DOI: 10.5061/dryad.d5j06
title: Data from: Wild worm embryogenesis harbors ubiquitous polygenic modifier variation

description: Embryogenesis is an essential and stereotypic process that nevertheless
 evolves among species. Its essentiality may favor the accumulation of
 cryptic genetic variation (CGV) that has no effect in the wild-type but
 that enhances or suppresses the effects of rare disruptions to gene
 function. Here, we adapted a classical modifier screen to interrogate the
 alleles segregating in natural populations of C. elegans: we induced gene
 knockdowns and used quantitative genetic methodology to examine how
 segregating variants modify the penetrance of embryonic lethality. Each
 perturbation revealed CGV, indicating that wild-type genomes harbor myriad
 genetic modifiers that may have little effect individually but which in
 aggregate can dramatically influence penetrance. Phenotypes were mediated
 by many modifiers, indicating high polygenicity, but the alleles tend to
 act very specifically, indicating low pleiotropy. Our findings demonstrate
 the extent of conditional functionality in complex trait architecture.
description: Embryonic lethality
 dataThis is a tab-delimited
 text file with one header row, 27,360 data rows, and 19 columns. Each data
 row corresponds to a unique image taken of a well in a 96-well plate, in
 which there are (potentially) adult worms, dead embryos, and living
 larvae. The column headers are: adults_man (the number of adults in the
 image, manually counted by a human); eggs_man (the score of the abundance
 of dead embryos in the image, from 0 to 9, scored manually by a human);
 larvae_man (the score of the abundance of living larvae in the image, from
 0 to 9, scored manually by a human); strain (the worm strain); vector (the
 gene targeted by RNAi, or in the case of "empty," the negative
 control RNAi clone); date (the one of three date batches in which the
 experiments were conducted); well_row (the row, from A to H, in a 96-well
 plate, in which the well was located); well_col (the column, from 1 to 12,
 in a 96-well plate, in which the well was located); fol_strain (the
 grouping, from a to c, to which the worm strain in this image belonged
 when it was dispensed into the 96-well plates; strains were dispensed in
 sets of 8, as each plate has 8 rows); fol_lib (the RNAi library, from 1 to
 4, to which the bacteria in this well belonged when it was dispensed);
 fol_bac_rep (the batch of bacterial culture, either "car,"
 "gre," or "roy" that was dispensed into this well;
 from a single bacterial library, three replicate culture batches were
 grown in three deep-well 96-well plates, from which the RNAi bacteria were
 dispensed into the experimental plates); fol_plate_rep (the replicate
 plate number, from 1 to 8; each experimental condition of worm strain and
 RNAi vector was replicated 8 times, across the three replicate batches of
 bacterial culture); image (the image number, from 1 to 96, in a 96-well
 plate, assigned by the image capture software); adult_area (the number of
 pixels assigned to the "adult" category by the DevStaR
 algorithm); larva_area (the number of pixels assigned to the
 "larva" category by the DevStaR algorithm); egg_area (the number
 of pixels assigned to the "embryo" category by the DevStaR
 algorithm); adults (the count of adults in the image by the DevStaR
 algorithm); larvae (the count of living larvae in the image by the DevStaR
 algorithm); eggs (the count of dead embryos in the image, determined by
 dividing egg_area by 70). NA values in the manually scored columns
 (adults_man, eggs_man, larvae_man) indicate that the well failed to grow a
 mature culture of worms. This is often due to somatic lethality of the
 targeted gene (e.g. the somatic control vector tba-2), or to fungal
 contamination. Because these images were checked by a human eye, rows with
 NAs in the manual columns should be excluded from most
 analyses.emb_leth_data.txt