WormMine: LifeStage WBls:0000024

• Definition: The first stage larva. At 25 Centigrade, it ranges 14-25.5 hours after fertilization, 0-11.5 hours after hatch.
• Primary Identifier: WBls:0000024
• Public Name: L1 larva Ce

5 Anatomy Terms

Definition	Name	Synonym	Primary Identifier
Epidermal layer.	hypodermis	epidermis	WBbt:0005733
type of cells that make up muscle layers in the pharynx.	pharyngeal muscle cell		WBbt:0005451
organ producing either sperm or ova.	gonad		WBbt:0005175
Neuron class of one pharyngeal interneuron, anterior sensory.	I3 neuron	I3	WBbt:0004742
type of 95 cells that make up muscles of the body wall.	body wall muscle cell	body muscle cell	WBbt:0006804

2 Contained In

Remark	Definition	Other Name	Public Name	Primary Identifier
	A developmental life stage of the nematode Caenorhabditis elegans that occurs from egg hatching until adulthood.		larva Ce	WBls:0000023
	The first stage larva of nematodes.		L1 larval stage	WBls:0000106

257 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_upregulated_neural
	Transcripts of coding genes that showed significantly decreased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_depleted_coding-RNA
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:all-neurons_L1-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:AVE-neuron_L1-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:bodywall-muscle_L1-larva_expressed
	Genes that were downregulated in lin-15B(n744).	For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis.	WBPaper00038168:lin-15B(n744)_downregulated
	Genes that were upregulated in lin-15B(n744).	For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis.	WBPaper00038168:lin-15B(n744)_upregulated
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards total RNA.	Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference.	WBPaper00045974:NSM_enriched_totalRNA_RNAseq
	Transcripts that showed significantly decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage.	DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed.	WBPaper00048971:daf-16(mgDf50)_downregulated_L1
	Transcripts that showed significantly increased expression in pry-1(mu38) animals comparing to in N2 at L1 larva stage.	DESeq, FDR < 0.05	WBPaper00055626:pry-1(mu38)_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:coelomocytes_L1-larva_expressed
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to tiling array analysis towards total RNA.	A linear model and moderated t-statistic were used to determine differentially expressed genes as implemented by the limma package (v3.21.4). Enriched list contains only genes significantly enriched in the NSM neurons versus the reference <=1.5X and <= 5% FDR.	WBPaper00045974:NSM_enriched_totalRNA_tiling
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:hypodermis_L1-larva_expressed
	Transcripts of coding genes that showed significantly increased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_enriched_coding-RNA
EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at 3 h after the third UVC dose (51h), which is also 3 h after being placed on food.	Genes differentially expressed under EtBr treatment without UVC exposure vs after UVC exposure but without EtBr treatment at the -3h timepoint (3 h after the third UVC dose (51h), which is also 3 h after being placed on food).	Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first.	WBPaper00041939:EtBr-exposed_vs_UVC-exposed_51h
UVC-EtBr-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total) and exposed to EtBr (5ug/mL in agar).) vs EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) at just prior to the second UVC dose (24h).	Genes differentially expressed under UVC exposure and EtBr treatment vs under EtBr treatment but without UVC exposure at the -25h timepoint (just prior to the second UVC dose (24h)).	Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first.	WBPaper00041939:UVC-EtBr-exposed_vs_EtBr-exposed_24h
	Genes that are down-regulated in elt-2(ca15) larvae compared to elt-2(ca15);elt-7(tm840) larvae.	RNA-seq count data were filtered for detected genes (> 10 counts across all samples) and analyzed using DESeq. 2 with Cook's cutoff filtering set to FALSE. Genes were counted as differentially expressed if they registered a Benjamini-Hochberg corrected p-value less than 0.05 and a log2-fold change greater than 1.2 between any pair-wise conditional comparison.	WBPaper00053606:elt-2(ca15)_vs_elt-2(ca15);elt-7(tm840)_doenregulated
	Genes that are up-regulated in wild-type N2 larvae compared to elt-2(ca15) larvae.	RNA-seq count data were filtered for detected genes (> 10 counts across all samples) and analyzed using DESeq. 2 with Cook's cutoff filtering set to FALSE. Genes were counted as differentially expressed if they registered a Benjamini-Hochberg corrected p-value less than 0.05 and a log2-fold change greater than 1.2 between any pair-wise conditional comparison.	WBPaper00053606:N2_vs_elt-2(ca15)_upregulated
	Transcripts depleted in RIS neurons comparing to in all cells.	edgeR 3.24.3, FDR < 0.01	WBPaper00058969:RIS_depleted
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:A-class-motor-neurons_L1-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:AVA-neuron_L1-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:dopaminergic-neurons_L1-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:GABAergic-motor-neurons_L1-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:intestine_L1-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:pharyngeal-muscle_L1-larva_expressed
Acidic Environment: PH 4.33 vs. PH 6.33.	Transcripts that showed significantly increased expression after 3 hours of exposure to acidic environment (PH 4.33), comparing to control animals exposed to PH 6.33 environment.	DESeq2 (1.16.1). The Benjamini and Hochberg's approach was used to adjust the resulting P-values to control the false discovery rate. Corrected value of P < 0.05 and fold change > 2 were set as the threshold for significantly differential expression.	WBPaper00060434:pH4.33_vs_pH6.33_uprgulated
feeding/starvation	A large cluster of genes up-regulated during early larval development..	For each average expression value, the larger of the model-based error and empirical error was reported. ANOVA and T-tests were also computed in Rosetta Resolver using the reported errors. Expression values, errors, and P-values corresponding to transcript detection, ANOVAs, and T-tests were exported from Rosetta Resolver and analyzed elsewhere.	WBPaper00032948:FedUp
control(maintained under normal lab light (mostly dark, in incubators).) vs EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) at just prior to the second UVC dose (24h).	Genes differentially expressed in control vs under EtBr treatment without UVC exposure, at the -25h timepoint.	Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first.	WBPaper00041939:control_vs_EtBr-exposed_24h
control(maintained under normal lab light (mostly dark, in incubators).) vs EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) at just prior to the third UVC dose (48h).	Genes differentially expressed in control vs under EtBr treatment without UVC exposure, at the -1h timepoint.	Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first.	WBPaper00041939:control_vs_EtBr-exposed_48h

2274 Expression Patterns

• Primary Identifier: Expr8361
• Remark: Picture: Figure 1.
• Pattern: GFP expression initiated in the early gastrula. Robust expression of Prncs-1::GFP was observed in the midgut (E cell lineage) starting at the 28-cell stage and continuing into adulthood. By the comma stage, fluorescence was also visible in the embryo periphery in cells that give rise to hypodermis. In L1 larva and subsequent stages, strong expression of GFP was seen in hypodermal cells, including Hyp 7 syncytium and head and tail hypodermis. The expression pattern was identical in hermaphrodites and males, but adult hermaphrodites displayed fluorescence in vulval epithelium. Expression was absent in seam cells, nervous system, and pharynx. The Prncs-1::GFP reporter showed increased expression during starvation. Although fluorescence intensity was enhanced under starved conditions, the spatial expression pattern was unchanged. Expression of the Prncs-1::GFP transgene was also enhanced in males. An ~2.5-fold increase in rncs-1 expression in total RNA prepared from wild-type, well fed males, compared with hermaphrodites.

• Primary Identifier: Expr4899
• Remark: Picture: Figure 2.
• Pattern: Levels of the drh-3 transcripts in animals at adult stages were approximately threefold higher than that in larval nematodes.

• Primary Identifier: Expr4890
• Remark: Picture: Fig 5.
• Pattern: Several globin genes (C06E4.7, C09H10.8, C36E8.2, C52A11.2, F52A8.4, R01E6.6, R13A1.8, R90.5, and W01C9.5) are similarly upregulated in L3 and dauers relative to young adults, although some reach significance in dauers only. Many genes exhibited more than 2- fold upregulation but didn't reach statistical significance because strong upregulation was only seen in 2 biological replicates, A significant downregulation in L3 stage relative to young adults was observed for C26C6.7, T22C1.2 and ZK637.13. A similar trend was seen in dauers. C26C6.7 was the only globin which exressed at a significantly higher level in dauers relative to L3. Quantitative real-time RT-PCR experiments were done to compare the relative bundance of all 33 globins in wild type adults. Results demonstrate T22C1.2 and ZK637.13 are expressed at substantially higher levels. The difference with the other globins ranges within 1-3 orders of magnitude.

• Primary Identifier: Expr4883
• Remark: Picture: Fig. 4A.
• Pattern: Low GFP signals were detected exclusively in the intestinal cells of late embryos, L1L4, and adult hermaphrodites.

• Primary Identifier: Expr4874
• Remark: Picture: Figure 4D, 4E. nfyb-1 and nfyc-1 displayed identical expression patterns.
• Pattern: nfyb-1 was expressed in many cells in the developing embryo. At the larval stages, the expression level of nfyb-1 was reduced in most somatic cells except in some head neurons and in the developing hermaphrodite vulva and male tail.
• Subcellular Localization: NFYB-1 was localized in both the nucleus and the cytoplasm.

• Primary Identifier: Expr4875
• Remark: Picture: Figure 4D, 4E. nfyb-1 and nfyc-1 displayed identical expression patterns.
• Pattern: nfyc-1 was expressed in many cells in the developing embryo. At the larval stages, the expression level of nfyc-1 was reduced in most somatic cells except in some head neurons and in the developing hermaphrodite vulva and male tail.
• Subcellular Localization: NFYC-1 was localized in both the nucleus and the cytoplasm.

• Primary Identifier: Expr4876
• Remark: Picture: Figure 4H, 4I.
• Pattern: The expression of nfya-2 was restricted to few tissues, including the spermatheca, some neurons in the head and other body regions. Notably, it was highly expressed in intestine cells at all developmental stages.
• Subcellular Localization: NFYA-2 localized to the nucleus.

• Primary Identifier: Expr4873
• Remark: Picture: Figure 4A, B, C.
• Pattern: NFYA-1 was localized to the nucleus and was ubiquitously expressed in all nuclei at all developmental stages. In larvae and adult animals, strong expression of nfya-1 was observed in the head ganglia neurons and also in the developing hermaphrodite vulva and mail tail, while its expression was lower in most somatic cells.
• Subcellular Localization: NFYA-1 was localized to the nucleus.

• Primary Identifier: Expr4838
• Remark: Picture: Figure 8 C and D.
• Pattern: The major site of agrin expression was around the pharynx and the staining was particularly enriched in the anterior part. The posterior bulb was labeled more weakly correlating with the fainter GFP reporter expression in the posterior part. Polyclonal antiserum staining resulted in the same staining pattern in wild type worms of different developmental stages. Young larvae (L1) generally showed stronger agrin staining compared to young adults. In addition to the pharynx staining in the wild type worms, the polyclonal antiserum stained the gut lumen both in the wild type worms as well as in the agrin mutants, but not when preimmune serum was used. The staining of the lumen of the gut represents an unrelated cross-reactivity of the antiserum, possibly corresponding to the background bands detected on the western blots.
• Subcellular Localization: Agrin was detected in the basal lamina around the pharynx procorpus and anterior bulb. Posterior bulb staining was weaker possibly due to poor antibody penetration.

• Primary Identifier: Expr4836
• Remark: Picture: Figs. 4A-D.
• Pattern: In hermaphrodites, the expression of bro-1 was restricted to seam cells. Its expression was first detected at bean-stage embryos and persisted throughout the developmental stages. In the male tail, bro-1 was also expressed in the ray precursor cells.
• Subcellular Localization: GFP::BRO-1 was localized to both the cytoplasm and the nucleus.

• Primary Identifier: Expr4837
• Remark: Picture: Figure 5.
• Pattern: Fluorescence started to be visible in two cells of young embryos at around the 64 AB cell stage. Towards the end of gastrulation expression was visible in about 40 cells throughout the embryo including neuronal precursors, ventral hypodermal cells, and pharyngeal precursor cells. At the 1 to 2 fold stages fluorescence was observed in IL1 neurons (the identity was determined post-embryonically), the nine buccal epidermal cells, and additional cells in the head, most likely arcade cells. Transient expression was also observed in embryonic motoneurons (no longer visible in 3 fold stage embryos) and in a few apoptotic cells in the head. Based on their position they could be the sister cells of some of the IL1 neurons, which are known to undergo programmed cell death at this developmental stage. At the 3 fold stage expression was restricted to the buccal epidermal cells, most of the arcade cells (3 anterior and the DL and DR posterior arcade cells), and the six IL1 neurons. The two lateral IL1 neurons expressed the marker only weakly also in the L1 larval stage (but not later during development), whereas the dorsal and ventral IL1 neurons expressed GFP strongly throughout all larval stages and in the adults. Starting from the L1 larval stage expression could also be observed in the posterior cells of the gut. Starting from the L2 stage, when gonad development and migration begins, fluorescence became also visible in the distal tip cells of the gonad.

• Primary Identifier: Expr4829
• Remark: Picture: Fig. 6A, 6B. Reporter gene fusion type not specified.
• Pattern: Exclusively expressed throughout the nervous system in C. elegans. F25B3.3::gfp is a postmitotic pan-neuronal marker, i.e. its onset of expression is observed after the terminal division of neurons (around 450 minutes of embryonic development).

• Primary Identifier: Expr4821
• Remark: Picture: Fig. 10, A and B.
• Pattern: The hex-1 promoter was particularly active in coelomocytes as well as in neurons of the pharyngeal region and nerve cord, as compared with the head and tail pattern observed in strain BC14144 (see Expr6695). Expressed throughout the life-cycle.

• Primary Identifier: Expr4822
• Remark: Picture: Fig. 10, C.
• Pattern: The hex-2::gfp construct appeared to be active in the hypodermal cells, vulval toroids, and various adult head and tail neurons, Expressed throughout the life-cycle.

• Primary Identifier: Expr4823
• Remark: Picture: Fig. 10 H.
• Pattern: The hex-3 construct was expressed in gut granules. Expressed throughout the life-cycle.

• Primary Identifier: Expr4824
• Remark: Picture: Fig. 10 I.
• Pattern: The hex-4::gfp line displayed staining of seam cells in late embryos and L1 larvae. Expression was restricted to the embryonal and L1 stages.

• Primary Identifier: Expr4825
• Remark: Picture: Fig. 10, J and K.
• Pattern: Expression of hex-5 was restricted to certain cells at the 3-fold stage but was also present in the vulval, head (muscle), and tail regions in larval and adult worms. Expressed throughout the life-cycle.

• Primary Identifier: Expr4818
• Remark: Picture: Fig. 1A, 1B, 1C.
• Pattern: aqp-8 localized exclusively to the excretory system of the worm. Expression of aqp-8 also appears to be localized to an additional cell. The aqp-8p::GFP-PEST-expressing worms displayed an identical spatial pattern to the worms carrying the usual aqp-8::GFP construct, but due to the short half-life of the GFP-PEST construct, authors were able to determine that aqp-8 is transcribed only in the interval between the first larval stage and early adulthood. The relative levels of expression in the excretory cell and the excretory gland cell appeared to be similar to each other. Expression patterns derived from extrachromosomal arrays may be confounded by somatic loss of the transgene (leading to mosaically expressing transgenes). Therefore, the expression pattern of aqp-8 was confirmed by generating a genome-integrated aqp-8p::GFP transgenic line to prevent the sporadic loss of the transgene in somatic tissue.

• Primary Identifier: Expr4812
• Remark: Picture: Figure 7A, Figure 7, C and D.
• Pattern: RDY-2 has a distribution very similar to that of VHA-5 in the excretory canal and the epidermis. Specifically, expression was seen in the lining of the excretory canal and excretory duct, but not around the excretory pore. As no expression was seen around the excretory cell body, authors conclude that RDY-2 is localized at the apical side of the canal, as reported for VHA-5 (see Expr4811). RDY-2 had a distribution in the epidermis similar to that of VHA-5 and was also excluded from seam cells. RDY-2 expression became progressively fainter after the L1 stage. In addition, authors found RDY-2 expressed in the sheath cells associated with head and tail sensory organs. Three-dimensional reconstructions showed that VHA-5 and RDY-2 formed a sixfold symmetrical pattern, which includes a larger spot that presumably corresponds to the amphid.
• Subcellular Localization: Localized at the apical side of the excretory canal. In the amphid sheath cell, VHA-5 and RDY-2 were found in the most distal part of the cell lining the sheath pocket, which can be equated to its apical side.

• Primary Identifier: Expr4813
• Remark: Picture: Figure 7, C and D.
• Pattern: Expression was observed throughout development, starting at midembryogenesis. VHA-5 was also detected at the lumen of the vulva and rectum. In addition, authors found VHA-5 expressed in the sheath cells associated with head and tail sensory organs. Three-dimensional reconstructions showed that VHA-5 and RDY-2 formed a sixfold symmetrical pattern, which includes a larger spot that presumably corresponds to the amphid.
• Subcellular Localization: In the amphid sheath cell, VHA-5 was found in the most distal part of the cell lining the sheath pocket, which can be equated to its apical side.

• Primary Identifier: Expr4690
• Remark: Reporter gene fusion type not specified.
• Pattern: It was observed that the fusion gene expression continued from embryonic and post-embryonic stages. At embryonic stage, several cells were stained in post-gastrulating embryos whereas in postembryonic stages staining of cells was seen from L1 to young adults.

• 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: Expr4687
• Pattern: Embryonic expression of pgp-2::gfp was first seen in the daughters of the E blastomere (E2 stage), which generate the intestine. Intestinal expression persisted through embryogenesis and into adulthood. Rarely, weak expression of pgp-2::gfp was detected in embryonic and adult hypodermal cells. Pharyngeal or AWA expression of the pgp-2::gfp reporter were never detected.

• Primary Identifier: Expr4689
• Pattern: It was found that the amount of transcript of tbg-1 varies significantly in different stages during the development. In embryos the expression of the gene was high; it has extremely low level of gene expression during L1 larval stage, increased from L2 to L4 stages and showed the maximum expression in young adult stage. In gravid adult stage, the expression was more than that of embryos.

• Primary Identifier: Expr4683
• Pattern: hlh-29/hlh-28 mRNA is present at all developmental stages and does not vary significantly during later larval stages. Embryos and early L1-stage larvae produce significantly more hlh-29/hlh-28 RNA than later larvae. In separate assays from three independent cDNA samples, L1-stage larvae produced an average of 3 1/2 times more hlh-29 RNA than did L4 stage larvae and adults.

• 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: Expr4791
• Remark: Reporter gene fusion type not specified.
• Pattern: The glt-7::gfp fusion shows strong expression in the excretory canal cell from embryonic to larval stages. Strikingly, there was a complete disappearance of the glt-7::gfp signal in most adult animals.

• Primary Identifier: Expr4793
• Pattern: For all arrays examined, the reporter gene was expressed exclusively in hypodermal cells. In males, expression of dpy-5::gfp generally resembles that of hermaphrodites. Fluorescence is observed within the head and tail hypodermal cells, the P cells and hyp7, and is absent or of low abundance within the seam cells. This is more easily seen in a higher magnification of the tail region in which GFP is notably absent in the V5-derived seam cell, yet abundant in its sister set cell and the V6- and T-derived specialized hypodermal cells that envelope the sensory rays used in copulation. In summary, expression of the dpy-5::gfp reporter gene in the hypodermal cells begins in L1, and continues throughout larval development, ending in adulthood. In seam cells, expression is variable, suggesting that it may be regulated differently than in the hypodermal cells.

• Primary Identifier: Expr4796
• Remark: Reporter gene fusion type not specified.
• Pattern: cnx-1 was expressed ubiquitously in every blastomere of the embryos up to the gastrulation stage but expression became gradually restricted to the head and tail regions at the comma stage during embryogenesis. During post-embryonic development, cnx-1 was expressed prominently in the H-shaped excretory cell, in the neurons of head and tail, in the dorsal and ventral nerve cords, and in the spermatheca. cnx-1 expression was also observed in the spicules of the male tail. The two head neurons expressing cnx-1 are ASK and ADL, and two tail neurons are PHA and PHB. Therefore, cnx-1 is expressed in head neurons including ASK and ASI chemosensory neurons and tail neurons including PHA and PHB.

• Primary Identifier: Expr4787
• Pattern: glt-1 is strongly expressed in body wall muscles from early developmental stages. Early in development glt-1 expression was seen in hypodermal cells. Towards adulthood, the GLT-1::GFP signal becomes more restricted to the head muscles.
• Subcellular Localization: In head muscles, bright GFP punctae seem to project from the cell soma towards the center of the nematode head

2 Followed By

Remark	Definition	Other Name	Public Name	Primary Identifier
	The second stage larva. At 25 Centigrade, it ranges 25.5-32.5 hours after fertilization, 11.5-18.5 hours after hatch.		L2 larva Ce	WBls:0000027
	The stage when an animal shifts from L1 larva to L2 larva. It includes the synthesis of new cuticle, cease of phrayngeal pumping during a lethargus stage, and the shed off of old cuticle.		L1-L2 molt Ce	WBls:0000026

1 Preceded By

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

4 Sub Stages

Remark	Definition	Other Name	Public Name	Primary Identifier
	The stage that begins right after hatching and before development proceeds after feeding. A newly hatched L1 larva contains 558 cells.		newly hatched L1 larval stage Ce	WBls:0000801
	The time period encompassing the 820th minute post first cleavage at 20 Centigrade with respect to Sulston's lineage tree.		820 min post first-cleavage Ce	WBls:0000701
	The time period encompassing the 830th minute post first cleavage at 20 Centigrade with respect to Sulston's lineage tree.		830 min post first-cleavage Ce	WBls:0000702
	The time period encompassing the 850th minute post first cleavage at 20 Centigrade with respect to Sulston's lineage tree.		850 min post first-cleavage Ce	WBls:0000703