He et al., 2014
Effect of Genetic Variation in a Drosophila Model of Diabetes-Associated Misfolded Human Proinsulin
[10.1534/genetics.113.157800]

Description

Eye area (pixels) was measured on F1 males from crosses of 177 DGRP lines to a GMR-Gal4, UAS-hINS^C96Y strain, a Drosophila model of diabetes-associated misfolded human proinsulin (smaller eyes are more degenerate). A GWAS on 154 lines found a peak in sulfateless.

Comments from curator

Phenotyping data comes from the Supporting Information of the paper (journal page, also on PMC; files taken from the Europe PMC supplementary files):
- Table S1 (TableS1.txt): raw data, the total eye area of each F1 male measured, with the Bloomington stock number of the DGRP line of the cross (2,671 flies, 178 crosses). Used for the raw dataset.
- Table S2 (TableS2.txt): the 154 DGRP lines used in the GWAS (RAL name and Bloomington stock number).

These are F1 phenotypes, not phenotypes of the inbred DGRP lines: virgin females of a tester strain (w; P{GMR-Gal4}, P{UAS-hINS^C96Y}/CyO, with GMR-Gal4 and UAS-hINS^C96Y recombined on chromosome 2) were crossed to males of each DGRP line. The F1 express the diabetes-causing mutant human preproinsulin hINS^C96Y in the developing eye, where it causes cell death and a smaller adult eye, so their eye area measures how much the heterozygous DGRP background modifies the degeneration (smaller eyes are more degenerate). The F1 males get their X chromosome from the tester mother. Each value is assigned to the DGRP father line, as in the authors' GWAS, and the cross is given in the phenotype name (_xhINSC96Y).

Crosses were reared at 25°C. Total eye area was measured as in Park et al. 2014 (3- to 5-day-old adults, eyes photographed under a stereomicroscope and measured with ImageJ), in screen pixels at the same microscope setting (the paper gives no conversion to µm²). Only males were measured, because they show a more severe phenotype than females. F1 females were also measured for 38 lines (r = 0.8 with the males, Figure S2), but these values are not published.

The raw dataset has one row per F1 male (sex M), with EyeArea_xhINSC96Y: 10 to 30 flies per cross (median 15), 177 DGRP lines. The line means range from 8,606 pixels (DGRP_639) to 58,630 pixels (DGRP_359), which the paper describes as 13% to 86% of the wild-type eye area. The crosses explain 58.6% of the variance of Table S1 (one-way ANOVA), as in the paper. The authors' GWAS used the mean eye area of the 154 crosses with lines sequenced in DGRP freeze 1 (Table S2; single-marker regression and EMMAX mixed model, about 1.6 million SNPs with MAF > 5%) and found a peak in an intron of sulfateless (sfl). The 23 other lines were not in the GWAS.

DGRP lines: the Bloomington stock numbers were mapped to DGRP lines. Three stocks are retired or were re-deposited under new numbers: 28177 is DGRP_352 and 28222 is DGRP_737 (named in Table S2; now Bloomington 83728 and 83729), and 25196 is DGRP_514 (a Core 40 line no longer at Bloomington; FlyBase lists DGRP_25196 as a synonym of DGRP-514). Stock 28120 (10 flies) is not a DGRP stock (in Bloomington's catalogue it is w*; P{lacW}bgm¹, and the DGRP series starts at 28122) and is not in Table S2, so it was dropped: the paper's 178 crosses are 177 lines here.

Of note: for DGRP_639, 7 of its 17 values appear twice in Table S1 (e.g. 14,503 and 17,294 pixels), which suggests duplicated entries (its 10 distinct values have a mean of 8,247 pixels, vs 8,606 with all 17). The values are uploaded as published. Not uploaded: the RNAi and mutant crosses (VDRC lines, ttv and botv mutants; not DGRP lines) and the allele-specific expression of sfl in F1 hybrids between DGRP lines (molecular data, Figures 5 and 6).

The companion paper Park et al. 2014 (DGRPool study 154) used the same tester on 38 Core lines and gives per-line means for both sexes. Its male means correlate with the line means of this study at r = 0.999 (37 of its 38 lines), but are 5% to 17% smaller, so the values are not identical.

177 DGRP lines 171 genotyped 6 not_genotyped

DGRP_021 DGRP_026 DGRP_028 DGRP_038 DGRP_040 DGRP_041 DGRP_042 DGRP_045 DGRP_057 DGRP_059 DGRP_069 DGRP_073 DGRP_075 DGRP_083 DGRP_085 DGRP_088 DGRP_091 DGRP_101 DGRP_105 DGRP_109 DGRP_129 DGRP_136 DGRP_138 DGRP_142 DGRP_149 DGRP_153 DGRP_158 DGRP_161 DGRP_176 DGRP_177 DGRP_189 DGRP_195 DGRP_208 DGRP_217 DGRP_223 DGRP_227 DGRP_228 DGRP_229 DGRP_233 DGRP_235 DGRP_237 DGRP_239 DGRP_256 DGRP_272 DGRP_280 DGRP_287 DGRP_301 DGRP_303 DGRP_304 DGRP_307 DGRP_309 DGRP_310 DGRP_313 DGRP_315 DGRP_318 DGRP_320 DGRP_321 DGRP_324 DGRP_325 DGRP_332 DGRP_335 DGRP_336 DGRP_338 DGRP_340 DGRP_350 DGRP_352 DGRP_356 DGRP_357 DGRP_358 DGRP_359 DGRP_360 DGRP_362 DGRP_365 DGRP_367 DGRP_371 DGRP_373 DGRP_374 DGRP_375 DGRP_377 DGRP_378 DGRP_379 DGRP_380 DGRP_381 DGRP_382 DGRP_383 DGRP_385 DGRP_386 DGRP_387 DGRP_391 DGRP_398 DGRP_399 DGRP_405 DGRP_406 DGRP_409 DGRP_426 DGRP_427 DGRP_437 DGRP_439 DGRP_440 DGRP_441 DGRP_443 DGRP_461 DGRP_486 DGRP_491 DGRP_492 DGRP_502 DGRP_508 DGRP_509 DGRP_513 DGRP_514 DGRP_517 DGRP_530 DGRP_531 DGRP_535 DGRP_554 DGRP_555 DGRP_563 DGRP_584 DGRP_589 DGRP_595 DGRP_639 DGRP_642 DGRP_646 DGRP_703 DGRP_705 DGRP_707 DGRP_712 DGRP_714 DGRP_716 DGRP_721 DGRP_730 DGRP_732 DGRP_737 DGRP_738 DGRP_748 DGRP_761 DGRP_765 DGRP_774 DGRP_776 DGRP_783 DGRP_786 DGRP_787 DGRP_790 DGRP_796 DGRP_799 DGRP_801 DGRP_802 DGRP_805 DGRP_808 DGRP_810 DGRP_812 DGRP_818 DGRP_819 DGRP_820 DGRP_821 DGRP_822 DGRP_837 DGRP_843 DGRP_849 DGRP_850 DGRP_852 DGRP_853 DGRP_855 DGRP_857 DGRP_859 DGRP_861 DGRP_879 DGRP_882 DGRP_884 DGRP_887 DGRP_890 DGRP_894 DGRP_897 DGRP_900 DGRP_908 DGRP_911 DGRP_913

Datasets

Dataset	Phenotypes	DGRP lines
Raw dataset #1	1 phenotypes EyeArea_xhINSC96Y	177 DGRP lines DGRP_021 DGRP_026 DGRP_028 DGRP_038 DGRP_040 DGRP_041 DGRP_042 DGRP_045 DGRP_057 DGRP_059 DGRP_069 DGRP_073 DGRP_075 DGRP_083 DGRP_085 DGRP_088 DGRP_091 DGRP_101 DGRP_105 DGRP_109 DGRP_129 DGRP_136 DGRP_138 DGRP_142 DGRP_149 DGRP_153 DGRP_158 DGRP_161 DGRP_176 DGRP_177 DGRP_189 DGRP_195 DGRP_208 DGRP_217 DGRP_223 DGRP_227 DGRP_228 DGRP_229 DGRP_233 DGRP_235 DGRP_237 DGRP_239 DGRP_256 DGRP_272 DGRP_280 DGRP_287 DGRP_301 DGRP_303 DGRP_304 DGRP_307 DGRP_309 DGRP_310 DGRP_313 DGRP_315 DGRP_318 DGRP_320 DGRP_321 DGRP_324 DGRP_325 DGRP_332 DGRP_335 DGRP_336 DGRP_338 DGRP_340 DGRP_350 DGRP_352 DGRP_356 DGRP_357 DGRP_358 DGRP_359 DGRP_360 DGRP_362 DGRP_365 DGRP_367 DGRP_371 DGRP_373 DGRP_374 DGRP_375 DGRP_377 DGRP_378 DGRP_379 DGRP_380 DGRP_381 DGRP_382 DGRP_383 DGRP_385 DGRP_386 DGRP_387 DGRP_391 DGRP_398 DGRP_399 DGRP_405 DGRP_406 DGRP_409 DGRP_426 DGRP_427 DGRP_437 DGRP_439 DGRP_440 DGRP_441 DGRP_443 DGRP_461 DGRP_486 DGRP_491 DGRP_492 DGRP_502 DGRP_508 DGRP_509 DGRP_513 DGRP_514 DGRP_517 DGRP_530 DGRP_531 DGRP_535 DGRP_554 DGRP_555 DGRP_563 DGRP_584 DGRP_589 DGRP_595 DGRP_639 DGRP_642 DGRP_646 DGRP_703 DGRP_705 DGRP_707 DGRP_712 DGRP_714 DGRP_716 DGRP_721 DGRP_730 DGRP_732 DGRP_737 DGRP_738 DGRP_748 DGRP_761 DGRP_765 DGRP_774 DGRP_776 DGRP_783 DGRP_786 DGRP_787 DGRP_790 DGRP_796 DGRP_799 DGRP_801 DGRP_802 DGRP_805 DGRP_808 DGRP_810 DGRP_812 DGRP_818 DGRP_819 DGRP_820 DGRP_821 DGRP_822 DGRP_837 DGRP_843 DGRP_849 DGRP_850 DGRP_852 DGRP_853 DGRP_855 DGRP_857 DGRP_859 DGRP_861 DGRP_879 DGRP_882 DGRP_884 DGRP_887 DGRP_890 DGRP_894 DGRP_897 DGRP_900 DGRP_908 DGRP_911 DGRP_913	Download