WormMine: AnatomyTerm WBbt:0003999

• Definition: Amphid neuron, prob. chemosensory
• Name: ADFR
• Primary Identifier: WBbt:0003999
• Synonym: lineage name: ABpraaappaa

1 Children

Definition	Name	Synonym	Primary Identifier
nucleus of pedigree ABpraaappaa	ABpraaappaa nucleus		WBbt:0001630

2 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Top 300 transcripts enriched in ADFL, ADFR, AWBL, AWBR 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:ADF_AWB
	Top 300 transcripts enriched in ADFL, ADFR 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:ADF

165 Expression Patterns

• Primary Identifier: Expr4817
• Remark: Picture: Fig. 2G.
• Pattern: In wild-type animals, GFP was observed in all identified serotonergic and dopaminergic neurons and many muscle cells. Please note: this strain -JY739- shows expression in biogenic amine neurons and the epidermis, not in muscle cells (Loer et al., 2015. Genetics. WBPaper00046585, Expr12165).

• Primary Identifier: Expr4693
• Remark: nsy-5 = T16H5.1.
• Pattern: A GFP reporter transgene with 5.8 kb of the nsy-5 promoter was expressed exclusively in sensory neurons and interneurons in the head and tail. The neurons that expressed nsy-5::GFP included AWC, ASH, AFD, ASI, ADL, ASK, BAG, AWB, and ADF (head sensory neurons); ADA, AIZ, RIC, AIY, and AIM (head interneurons); PHA and PHB (tail sensory neurons); and PVC and PVQ (tail interneurons). Expression began about halfway through embryogenesis, was strongest in late embryogenesis and the L1 larval stage, and faded thereafter. Adults maintained weak expression in several neurons, including ASH but not AWC.

• Primary Identifier: Expr4403
• Pattern: Strong and consistent expression was observed in a limited number of neurons in the head and tail and coelomocytes. Weaker and/or inconsistent expression of TTX-7::EGFP was detected in nerve cord motor neurons, intestine, and somatic gonad. The head neurons expressing ttx-7::EGFP include AFD and RIA neurons. Also expressed in ASH, ASE, ASJ, AWC, ADF, ADL, ASI, ASK, AWB, VNC motor neurons, etc.
• Subcellular Localization: TTX-7::EGFP was diffusely expressed in the cytoplasm and was not localized to any specific subcellular compartment.

• Primary Identifier: Expr4227
• Remark: Reporter gene fusion type not specified.
• Pattern: Expressed in NSM and ADF neurons.

• Primary Identifier: Expr8656
• Remark: Picture: Fig 3.
• Pattern: The fusion protein encoded by the transgene was preferentially detected in several tissues including the nervous system. However, its presence was not uniform. Within the nervous system, ELPC-1::GFP was seen predominantly in a pair of neurons that control egg-laying, the HSNs, and in chemosensory neurons in the head. Within the latter class of neurons, the ELPC-1::GFP level was particularly high in the ASE, ADF and ASK pairs of neurons. Outside of the nervous system, a strong ELPC-1::GFP signal was seen in the pharynx and the vulva. In all animals examined, ELPC-1::GFP expression was also seen in the two CAN cells.
• Subcellular Localization: In the nervous system, expression was seen both within the cell bodies and along the entire lengths of the neuronal processes. Outside of the nervous system, in all cells in which ELPC-1::GFP was seen, fluorescence was restricted to the cytoplasm.

• Primary Identifier: Expr15649

• Primary Identifier: Expr3175
• Pattern: Expressed in ADF, ADL, AFD, ASE, ASG, ASH, ASI, ASJ, ASK, AWA, AWB, AWC, BAG, PHA, PHB, URX, intestine.

• Primary Identifier: Expr8976
• Remark: Picture: Fig 4E to 4H. npr-5 = Y58G8A.4 in this paper.
• Pattern: The npr-5p::RFP transgene was expressed in a subset of amphid neurons (ADF, ASE, ASG, ASI, ASJ, ASK, AWA, AWB) in the inner labial neuron IL2, in the interneurons AIA and AUA, and in the phasmids (PHA, PHB). Outside the nervous system, npr-5p::RFP was expressed in head, neck, and body muscles throughout larval and adult development.

• Primary Identifier: Marker42
• Remark: Picture: Figure 8A. Reporter gene fusion type not specified.
• Pattern: Expressed in ASE neurons, also expressed in the AFD or ADF neuron classes.

• Primary Identifier: Expr8247
• Remark: Picture: Figure 5D.
• Pattern: Pmgl-3::gfp was expressed in NSM, ADF, ASE, and AWC amphid sensory neurons, and the RIB and RIC interneurons. Occasional expression in BAG-ciliated neurons was also noted.

• Primary Identifier: Expr15388

• Primary Identifier: Expr11753
• Remark: genomic

• Primary Identifier: Expr12168
• Pattern: qdpr-1 was expressed in the epidermis -similar to what observed in cat-4 transgenics- but was not highly expressed in 5HT and DA neurons. These transgenics all also showed some expression of varying intensity in other cells (non-epidermal cells, and non-5HT and non-DA neurons in the head and body). A qdpr-1 full-length translational fusion was expressed in several known 5HT and DA neurons, including NSMs, ADFs, CEPs, and other cells.

• Primary Identifier: Expr11444
• Remark: Reporter gene fusion not specified.
• Pattern: Not expressed in NSM nor HSN. Expressed in several dim cells in the head (ADF?) tail and head hypodermal cells.

• Primary Identifier: Expr3169
• Pattern: Expressed in ADF, ADL, ASH, ASI, ASJ, ASK, PHA, PHB.

• Primary Identifier: Expr3185
• Pattern: Expressed in ADF, ADL, ASE, ASG, ASH, ASI, ASJ, ASK, PHA, PHB, URX, labial neurons.

• Primary Identifier: Expr15558

• Primary Identifier: Expr1688
• Remark: The cellular expression pattern for nlp-3 fragments was indistinguishable from the cellular expression pattern for nlp-3 subcloned constructs. Transgenic lines were generated by coinjection of the nlp::gfp construct (5070 ng/ul) and lin-15 rescue construct (pJM24,100 ng/ul) into lin-15(n765ts) animals. At least two independent transgenic lines were analyzed for each nlp gene; 5-10 animals were scored per line. 1,1'-Dioctadecyl-3,3,3',3 -tetramethylindodicarbocyanine perchlorate (Molecular Probes) was used to stain amphid and phasmid neurons to facilitate identification.
• Pattern: Expressed in ADF, ASE, ASH, AWB, ASJ, BAG, HSN, I1, I2, I3, I4, MI, M3, NSMR, 3 head neurons, VNC, oocytes, I6, M2, pm1VL, intestine.

• Primary Identifier: Expr15571

• Primary Identifier: Expr15572

• Primary Identifier: Expr15573

• Primary Identifier: Expr15579

• Primary Identifier: Expr15586

• Primary Identifier: Expr15651

• Primary Identifier: Expr15652

• Primary Identifier: Expr15589

• Primary Identifier: Expr15591

• Primary Identifier: Expr12196
• Pattern: To determine where lite-1 is expressed and identify likely sites of lite-1 function, the authors generated and examined worms carrying one of four transgenes derived from the wild-type lite-1 locus: a genomic fragment (lite-1 genomic), a transcriptional fusion (lite-1prom::gfp), a C-terminal translational fusion (lite-1prom::lite-1::gfp), and an N-terminal translational fusion (lite-1prom::gfp::lite-1). GFP expression was observed in a total of 29 cells: pharyngeal neurons M1, M4, M5, and MI; non-pharyngeal neurons ASK, ADL, ASI, ASH, AVG, AVB, RIM, ADF, PHA, PHB, and PVT; and non-neuronal cells Hyp3 (hypoderm), AMso (amphid socket cells), and PHso (phasmid socket cells). AVB was observed only with the C-terminal fusion transgene, and RIM and ADF were observed only with the transcriptional fusion transgene. lite-1 expression in AVG and PVT was previously reported.

• Primary Identifier: Expr15598

• Primary Identifier: Expr15604

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

6 Parents

Definition	Name	Synonym	Primary Identifier
neuron with its cell body situated in the head, excluding the pharynx.	head neuron		WBbt:0006751
cell that exists in and is part of an embryo.	embryonic cell		WBbt:0007028
embryonic cell	ABpraaappa		WBbt:0006483
Neuron class of two neurons that have dual ciliated endings in the amphid sensillum. The endings are in the amphid channel, which is open to the outside. Processes from lateral cell bodies enter the ventral cord via the amphidial commissures and turn anteriorly to enter the nerve ring. The processes of ADF run near the outside surface and posterior face of the ring, in close association with those of AIZ. They meet at the dorsal mid-line and terminate; there is a gap junction at the point or contact. The main synaptic output is to RIA and AIZ; there are also synapses to SMB, AUA and RIR, usually in dyadic combinations with RIA or AIZ. AWB synapses onto ADF in several places, and there are gap junctions to RIH, ADA and AIA.	ADF		WBbt:0005660
neuron type, cell body located in right lateral ganglion.	lateral ganglion right neuron		WBbt:0005100
	amphid right sensillum		WBbt:0005392