WormMine: AnatomyTerm WBbt:0003955

• Definition: Neuron class of one neuron, sends processes laterally and along dorsal cord.
• Name: ALA
• Primary Identifier: WBbt:0003955
• Synonym: lineage name: ABalapppaaa

1 Children

Definition	Name	Synonym	Primary Identifier
nucleus of pedigree ABalapppaaa	ABalapppaaa nucleus		WBbt:0001647

5 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Top 300 transcripts enriched in ALA 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:ALA
	Single-cell RNA-Seq cell group 140_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:140_0
	Transcripts enriched in ALA according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:ALA_enriched
	Single-cell RNA-Seq cell group 139_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:139_0
	Single-cell RNA-Seq cell group 130 expressed in: ALA.	CellRanger, DecontX, Monocle3, Louvain algorithm.	WBPaper00065623:130

78 Expression Patterns

• Primary Identifier: Expr4684
• Pattern: GFP expression was detected at most developmental stages, with the spatial expression depending on the developmental stage of the animal. Neuronal expression of hlh-29 was detected in larvae and adults in both amphid and phasmid sockets, in the ALA and PVT neurons, in the chemosensory and mechanosensory neurons, ASI, ASK, PHA, and PQR, and in neurons of the anterior pharyngeal bulb. Weaker expression was also detected in the ASG chemosensory neurons in some transgenic lines. L1 animals show strong expression of hlh-29 in intestinal cells, and weaker expression in the rectal glands and the pharyngeal muscle cell PM1. By L3 stage, intestinal expression of the hlh-29::GFP is limited to the posterior intestinal cells, and PM1 expression is no longer detected. Expression is also detected in the ventral posterior coelomocytes in the later L3-stage larvae, and in the spermatheca and vulval muscles of L4 and adult animals.

• Primary Identifier: Expr15649

• Primary Identifier: Expr15558

• Primary Identifier: Expr15567

• Primary Identifier: Expr15571

• Primary Identifier: Expr15572

• Primary Identifier: Expr15573

• Primary Identifier: Expr15579

• Primary Identifier: Expr15586

• Primary Identifier: Expr15651

• Primary Identifier: Expr15589

• Primary Identifier: Expr13158

• Primary Identifier: Expr15591

• Primary Identifier: Expr15598

• Primary Identifier: Expr15604

• Primary Identifier: Expr14590
• Pattern: Embryonic expression of exc-7 was first observed at the bean stage. By reverse lineaging with use of SIMI-Biocell software, we confirm the identity of one of the expressing cells at this stage as the excretory canal cell. In L1 animals, broad expression in the head, ventral nerve cord (VNC), and tail was observed. In young adults, expression is notably observed in vulva cells. In the nervous system specifically, expression is observed in many neurons throughout the body, but unlike Drosophila Elav, exc-7::gfp it is not panneuronally expressed. We confirmed previously reported expression in cholinergic VNC MNs, but absence of GABAergic VNC MNs, consistent with previous reports (Fujita et al., 1999; Loria et al., 2003) and consistent with exc-7 functioning in cholinergic, but not GABAergic neurons to control alternative splicing (Norris et al., 2014). exc-7::gfp is also expressed in some non-neuronal cell types, including muscle and hypodermis, but not in the gut. A previous report showed that exc-7 is only transiently and weakly expressed in the excretory cell, which, based on exc-7's excretory mutant phenotype, has puzzled researchers (Fujita et al., 2003). We find that the gfp tagged exc-7 locus is strongly and continuously expressed in the excretory canal cell.

• Primary Identifier: Expr15608

• Primary Identifier: Expr15611

• Primary Identifier: Expr13508
• Pattern: Embryonic (bean and on) GLR cells, ALA?, muscle?

• Primary Identifier: Expr294
• Remark: Data modified according to Shawn Lockery's expression pattern curations.
• Pattern: Expressed in URX, ALA, some sensory neurons, interneurons, pharyngeal neurons and muscle.

• Primary Identifier: Expr14627
• Pattern: sax-3 was expressed in the muscles and many neurons, including ALA and PVD.

• Primary Identifier: Expr597
• Remark: Reporter gene fusion type not specified. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). tba-2 in this article is referred as alpha-2 tubulin, while the same authors referred it as tba-2 in later publications such as cgc2176.
• Pattern: Following hatching, 6 pharyngeal muscle cells stain becoming increasingly intense during larval and adult development. 6-7 neurons are stained in the ventral cord identified as DB motor neurons. Late larval and adult stages, staining of the set of DB and VB motor neurons in the ventral cord and their axonal processes along the ventral cord shows higher intensity of staining in late larval and adult stages. At L4, Pharyngeal muscles and the motor neurons show intense staining in L4 and adult stages. Fusion gene expressed in intestinal nuclei showing a gradient of expression, high staining in the posterior most intestinal nuclei in the tail region to a lower intensity of staining in the anterior intestinal nuclei. Intestinal staining decreases (L3-L4) and adult stages. Staining is detected in entire intestinal organ. Expression in neurons includes a set of DB and VB (19 cells) in the ventral nerve cord, a pair of posterior mechanosensory receptor neuron PLML and PLMR a single interneuron PVT in the pre-anal ganglion and a single neuron ALA in dorsal ganglion in the head.

• Primary Identifier: Expr716
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: Expression observed in most or all neurons at high levels as well as in some hypodermal and muscle cells. In most neurons, sax-3::GFP expression is transient, peaking during the period of axon outgrowth. Highest level of expression is observed in the embryo, particularly during the initial period of axon outgrowth at 350-400 min (comma-stage). At comma-stage high level of expression is observed in anterior embryo, including most developing neurons of the nerve ring and a swath of ventral cells that includes the developing motor neurons of the ventral nerve cord and posterior neurons such as PVQ. Lower level of expression is observed in the epidermal cells. 200-400 - cell stage; 200-300 min of development: Expression seen in all epidermal cells at low level. 3-fold stage; >500 min of development: Expression seen in muscles that extend from nerve ring to the anterior tip of the head. L1: Expression in motor neurons in the head including RMD, RMG, SMD, SIA and SIB neurons; projection interneurons in the head and tail, including AVA, AVB, PVC, AVD, PVQ and ALA neurons; and the sensory OLQ neuron. This neuronal expression diminishes throughout postembryonic development. During L1, expression persists in the head muscles and appears in muscles along the body wall, with ventral muscles expressing more strongly than posterior muscles. This expression continues until the adult stage. Epidermal expression was rarely seen in larval stages. L2: Expression observed in HSN motor neurons. HSN motor neurons extends a growth cone (axon from their lateral cell bodies) towards the ventral midline and expression is at its highest at this point. L3: Expression observed in the axon reaching the ventral nerve cord. L4: Expression continues in HSN, when HSN axon grows anteriorly to the head. Adult: Expression decreases in HSN at this stage after the completion of HSN axon outgrowth. In addition expression observed in motor neurons, interneurons and sensory neurons listed above also postembryonic ventral cord motorneurons, some interneurons from the tail and head, body wall and vulval muscles.

• Primary Identifier: Expr15402

• Primary Identifier: Expr15406

• Primary Identifier: Expr13810
• Pattern: cnx-1 promoter-driven GFP was ubiquitously expressed in large numbers of neurons in the tail, head, and vulva. Furthermore, cnx-1 promoter-driven mCherry proteins were colocalized with the ALA-specific ver-3 promoter-driven GFP, suggesting that CNX-1 was expressed in ALA neurons.

• Primary Identifier: Expr14626
• Pattern: Promoter reporter assays confirmed that sax-7 was expressed in the hypodermal cells and the neurons, including ALA and PVD.

• Primary Identifier: Expr15344

• Primary Identifier: Expr15564

• Primary Identifier: Expr15570

11 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 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

4 Parents

Definition	Name	Synonym	Primary Identifier
neuron with its cell body situated in the head, excluding the pharynx.	head neuron		WBbt:0006751
ganglion that lies beside the nerve ring in the head. It contains neuron cell bodies that send their neuronal processes into the ring and longitudinal nerves, but form no local neuropil separate from the nerve ring. The dorsal ganglion is in close contact with the dorsal hypodermal cord.	dorsal ganglion		WBbt:0005214
cell that exists in and is part of an embryo.	embryonic cell		WBbt:0007028
embryonic cell	ABalapppaa		WBbt:0006703