DOI: 10.5061/dryad.1rn8pk15n
title: Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae

description: What constraints govern the evolution of gene expression patterns across
 development remains a fundamental question. Single-cell RNA-sequencing can
 detail these constraints by systematically profiling homologous cells. The
 conserved invariant embryonic lineage of C. elegans and C. briggsae makes
 them ideal for comparing cell-type gene expression across evolution.
 Measuring the spatiotemporal divergence of gene expression across
 embryogenesis, we find a high level of similarity in gene expression
 programs between species despite tens of millions of years of evolutionary
 divergence. Nonetheless, thousands of genes show divergence in their
 cell-type-specific expression patterns, with enrichment for functions in
 environmental response and behavior. Neuronal cell types show higher
 divergence than others, such as the intestine and germline. This work
 identifies likely constraints on the evolution of developmental gene
 expression.
description: # Lineage-resolved analysis of embryonic gene expression evolution in *C.
 elegans* and *C. briggsae* Dataset DOI:
 [10.5061/dryad.1rn8pk15n](10.5061/dryad.1rn8pk15n) ## Description of the
 data and file structure ### Files and variables #### File: config.yml
 **Description:** Config file needed for VisCello #### File: clist.rds
 **Description:** Cello list of UMAP projections #### File: cell\_plots.zip
 **Description:** Collection of plots describing each progenitor and
 terminal cell types. Below are the elements in the plots: 1. The relative
 TPM of every gene in *C. elegans* and *C. briggsae*. Whether a gene is a
 cell-type marker within that species or both is labeled. 2. A barplot of
 the cell-type markers from *C. elegans* binned by their WormCat gene
 category. Ontop is their fold-enrichment and below is their count. 3. The
 top cell-type markers that are shared between species (black outline),
 private to *C. elegans* (green), or private to *C. briggsae* (blue). The
 private markers can also include genes that weren't annotated as
 being directly orthologous between the species. 4. A bunch of cell type
 metrics, where the values for that cell type are shown in green for *C.
 elegans* and blue for *C. briggsae* (red for both) ontop of the dataset
 wide distribution. * Cell count: number of cells in the dataset. * The
 number of genes ‘detected’ in that cell type. Calculated by generating
 1000 bootstraps of the TPM, then selecting genes whose 95% lower CI
 doesn’t intersect 0. * The toal number of markers of that cell-type. * How
 many of the markers of that cell-type are just in one species versus the
 total markers (shared + private). * Gini coefficient: A measure of
 inequality that shows how evenly distributed the TPM values are (0 = even,
 1 = skewed). * The number of UMI-collapsed sequencing reads that are
 associated with the cell-type. * Jensen-Shannon Distance: Metric of
 distance between the two species cell transcriptomes. * Pearson
 Correlation: Metric of similarity between the two species cell
 transcriptomes. * Cosine distance: Metric of distance between the two
 species cell transcriptomes using one minus the cosine angle. * The number
 of differentially expressed genes between the species. #### File:
 cbr\_markers.txt **Description:** Gene markers identified in *C.
 briggsae.* Values that are NA for the *C. elegans* columns are because of
 a lack of 1:1 orthology between the genes. * p_val.species - The
 unadjusted p-value between the cells of that cell-type and the cells of
 rest of the dataset for that species. * avg_log2FC.species - The log2
 fold-change between the cells of that cell-type and the cells of rest of
 the dataset for that species. * pct.1.species - The fraction of cells for
 which this gene was detected in that cell-type for that species. *
 pct.2.species - The fraction of cells for which this gene was detected in
 the rest of the cells in the dataset for that species. * p_val_adj.species
 - The adjusted p-value between the cells of that cell-type and the cells
 of rest of the dataset for that species. * cell_type - The cell-type in
 which the gene was tested for its marker status. * gene - The gene that
 was tested for its marker status. * cell_gene - The joint name of the cell
 type and the gene. * p_val.other_species - If the gene was tested in the
 other species for its marker status, the values for that test are shown
 here. * avg_log2FC.other_species - If the gene was tested in the other
 species for its marker status, the values for that test are shown here. *
 pct.1.other_species - If the gene was tested in the other species for its
 marker status, the values for that test are shown here. *
 pct.2.other_species - If the gene was tested in the other species for its
 marker status, the values for that test are shown here. *
 p_val_adj.other_species - If the gene was tested in the other species for
 its marker status, the values for that test are shown here. *
 cel_tpm_log2fc - The log2FC using the TPM pseudobulk values instead of the
 single-cell estimates. * cbr_tpm_log2fc - The log2FC using the TPM
 pseudobulk values instead of the single-cell estimates. *
 cel_tpm_log2fc_just_pro - The log2FC using the TPM pseudobulk values from
 just the progenitor cell types instead of the single-cell estimates. NA
 values in this columns are either due to a lack of orthology or the gene
 not being expressed in the progenitors. * cbr_tpm_log2fc_just_pro - The
 log2FC using the TPM pseudobulk values from just the progenitor cell types
 instead of the single-cell estimates. NA values in this columns are either
 due to a lack of orthology or the gene not being expressed in the
 progenitors. * cel_tpm - The TPM of that gene in that cell-type for *C.
 elegans*. * cbr_tpm - The TPM of that gene in that cell-type for *C.
 briggsae*. * cel_max_tpm_term - The maximum TPM of that gene in terminal
 cell types for *C. elegans*. * cbr_max_tpm_term - The maximum TPM of that
 gene in terminal cell types for *C. briggsae*. * cel_max_tpm_pro - The
 maximum TPM of that gene in progenitor cell types for *C. elegans*. *
 cbr_max_tpm_pro - The maximum TPM of that gene in progenitor cell types
 for *C. briggsae*. * cel_mean_tpm_term - The mean TPM of that gene in
 terminal cell types for *C. elegans*. * cbr_mean_tpm_term - The mean TPM
 of that gene in terminal cell types for *C. briggsae*. * cel_mean_tpm_pro
 - The mean TPM of that gene in progenitor cell types for *C. elegans*. *
 cbr_mean_tpm_pro - The mean TPM of that gene in progenitor cell types for
 *C. briggsae*. * cel_tau_pro - The broadness of the gene expression
 pattern in just progenitor cell types for *C. elegans*. * cbr_tau_pro -
 The broadness of the gene expression pattern in just progenitor cell types
 for *C. briggsae*. * cel_tau_term - The broadness of the gene expression
 pattern in just terminal cell types for *C. elegans*. * cbr_tau_term - The
 broadness of the gene expression pattern in just terminal cell types for
 *C. briggsae*. * cel_tau_joint - The broadness of the gene expression
 pattern across the dataset for *C. elegans*. * cbr_tau_joint - The
 broadness of the gene expression pattern across the dataset for *C.
 briggsae*. * gene.type - Whether the gene in shared between species, or is
 specific to one or the other. * orthology_conf - The confidence in the
 orthology classification * OG - The orthogroup name for this gene. *
 cel_OG_count - The number of genes from *C. elegans* in this orthogroup. *
 cbr_OG_count - The number of genes from *C. briggsae* in this orthogroup.
 * WormCat.1 - The WormCat (Holdorf, et al., 2020) category of this gene at
 a tier one level. * WormCat.2 - The WormCat category of this gene at a
 tier two level. * WormCat.3 - The WormCat category of this gene at a tier
 three level. * in_species - Whether this gene marker is also a marker in
 the other species. #### File: cell\_data\_bins.txt **Description:** Cell
 data, calculated on progenitor and terminal cell type bins * cell-type -
 The name of the cell type. * cell_type_bin - The cell type time bins
 associated with this cell type. * cell_class - The tissue subset the cell
 is a part of. * jsd_median - The median Jensen-shannon distance between
 the transcriptomes of the homologous cell-types between *C. elegans* and
 *C. briggsae*, calculated on 1000 bootstraped TPM values. * jsd_lower -
 The lower 95% confidence-interval of the Jensen-shannon distance between
 the transcriptomes of the homologous cell-types between *C. elegans* and
 *C. briggsae*, calculated on 1000 bootstraped TPM values. * jsd_upper -
 The upper 95% confidence-interval of the Jensen-shannon distance between
 the transcriptomes of the homologous cell-types between *C. elegans* and
 *C. briggsae*, calculated on 1000 bootstraped TPM values. * cor_median -
 The median pearson correlation between the transcriptomes of the
 homologous cell-types between *C. elegans* and *C. briggsae*, calculated
 on 1000 bootstraped TPM values. * cor_lower - The lower 95%
 confidence-interval of the Pearson correlation between the transcriptomes
 of the homologous cell-types between *C. elegans* and *C. briggsae*,
 calculated on 1000 bootstraped TPM values. * cor_upper - The upper 95%
 confidence-interval of the Pearson correlation between the transcriptomes
 of the homologous cell-types between *C. elegans* and *C. briggsae*,
 calculated on 1000 bootstraped TPM values. * cos_median - The median
 cosine angle between the transcriptomes of the homologous cell-types
 between *C. elegans* and *C. briggsae*, calculated on 1000 bootstraped TPM
 values. * cos_upper - The lower 95% confidence-interval of the cosine
 angle between the transcriptomes of the homologous cell-types between *C.
 elegans* and *C. briggsae*, calculated on 1000 bootstraped TPM values. *
 cos_lower - The upper 95% confidence-interval of the cosine angle between
 the transcriptomes of the homologous cell-types between *C. elegans* and
 *C. briggsae*, calculated on 1000 bootstraped TPM values. *
 cel_gini_median - *C. elegans* gini coefficient, calculated on calculated
 on 1000 bootstraped TPM values. * cbr_gini_median - *C. briggsae* gini
 coefficient, calculated on calculated on 1000 bootstraped TPM values. *
 cel_gini_upper - *C. elegans* upper 95% confidence-interval gini
 coefficient, calculated on calculated on 1000 bootstraped TPM values. *
 cel_gini_lower - *C. elegans* lower 95% confidence-interval gini
 coefficient, calculated on calculated on 1000 bootstraped TPM values. *
 cbr_gini_upper - *C. briggsae* upper 95% confidence-interval gini
 coefficient, calculated on calculated on 1000 bootstraped TPM values. *
 cbr_gini_lower - *C. briggsae* lower 95% confidence-interval gini
 coefficient, calculated on calculated on 1000 bootstraped TPM values. *
 cel_markers - Number of *C. elegans* markers. * cbr_markers - Number of
 *C. briggsae* markers. * cel_markers_common - Number of *C. elegans*
 shared markers. * cbr_markers_common - Number of *C. briggsae* shared
 markers. * cel_markers_non_one_to_one - Number of markers that are private
 to *C. elegans*. * cbr_markers_non_one_to_one - Number of markers that are
 private to *C. briggsae*. * genes_detected_bootstrap_cel - Number of genes
 detected using binarization using the 95% CI on bootstrapped TPM. *
 genes_detected_bootstrap_cbr - Number of genes detected using binarization
 using the 95% CI on bootstrapped TPM. * cel_cell_count - Cell count for
 *C. elegans*. * cbr_cell_count - Cell count for *C. briggsae*. *
 cel_median_umi - Median number of UMI per cell. * cbr_median_umi - Median
 number of UMI per cell. * deg - How many differentially expressed between
 homologous cell type between *C. elegans* and *C. briggsae*. *
 lineage_group - Naming of progenitor cell groups (Not applicable for
 terminally differentiated cell types). * div_stage - The embryonic stage
 of that cell type. * min_cell_count - The minimum cell count from either
 species. * embryo_time - The mean embryo time of that cell type. ####
 File: cell\_data\_mean.txt **Description:** Cell data, calculated on
 progenitor and the mean values of terminal cell type bins * cell-type -
 The name of the cell type. * cell_type_bin - The cell type time bins
 associated with this cell type. * cell_class - The tissue subset the cell
 is a part of. * jsd_median - The median Jensen-shannon distance between
 the transcriptomes of the homologous cell-types between *C. elegans* and
 *C. briggsae*, calculated on 1000 bootstraped TPM values. * jsd_lower -
 The lower 95% confidence-interval of the Jensen-shannon distance between
 the transcriptomes of the homologous cell-types between *C. elegans* and
 *C. briggsae*, calculated on 1000 bootstraped TPM values. * jsd_upper -
 The upper 95% confidence-interval of the Jensen-shannon distance between
 the transcriptomes of the homologous cell-types between *C. elegans* and
 *C. briggsae*, calculated on 1000 bootstraped TPM values. * cor_median -
 The median pearson correlation between the transcriptomes of the
 homologous cell-types between *C. elegans* and *C. briggsae*, calculated
 on 1000 bootstraped TPM values. * cor_lower - The lower 95%
 confidence-interval of the Pearson correlation between the transcriptomes
 of the homologous cell-types between *C. elegans* and *C. briggsae*,
 calculated on 1000 bootstraped TPM values. * cor_upper - The upper 95%
 confidence-interval of the Pearson correlation between the transcriptomes
 of the homologous cell-types between *C. elegans* and *C. briggsae*,
 calculated on 1000 bootstraped TPM values. * cos_median - The median
 cosine angle between the transcriptomes of the homologous cell-types
 between *C. elegans* and *C. briggsae*, calculated on 1000 bootstraped TPM
 values. * cos_upper - The lower 95% confidence-interval of the cosine
 angle between the transcriptomes of the homologous cell-types between *C.
 elegans* and *C. briggsae*, calculated on 1000 bootstraped TPM values. *
 cos_lower - The upper 95% confidence-interval of the cosine angle between
 the transcriptomes of the homologous cell-types between *C. elegans* and
 *C. briggsae*, calculated on 1000 bootstraped TPM values. *
 cel_gini_median - *C. elegans* gini coefficient, calculated on calculated
 on 1000 bootstraped TPM values. * cbr_gini_median - *C. briggsae* gini
 coefficient, calculated on calculated on 1000 bootstraped TPM values. *
 cel_gini_upper - *C. elegans* upper 95% confidence-interval gini
 coefficient, calculated on calculated on 1000 bootstraped TPM values. *
 cel_gini_lower - *C. elegans* lower 95% confidence-interval gini
 coefficient, calculated on calculated on 1000 bootstraped TPM values. *
 cbr_gini_upper - *C. briggsae* upper 95% confidence-interval gini
 coefficient, calculated on calculated on 1000 bootstraped TPM values. *
 cbr_gini_lower - *C. briggsae* lower 95% confidence-interval gini
 coefficient, calculated on calculated on 1000 bootstraped TPM values. *
 cel_markers - Number of *C. elegans* markers. * cbr_markers - Number of
 *C. briggsae* markers. * cel_markers_common - Number of *C. elegans*
 shared markers. * cbr_markers_common - Number of *C. briggsae* shared
 markers. * cel_markers_non_one_to_one - Number of markers that are private
 to *C. elegans*. * cbr_markers_non_one_to_one - Number of markers that are
 private to *C. briggsae*. * genes_detected_bootstrap_cel - Number of genes
 detected using binarization using the 95% CI on bootstrapped TPM. *
 genes_detected_bootstrap_cbr - Number of genes detected using binarization
 using the 95% CI on bootstrapped TPM. * cel_cell_count - Cell count for
 *C. elegans*. * cbr_cell_count - Cell count for *C. briggsae*. *
 cel_median_umi - Median number of UMI per cell. * cbr_median_umi - Median
 number of UMI per cell. * deg - How many differentially expressed between
 homologous cell type between *C. elegans* and *C. briggsae*. *
 lineage_group - Naming of progenitor cell groups (Not applicable for
 terminally differentiated cell types). * div_stage - The embryonic stage
 of that cell type. * min_cell_count - The minimum cell count from either
 species. * embryo_time - The mean embryo time of that cell type. ####
 File: gene\_data.txt **Description:** Gene data information. For genes
 that are poorly sampled, some of the distance and broadness metrics may be
 NA, meaning there was not enough information to make a conclusion. For
 columns that come from matching with other datasets, NA values refer to
 where no match was able to be made due to gene naming differences. *
 jsd_median_term - Jensen-Shannon distance calculated on 1000x bootstraps
 of the terminal cell type TPM values * pcor_median_term - Pearson
 correlation calculated on 1000x bootstraps of the terminal cell type TPM
 values * scor_median_term - Spearman correlation calculated on 1000x
 bootstraps of the terminal cell type TPM values * cos_median_term - Cosine
 angle calculated on 1000x bootstraps of the terminal cell type TPM values
 * cel_tau_median_term - *C. elegans* Tau calculated on 1000x bootstraps of
 the terminal cell type TPM values * cbr_tau_median_term - *C. briggsae*
 Tau calculated on 1000x bootstraps of the terminal cell type TPM values *
 jsd_median_pro - Jensen-Shannon distance calculated on 1000x bootstraps of
 the progenitor cell type TPM values * pcor_median_pro - Pearson
 correlation calculated on 1000x bootstraps of the progenitor cell type TPM
 values * scor_median_pro - Spearman correlation calculated on 1000x
 bootstraps of the progenitor cell type TPM values * cos_median_pro -
 Cosine angle calculated on 1000x bootstraps of the progenitor cell type
 TPM values * cel_tau_median_pro - *C. elegans* Tau calculated on 1000x
 bootstraps of the progenitor cell type TPM values * cbr_tau_median_pro -
 *C. briggsae* Tau calculated on 1000x bootstraps of the progenitor cell
 type TPM values * jsd_median_joint - Jensen-Shannon distance calculated on
 1000x bootstraps of the joint cell type TPM values * pcor_median_joint -
 Pearson correlation calculated on 1000x bootstraps of the joint cell type
 TPM values * scor_median_joint - Spearman correlation calculated on 1000x
 bootstraps of the joint cell type TPM values * cos_median_joint - Cosine
 angle calculated on 1000x bootstraps of the joint cell type TPM values *
 cel_tau_median_joint - *C. elegans* Tau calculated on 1000x bootstraps of
 the joint cell type TPM values * cbr_tau_median_joint - *C. briggsae* Tau
 calculated on 1000x bootstraps of the joint cell type TPM values *
 cel_max_tpm_term - *C. elegans* maximum TPM value across all terminal cell
 types * cbr_max_tpm_term - *C. briggsae* maximum TPM value across all
 terminal cell types * max_tpm_term - Maximum TPM value across all terminal
 cell types across species * cel_max_tpm_pro - *C. elegans* maximum TPM
 value across all progenitor cell types * cbr_max_tpm_pro - *C. briggsae*
 maximum TPM value across all progenitor cell types * max_tpm_pro - Maximum
 TPM value across all progenitor cell types across species * elegans_id -
 *C. elegans* WBGene name * elegans_gene_long_name - *C. elegans*
 transcript name * briggsae_id - *C. briggsae* WBGene name *
 briggsae_gene_short_name - *C. briggsae* gene short name *
 briggsae_gene_long_name - *C. briggsae* transcript name * orthology_conf -
 Confidence in the orthology assignment with 1:1 being the highest,
 followed by confident canonical then canonical * percent_identity -
 Percent identity in a Smith-Waterman alignment between *C. elegans* and
 *C. briggsae* * percent_similarity - Percent similarity in a
 Smith-Waterman alignment between *C. elegans* and *C. briggsae* * syntenic
 - Whether the gene has been found to be syntenic between species * OG -
 The orthogroup number for reference with the orthogroup supplementary
 table * cel_OG_count - Number of *C. elegans* genes in the orthogroup *
 cbr_OG_count - Number of *C. briggsae* genes in the orthogroup * WormCat.1
 - WormCat tier one term * WormCat.2 - WormCat tier two term * WormCat.3 -
 WormCat tier three term * omega - The dN/dS values calculated in this
 study * Cutter_Ka - Ka values calculted in Tu et al. 2015 * Cutter_Ks - Ks
 values calculted in Tu et al. 2015 * Cutter_Ka.Ks - Ka/Ks values calculted
 in Tu et al. 2015 * PS.Value - Phylostrata values calculated in Ma et al.,
 2023 * PS.Name - Phylostrata names calculated in Ma et al., 2023 *
 maternal - Whether the gene was maternally inherited according to have an
 expression above zero in the first cell division from Tintori et al., 2016
 #### File: cel\_markers.txt **Description:** Gene markers of cell type
 calculated in *C. elegans.* Values that are NA for the *C. briggsae*
 columns are because of a lack of 1:1 orthology between the genes. *
 p_val.species - The unadjusted p-value between the cells of that cell-type
 and the cells of rest of the dataset for that species. *
 avg_log2FC.species - The log2 fold-change between the cells of that
 cell-type and the cells of rest of the dataset for that species. *
 pct.1.species - The fraction of cells for which this gene was detected in
 that cell-type for that species. * pct.2.species - The fraction of cells
 for which this gene was detected in the rest of the cells in the dataset
 for that species. * p_val_adj.species - The adjusted p-value between the
 cells of that cell-type and the cells of rest of the dataset for that
 species. * cell_type - The cell-type in which the gene was tested for its
 marker status. * gene - The gene that was tested for its marker status. *
 cell_gene - The joint name of the cell type and the gene. *
 p_val.other_species - If the gene was tested in the other species for its
 marker status, the values for that test are shown here. *
 avg_log2FC.other_species - If the gene was tested in the other species for
 its marker status, the values for that test are shown here. *
 pct.1.other_species - If the gene was tested in the other species for its
 marker status, the values for that test are shown here. *
 pct.2.other_species - If the gene was tested in the other species for its
 marker status, the values for that test are shown here. *
 p_val_adj.other_species - If the gene was tested in the other species for
 its marker status, the values for that test are shown here. *
 cel_tpm_log2fc - The log2FC using the TPM pseudobulk values instead of the
 single-cell estimates. * cbr_tpm_log2fc - The log2FC using the TPM
 pseudobulk values instead of the single-cell estimates. *
 cel_tpm_log2fc_just_pro - The log2FC using the TPM pseudobulk values from
 just the progenitor cell types instead of the single-cell estimates. NA
 values in this columns are either due to a lack of orthology or the gene
 not being expressed in the progenitors. * cbr_tpm_log2fc_just_pro - The
 log2FC using the TPM pseudobulk values from just the progenitor cell types
 instead of the single-cell estimates. NA values in this columns are either
 due to a lack of orthology or the gene not being expressed in the
 progenitors. * cel_tpm - The TPM of that gene in that cell-type for *C.
 elegans*. * cbr_tpm - The TPM of that gene in that cell-type for *C.
 briggsae*. * cel_max_tpm_term - The maximum TPM of that gene in terminal
 cell types for *C. elegans*. * cbr_max_tpm_term - The maximum TPM of that
 gene in terminal cell types for *C. briggsae*. * cel_max_tpm_pro - The
 maximum TPM of that gene in progenitor cell types for *C. elegans*. *
 cbr_max_tpm_pro - The maximum TPM of that gene in progenitor cell types
 for *C. briggsae*. * cel_mean_tpm_term - The mean TPM of that gene in
 terminal cell types for *C. elegans*. * cbr_mean_tpm_term - The mean TPM
 of that gene in terminal cell types for *C. briggsae*. * cel_mean_tpm_pro
 - The mean TPM of that gene in progenitor cell types for *C. elegans*. *
 cbr_mean_tpm_pro - The mean TPM of that gene in progenitor cell types for
 *C. briggsae*. * cel_tau_pro - The broadness of the gene expression
 pattern in just progenitor cell types for *C. elegans*. * cbr_tau_pro -
 The broadness of the gene expression pattern in just progenitor cell types
 for *C. briggsae*. * cel_tau_term - The broadness of the gene expression
 pattern in just terminal cell types for *C. elegans*. * cbr_tau_term - The
 broadness of the gene expression pattern in just terminal cell types for
 *C. briggsae*. * cel_tau_joint - The broadness of the gene expression
 pattern across the dataset for *C. elegans*. * cbr_tau_joint - The
 broadness of the gene expression pattern across the dataset for *C.
 briggsae*. * gene.type - Whether the gene in shared between species, or is
 specific to one or the other. * orthology_conf - The confidence in the
 orthology classification * OG - The orthogroup name for this gene. *
 cel_OG_count - The number of genes from *C. elegans* in this orthogroup. *
 cbr_OG_count - The number of genes from *C. briggsae* in this orthogroup.
 * WormCat.1 - The WormCat (Holdorf, et al., 2020) category of this gene at
 a tier one level. * WormCat.2 - The WormCat category of this gene at a
 tier two level. * WormCat.3 - The WormCat category of this gene at a tier
 three level. * in_species - Whether this gene marker is also a marker in
 the other species. #### File: deg.txt **Description:** A list of all
 differentially expressed genes between *C. elegans* and *C. briggsae*. To
 identify genes differentially expressed between *C. elegans* and *C.
 briggsae* within the homologous cell-types, we used Seurat V5. A Wilcoxon
 Rank Sum test was run between the cells of that cell-type from *C.
 elegans* against the cells of that cell-type from *C. briggsae*. The data
 have been filtered for an adjusted p-value less than 0.05 and a log2
 fold-change of greater than 1 or less than -1. The columns in the table
 are as below: * p_val - The unadjusted p-value between *C. elegans* cells
 and *C. briggsae* cells for that gene in that cell-type. * avg_log2FC -
 The log2 fold-change between *C. elegans* cells and *C. briggsae* cells
 for that gene in that cell-type. * pct.1 - The fraction of cells for which
 this gene was detected in *C. elegans*. * pct.2 - The fraction of cells
 for which this gene was detected in *C. briggsae*. * p_val_adj- The
 adjusted p-value between *C. elegans* cells and *C. briggsae* cells for
 that gene in that cell-type. * cell_type - The cell-type in which the gene
 was tested for its differential expression. * gene - The gene that was
 tested for its differential expression. * cell_type_bin - The cell type
 bin that this differentially expressed gene was found in. * cel_tpm - The
 TPM of that gene in that cell-type for *C. elegans*. * cbr_tpm - The TPM
 of that gene in that cell-type for *C. briggsae*. #### File:
 cbr\_tpm\_out.txt **Description:** The summary expression values for every
 gene in *C. elegans*. Available here is the expression value of every gene
 in the *C. elegans* genome, summarized as the transcripts per million
 (TPM) on pseudobulked progenitor and terminal cell-types. To evaluate the
 variation in the measurement of these TPM values, we have used
 bootstrapping to take samples of the cells and generate several confidence
 intervals on the cellular expression values. A gene can be thought of as
 confidently detected in that cell-type if its lower 95% confidence
 interval does not intersect zero. Additionally, we have assessed the
 percentage of cells from that cell-type that we were able to detect
 expression from. #### File: eset.rds **Description:** The cell and gene
 information for VisCello. **Meta data columns in the VisCello Objects:** *
 lineage - The manually annotated cell lineage. For ambiguities in division
 orientation, an x is used (e.g. MSx to refer to MSa and MSp). * cell_type
 - The terminal cell-type identities, manually annotated using homologous
 marker genes. * species - Whether the cell is from *C. elegans* or *C.
 briggsae.* * embryo_time - The estimated age of the embryo from which the
 cell was drawn. See Packer and Zhu et al., 2019 for more details on how
 this was calculated. <em>C. briggsae</em> embryo_time was
 estimated using the orthologous genes between the species. * dataset -
 Which collection batch the cells come from. * n_umi - The number of
 UMI-collapsed sequencing reads that are associated with the cell. *
 genotype - The genotype from which the cell came from. Some of the *C.
 elegans* cells are from mutant animals. * Wild-type *C. elegans*: N2 and
 VC2010 * Wild-type *C. briggsae*: AF16 * Mutant *C. elegans* for mec-3:
 VC2396 mec-3(gk1126). Mutants for mec-3 appear to be missing their touch
 neurons and markers of the touch neurons are not detected. * Mutant *C.
 elegans* for M03D4.4: VC4183 M03D4.4(gk5269[loxP + myo-2p::GFP::unc-54
 3' UTR + rps-27p::neoR::unc-54 3' UTR + loxP]). This mutant
 strain for M03D4.4 appears otherwise wild-type in cell composition and
 expression. * Mutant *C. elegans* for ceh-9: YL633 ceh-9(tm2747). This
 mutant strain for ceh-9 appears otherwise wild-type in cell composition
 and expression. * potential_low_quality_cell - Using a variety of manual
 annotation strategies, we have identified some cells that don't
 behave consistently across UMAP embeddings due to a variety of technical
 reasons. These have been left in the dataset as they often represent
 'normal cells', but have been labeled as being potentially
 low-quality. * high_background - The amount of background reads was
 estimated for every cell similar to Packer and Zhu et al., 2019. The cells
 labeled here as TRUE had a fraction of reads from background higher than
 0.75. * possible_doublet - Droplets that annotated as possibly containing
 two or more cells. Not all cells annotated as possible droplets are as
 such. Please see Packer and Zhu et al., 2019 for details on how the
 background was estimated. * packer_cell_type - Cell type annotation from
 Packer and Zhu et al., 2019. * packer_cell_subtype - Cell type annotation
 from Packer and Zhu et al., 2019. * packer_plot_cell_type - Cell type
 annotation from Packer and Zhu et al., 2019. * SizeFactor - A column used
 to estimate the library size. * smoothed_embryo_time - The estimated
 embryo time calculated as above, with an additional nearest neighbor
 smoothing algorithm to use the neighboring cell's embryo time and
 transcriptome to better approximate the age of the embryo. *
 embryo_time_bin - Binned smoothed embryo time with lt_100 meaning
 'less than 100' and gt_710 meaning 'greater than 710. *
 Gene Expression - Used to inspect gene expression. #### File:
 cel\_tpm\_out.txt **Description:** The summary expression values for every
 gene in *C. briggsae*. Available here is the expression value of every
 gene in the *C. briggsae* genome, summarized as the transcripts per
 million (TPM) on pseudobulked progenitor and terminal cell-types. To
 evaluate the variation in the measurement of these TPM values, we have
 used bootstrapping to take samples of the cells and generate several
 confidence intervals on the cellular expression values. A gene can be
 thought of as confidently detected in that cell-type if its lower 95%
 confidence interval does not intersect zero. Additionally, we have
 assessed the percentage of cells from that cell-type that we were able to
 detect expression from. #### File: gene\_plots.zip **Description:** A
 collection of summary plots for every gene that is shared in *C. elegans*
 and *C. briggsae* with some expression. Below are the elements in the
 plots: 1. Global UMAP showing the expression of your gene of interest. 2.
 Cell subset UMAP showing the expression of your gene of interest. The
 choice of which UMAP is shown is based on which cell-type shows maximum
 expression across all cell-types between the two species. 3. Terminal
 cell-type comparative TPM values shown in log2 space. The cell-types are
 summarized by their cell class. 4. Progenitor cell-type comparative TPM
 values shown in log2 space. The circle plots summarize the division
 patterns in the embryo. 5. A bunch of gene metrics, where the values for
 this gene is shown in red as a confidence interval (CI) range on top of
 the dataset wide distribution. These metrics are shown for the jointly
 estimated, terminal, and progenitor cell types. * Gene expression patern
 distance shown as the Jensen-Shannon Distance (JSD) calculated on the
 bootstrapped TPM values. The CI and median for the gene JSD was calculated
 on the bootstrap resampled TPM values. * The broadness of gene expression
 pattern shown as the Tau value for *C. elegans*. * The broadness of gene
 expression pattern shown as the Tau value for *C. briggsae*. #### File:
 briggsae\_WS290\_cistarget.zip **Description:** Database files for running
 SCENIC on *C. briggsae* expression data (WS290). Please see the following
 publication for how to run SCENIC using the enclosed feather databases:
 Van de Sande, B., Flerin, C., Davie, K. *et al.* A scalable SCENIC
 workflow for single-cell gene regulatory network analysis. *Nat Protoc*
 **15**, 2247–2276 (2020).
 [https://doi.org/10.1038/s41596-020-0336-2](https://doi.org/10.1038/s41596-020-0336-2) #### File: elegans\_WS290\_cistarget.zip **Description:** Database files for running SCENIC on *C. elegans* expression data (WS290). Please see the following publication for how to run SCENIC using the enclosed feather databases: Van de Sande, B., Flerin, C., Davie, K. *et al.* A scalable SCENIC workflow for single-cell gene regulatory network analysis. *Nat Protoc* **15**, 2247–2276 (2020). [https://doi.org/10.1038/s41596-020-0336-2](https://doi.org/10.1038/s41596-020-0336-2) ## Code/software Included are all codes to generate the summary metrics and visualizations presented in the associated manuscript. Additional code for the ShinyApp is also available here as a zip file. ## Access information Other publicly accessible locations of the data: * [https://github.com/livinlrg/C.elegans_C.briggsae_Embryo_Single_Cell](https://github.com/livinlrg/C.elegans_C.briggsae_Embryo_Single_Cell) * [https://github.com/livinlrg/cistarget_caenorhabditis](https://github.com/livinlrg/cistarget_caenorhabditis) * [https://github.com/livinlrg/cel_cbr_embryo_single_cell](https://github.com/livinlrg/cel_cbr_embryo_single_cell)