Comments from curator
Phenotyping data comes from the
Supplementary material of the paper (
journal page, "Supplementary materials" tab, file
S001667231100019X.xls):
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Supplementary Table 1a (sheet SupplTable1a-F_R): number of flies, mean lifespan and its standard error for 34 DGRP lines on full (F) and restricted (R) food.
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Supplementary Table 1b (sheet SupplTable1b-F+W_R+E_R+M): the same for 9 of these lines on full food with nutrient-free water (F+W), 8 lines on restricted food with methionine (R+M) and 6 lines on restricted food with essential amino acids (R+E).
Only these per-line values were published (no per-bottle or per-fly data), so the study has a summary dataset only. The lines are given as bare numbers (e.g. 208 = DGRP_208).
Design: 34 of the 40 core DGRP lines (from Bloomington). For each line and food, 30 females and 30 males collected less than 24 h after eclosion were kept together in 150 mL bottles at 26 °C and 75% humidity; food was replaced and dead flies were counted and sexed every other day until all flies were dead (2 blocks, 3-5 replicate bottles per line and food). Full food (F): 15% brewer's yeast, 5% sugar, 1.5% agar; restricted food (R): 5% yeast, 5% sugar, 1.5% agar. F+W: full food with a source of nutrient-free water (1 mL of 0.7% agar); R+M: restricted food with 1.5 mM methionine (0.225 g/L); R+E: restricted food with 0.225 g/L of each of 10 essential amino acids (R, H, I, L, K, M, F, T, W, V). Mean lifespan (days) and its standard error come from the authors' Kaplan-Meier analysis (JMP).
Sex: the supplementary table does not state the sex, but its values pool both sexes, so they are uploaded with sex NA: the N-weighted average of the line means equals the "Combined" row of every column; the overall lifespan reduction on full food (22.29 vs 29.77 days, -25%) lies between the paper's per-sex values (-23% in females, -28% in males); and the number of flies per line (median about 200) matches the paper's 100-150 flies per sex, line and food. Per-sex mean lifespans are only shown in Fig. 1 and were not digitised.
The summary dataset has, for each food (suffix
Y15 = full food, 15% yeast;
Y5 = restricted food, 5% yeast;
Y15Water = F+W;
Y5Met = R+M;
Y5EAA = R+E):
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mn_Lifespan_*: mean lifespan (days);
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se_Lifespan_*: its standard error;
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NFlies_* (obsolete, design information): the number of flies behind the mean (column "N", or "N Failed" for F+W, i.e. the number of deaths, all flies being followed until death).
The authors analysed the effect of dietary restriction (line-by-food interaction) with a mixed-model ANOVA on bottle-level data; no per-line restriction index was published and there was no GWAS. The lifespan response of a line to dietary restriction can be derived from mn_Lifespan_Y5 and mn_Lifespan_Y15.
Of note:- The paper (Fig. 1 legend) says that R+M and R+E were tested on six lines, but Supplementary Table 1b has R+M values for eight lines (DGRP_304 and DGRP_362 have R+M but no R+E values). The values are uploaded as published.
- The F+W, R+M and R+E lines were chosen among the 25 most viable of the 34 lines, so they are a biased subset (as stated in the paper), and their cohorts are smaller (25-71 flies per line and food).
- DGRP_427 (30 and 39 flies on full and restricted food) and DGRP_714 (43 flies on full food) have small cohorts.
Not uploaded, because no per-line values were published (figures or ANOVA tables only): the per-sex lifespans, median lifespan and Logistic-Makeham mortality parameters (Table 1), fecundity at days 5, 10 and 20 and the proportion of eggs developing into pupae (Figs 2 and 3, and Table 2). Supplementary Table 2 (amino acid content of the diets) is not a phenotype.
