Data from: Wild worm embryogenesis harbors ubiquitous polygenic modifier variation

Paaby AB, White AG, Riccardi DD, Gunsalus KC, Piano F, Rockman MV

Date Published: August 24, 2015

DOI: http://dx.doi.org/10.5061/dryad.d5j06

 

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Title Embryonic lethality data
Downloaded 11 times
Description This 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.
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When using this data, please cite the original publication:

Paaby AB, White AG, Riccardi DD, Gunsalus KC, Piano F, Rockman MV (2015) Wild worm embryogenesis harbors ubiquitous polygenic modifier variation. eLife 4: e09178. http://dx.doi.org/10.7554/eLife.09178

Additionally, please cite the Dryad data package:

Paaby AB, White AG, Riccardi DD, Gunsalus KC, Piano F, Rockman MV (2015) Data from: Wild worm embryogenesis harbors ubiquitous polygenic modifier variation. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.d5j06
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