Comments from curator
No new phenotype data: this study was rejected because no new phenotype was measured on DGRP lines.This is a multi-omics study of wing size. Its new data are molecular and genome-wide: the transcriptomes (BRB-seq) of the wing imaginal discs of wandering third-instar larvae of 32 DGRP lines, 16 with big and 16 with small wings, for females and males separately and in biological duplicate (128 samples; ArrayExpress
E-MTAB-7662; RNA levels of 10,017 genes in Dataset EV2). The authors associated these RNA levels, and the wing-disc protein levels of their previous study (
Okada et al. 2016, Nature Communications), with wing size (Datasets EV3 and EV4), and mapped eQTLs and pQTLs (Dataset EV7). These molecular results are not uploaded to DGRPool (see the repository identifiers). The RNAi validation of 20 size-associated genes (size ratio of the posterior to the anterior wing compartment, Fig 3 and Dataset EV6) was done on
hh-Gal4 > UAS-RNAi flies, not on DGRP lines.
The wing size traits of the 32 lines, listed in
Dataset EV1 (
Supplementary Information of the
paper;
PMC version), were not measured in this study: the Materials and Methods state that they were "previously measured and calculated" (Okada et al. 2016; Vonesch et al. 2016). They come from the adult wings and heads measured by
Vonesch et al. 2016 (
DGRPool study 34), as defined in the Methods of Okada et al. 2016:
-
absoluteCS: the raw wing centroid size (study 34, Wing_CentroidSize) minus the effects of food batch (study 34, Foodbatch) and of the homozygous In(2L)t and In(3R)Mo inversions estimated by a regression model (the sex effect is kept). It differs from the study 34 line means by one constant per food batch and inversion group (Pearson r = 0.999997).
-
relativeCS: the residual of the raw centroid size regressed on the interocular distance (study 34, Eye_Interocular_Dist), sex and food batch, i.e. the wing size relative to body size. Refitting this model on the study 34 line means reproduces it (Pearson r = 0.9998).
-
wing.size: the class of the line, B (big) or S (small), chosen from these values.
The same values were first published for 28 of the 32 lines in Supplementary Data 3 of
Okada et al. 2016, which also reused the data of Vonesch et al. 2016. The prediction of wing size in 143 DGRP lines (Fig 6C) also used the wing sizes of Vonesch et al. 2016.
A previous version of this study held Dataset EV1 as its summary dataset (64 rows: 32 lines, females and males). These values were checked and are identical to Dataset EV1, but since they are derived from study 34, the three phenotypes were renamed
mn_absoluteCS,
mn_relativeCS and
WingSizeClass (the old name wing.size is not valid) and made obsolete. The raw wing measurements of these lines are in study 34.
