Centigrade. Proliferate from 421 cells to 560 cells. The stage when embryo just finished gastrulation and is enclosing.		enclosing embryo Ce	WBls:0000013
	The C. elegans life stage spanning 100-290min after first cleavage at 20 Centigrade. Proliferate from 28 cells to 421 cells. Referring to the whole period of gastrulation.		gastrulating embryo Ce	WBls:0000010
	The C. elegans life stage spanning 0-350min after first cleavage at 20 Centigrade. Proliferate from 1 cell to 560 cells. From start of first cleavage until cleavage is over.		proliferating embryo Ce	WBls:0000004
	The C. elegans life stage spanning 520-620min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The shape of embryo is elongated and tripple fold. A stage between 2-fold embryo and fully-elongated embryo. Also called pretzel embryo or pretzel stage.		3-fold embryo Ce	WBls:0000020
	The C. elegans life stage spanning 420-460min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The shape of embryo is elongated and fold back 50%. A stage between comma embryo and 2-fold embryo.		1.5-fold embryo Ce	WBls:0000018
	The C. elegans life stage spanning 390-420min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The shape of embryo looks like a comma. A stage between bean embryo and 1.5-fold embryo.		comma embryo Ce	WBls:0000017
	The C. elegans life stage spanning 460-520min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The shape of embryo is elongated and double fold. A stage between 1.5-fold embryo and 3-fold embryo.		2-fold embryo Ce	WBls:0000019
	The C. elegans life stage spanning 350-390min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. Emrbyo elongation started but have not formed comma shape yet. The shape of embryo looks like a lima bean. A stage right before comma embryo. Also called lima embryo or lima bean stage.		bean embryo Ce	WBls:0000016
	The C. elegans life stage spanning 210-350min after first cleavage at 20 Centigrade. Proliferate from 421 cells to 560 cells. The stage before the fast cleavage of cells finishes.		late cleavage stage embryo Ce	WBls:0000014

3 Parents

Definition	Name	Synonym	Primary Identifier
embryonic cell	ABarpappa		WBbt:0006273
portion of anterior ganglion of somatic nervous system that is near or posteior to the metacorpus of pharynx.	anterior ganglion (post)		WBbt:0005371
Two embryonic hypodermal cells (XXXL, XXXR) that may provide a scaffold for the early organization of ventral bodywall muscles and the various socket cells in the lateral and ventral lips. Their cell bodies soon crawl posteriorly, and their processes separate the amphid nerve from the mechanosensory nerves in the late embryo. The XXX processes later retract, and the XXX cell bodies remain in the ventrolateral bodywall near the cell bodies of the posterior arcade and some socket cells where they perform a neurohumoral function, as they retain short processes bordering the pseudocoelom and contain some secretory vesicles.	XXX cell		WBbt:0007855