Bonfini et al., 2021
Multiscale analysis reveals that diet-dependent midgut plasticity emerges from alterations in both stem cell niche coupling and enterocyte size
[10.7554/elife.64125]

Description

Midgut length (total and regional) and width were measured on mated females of 200 DGRP lines after 5 days on a high-sugar or high-yeast diet; midguts were longer on high yeast in 184 of 188 lines. Mitotic cell counts and enterocyte area were also measured in 7 lines.

Comments from curator

Phenotyping data comes from the source data files of the Figures and data section of the article:
- Figure 1—source data 2 (elife-64125-fig1-data2-v2.csv, "Numeric data for Figure 1F and G"): one row per midgut of the DGRP panel, used for raw dataset 1.
- Figure 6—source data 1 (elife-64125-fig6-data1-v2.csv, "Numeric data for Figure 6A, Figure 6—figure supplement 1A, Figure 7A and Figure 7—figure supplement 1B"): one row per enterocyte of a panel of 7 DGRP lines, used for raw datasets 2 and 3.
The authors' R code is given in Supplementary file 2 (R markdown).

Mated females were moved at eclosion to one of two isocaloric diets, HS (high sugar: 11.85 g/L brewer's yeast, 168.1 g/L sucrose) or HY (high yeast: 105.9 g/L yeast, 74.1 g/L sucrose), and their midguts were dissected 5 days after eclosion. Tiled images of whole midguts were measured in FIJI (spline lines along the midgut for lengths, perpendicular to it for widths), in µm. All data are from females (sex F; the previous upload had sex NA). The diet is given by the suffix _HS or _HY of the phenotype names.

Raw dataset 1 (Figure 1F-G, 200 lines): one row per midgut, with the total midgut length (TotalLength, the sum of the three regional lengths), the length of the anterior, middle and posterior midgut (AntLength, MidLength, PostLength) and the width of the anterior and posterior midgut (AntWidth, PostWidth). The source codes the diet as x (HS) and y (HY), as in the authors' R code. The experiment was replicated three times (obsolete phenotype block: a, b, c), each replicate being dissected in several groups (code: a1-a6, b1-b5, c1-c3); additional_code and alias (line number + additional_code) are the authors' sample labels and Gut_Number numbers the midguts of a line, diet and group. These five design columns are kept as obsolete phenotypes. Changes to the source:
- 15 midguts without a DGRP line number (block c, group c3) were removed.
- 4 midguts of DGRP_563 have the diet coded "Y" instead of "y": they were taken as HY. The authors' code only used "y", so line 563 (1 HS and 4 HY midguts) was not part of their analyses.
- The authors removed 6 midguts with aberrant measurements ("samples that subsequently proved crazy": anterior width of 1000 µm or more, or middle length of 1500 µm or more; DGRP_038 HY, DGRP_228 HS and HY, DGRP_287 HS, DGRP_332 HS and DGRP_761 HY). All their measurements were set to NA.

The previous raw dataset on DGRPool was the source file as is, with the diet as a text phenotype, so the line means computed by DGRPool pooled the HS and HY midguts. It was replaced by the layout above, and its phenotypes anteriorLength, middleLength, posteriorLength, anteriorwidth, posteriorwidth, totalLength, diet and image (an empty column) were removed.

The authors analysed 188 lines: the lines measured on both diets, minus the 7 lines that are not among the genotyped DGRP lines (DGRP_190, 339, 343, 473, 556, 719 and 982; DGRP_240 to 243 were measured on HY only). The means computed from raw dataset 1 reproduce the paper for these 188 lines: midguts are longer on HY than on HS in 184 lines, the HY/HS ratio of mean total length ranges from 0.98 to 1.47 (median 1.18), and the HS-HY difference is significant in 132 lines (t-test per line, FDR 5%). The authors' R code also dropped 30 midguts that have a total length but no anterior width or middle length (R subset() removes NA rows). They are kept here, so the line means of TotalLength differ from those plotted in Figure 1F for 23 of the 376 line/diet combinations (by up to 0.21 mm). The paper's figures above are the same with or without them.

The authors' GWAS used, per line, the difference in total midgut length between diets (mean TotalLength_HY minus mean TotalLength_HS), with Wolbachia status and the difference in body weight between diets as covariates (the body weights were not published). Figure 1F shows the ratio mean TotalLength_HY / mean TotalLength_HS. Figure 1G shows the ratio of posterior to anterior length.

Raw datasets 2 and 3 (Figures 6A and 7A): 7 DGRP lines chosen as high (DGRP_362, 370) or low (DGRP_356, 502, 765, 853, 911) responders to diet, on the same diets and dissected at the same age, in three replicate experiments. Raw dataset 2 has one row per midgut (267 midguts, 13 to 27 per line and diet): total midgut length (MidgutLen, µm) and number of mitotic pH3⁺ cells counted in the midgut (PH3Cells). Raw dataset 3 has one row per enterocyte (7,871 cells, about 30 adjacent cells per midgut, outlined with an anti-mesh staining): enterocyte area (ECArea, µm²). The obsolete phenotypes Panel_GutID and EC_GutID (source column xLookup: Bloomington stock number, diet, midgut number, replicate) link each enterocyte to its midgut. Panel_Repeat/EC_Repeat and Panel_Cross are the replicate experiment and the parental vial set of the source. 4 midguts have no length and 1 has no pH3⁺ count (NA). The source columns Type and Type1 (responder class of the line) were not uploaded. In their figures, the authors averaged midgut length and pH3⁺ counts over the rows of the per-cell table (each midgut weighted by its number of measured cells), so their line means differ slightly from the per-midgut means computed by DGRPool.

The midgut RNA-seq of the paper (Canton-S, not DGRP lines) is in ArrayExpress (E-MTAB-10812).

Other external data available

E-MTAB-10812 3' RNA-seq of midguts of Canton-S females on high-sugar vs high-yeast diet (not DGRP lines)

200 DGRP lines 189 genotyped 11 not_genotyped

DGRP_021 DGRP_026 DGRP_028 DGRP_031 DGRP_032 DGRP_038 DGRP_040 DGRP_041 DGRP_042 DGRP_045 DGRP_048 DGRP_057 DGRP_059 DGRP_073 DGRP_075 DGRP_083 DGRP_085 DGRP_088 DGRP_091 DGRP_093 DGRP_100 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_181 DGRP_189 DGRP_190 DGRP_195 DGRP_208 DGRP_217 DGRP_223 DGRP_227 DGRP_228 DGRP_229 DGRP_233 DGRP_235 DGRP_237 DGRP_239 DGRP_240 DGRP_241 DGRP_242 DGRP_243 DGRP_256 DGRP_280 DGRP_287 DGRP_301 DGRP_303 DGRP_306 DGRP_307 DGRP_309 DGRP_310 DGRP_313 DGRP_315 DGRP_317 DGRP_318 DGRP_319 DGRP_320 DGRP_321 DGRP_324 DGRP_332 DGRP_335 DGRP_336 DGRP_338 DGRP_339 DGRP_340 DGRP_343 DGRP_348 DGRP_350 DGRP_352 DGRP_354 DGRP_355 DGRP_356 DGRP_357 DGRP_358 DGRP_359 DGRP_360 DGRP_361 DGRP_362 DGRP_365 DGRP_370 DGRP_371 DGRP_373 DGRP_374 DGRP_375 DGRP_377 DGRP_379 DGRP_380 DGRP_381 DGRP_382 DGRP_383 DGRP_385 DGRP_386 DGRP_390 DGRP_391 DGRP_392 DGRP_395 DGRP_397 DGRP_399 DGRP_405 DGRP_406 DGRP_409 DGRP_427 DGRP_437 DGRP_439 DGRP_440 DGRP_441 DGRP_443 DGRP_461 DGRP_473 DGRP_486 DGRP_491 DGRP_502 DGRP_505 DGRP_509 DGRP_517 DGRP_528 DGRP_530 DGRP_535 DGRP_551 DGRP_555 DGRP_556 DGRP_559 DGRP_563 DGRP_566 DGRP_584 DGRP_589 DGRP_595 DGRP_627 DGRP_630 DGRP_634 DGRP_639 DGRP_703 DGRP_705 DGRP_707 DGRP_712 DGRP_714 DGRP_716 DGRP_719 DGRP_721 DGRP_730 DGRP_732 DGRP_737 DGRP_738 DGRP_748 DGRP_757 DGRP_761 DGRP_765 DGRP_774 DGRP_776 DGRP_783 DGRP_786 DGRP_787 DGRP_790 DGRP_796 DGRP_801 DGRP_802 DGRP_804 DGRP_805 DGRP_808 DGRP_810 DGRP_812 DGRP_818 DGRP_819 DGRP_821 DGRP_822 DGRP_832 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_892 DGRP_894 DGRP_897 DGRP_900 DGRP_907 DGRP_908 DGRP_911 DGRP_913 DGRP_982

Datasets

Dataset	Phenotypes	DGRP lines
Raw dataset #1	12 phenotypes AntLength_HS AntLength_HY AntWidth_HS AntWidth_HY MidLength_HS MidLength_HY PostLength_HS PostLength_HY PostWidth_HS PostWidth_HY TotalLength_HS TotalLength_HY	200 DGRP lines DGRP_021 DGRP_026 DGRP_028 DGRP_031 DGRP_032 DGRP_038 DGRP_040 DGRP_041 DGRP_042 DGRP_045 DGRP_048 DGRP_057 DGRP_059 DGRP_073 DGRP_075 DGRP_083 DGRP_085 DGRP_088 DGRP_091 DGRP_093 DGRP_100 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_181 DGRP_189 DGRP_190 DGRP_195 DGRP_208 DGRP_217 DGRP_223 DGRP_227 DGRP_228 DGRP_229 DGRP_233 DGRP_235 DGRP_237 DGRP_239 DGRP_240 DGRP_241 DGRP_242 DGRP_243 DGRP_256 DGRP_280 DGRP_287 DGRP_301 DGRP_303 DGRP_306 DGRP_307 DGRP_309 DGRP_310 DGRP_313 DGRP_315 DGRP_317 DGRP_318 DGRP_319 DGRP_320 DGRP_321 DGRP_324 DGRP_332 DGRP_335 DGRP_336 DGRP_338 DGRP_339 DGRP_340 DGRP_343 DGRP_348 DGRP_350 DGRP_352 DGRP_354 DGRP_355 DGRP_356 DGRP_357 DGRP_358 DGRP_359 DGRP_360 DGRP_361 DGRP_362 DGRP_365 DGRP_370 DGRP_371 DGRP_373 DGRP_374 DGRP_375 DGRP_377 DGRP_379 DGRP_380 DGRP_381 DGRP_382 DGRP_383 DGRP_385 DGRP_386 DGRP_390 DGRP_391 DGRP_392 DGRP_395 DGRP_397 DGRP_399 DGRP_405 DGRP_406 DGRP_409 DGRP_427 DGRP_437 DGRP_439 DGRP_440 DGRP_441 DGRP_443 DGRP_461 DGRP_473 DGRP_486 DGRP_491 DGRP_502 DGRP_505 DGRP_509 DGRP_517 DGRP_528 DGRP_530 DGRP_535 DGRP_551 DGRP_555 DGRP_556 DGRP_559 DGRP_563 DGRP_566 DGRP_584 DGRP_589 DGRP_595 DGRP_627 DGRP_630 DGRP_634 DGRP_639 DGRP_703 DGRP_705 DGRP_707 DGRP_712 DGRP_714 DGRP_716 DGRP_719 DGRP_721 DGRP_730 DGRP_732 DGRP_737 DGRP_738 DGRP_748 DGRP_757 DGRP_761 DGRP_765 DGRP_774 DGRP_776 DGRP_783 DGRP_786 DGRP_787 DGRP_790 DGRP_796 DGRP_801 DGRP_802 DGRP_804 DGRP_805 DGRP_808 DGRP_810 DGRP_812 DGRP_818 DGRP_819 DGRP_821 DGRP_822 DGRP_832 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_892 DGRP_894 DGRP_897 DGRP_900 DGRP_907 DGRP_908 DGRP_911 DGRP_913 DGRP_982	Download
Raw dataset #2	4 phenotypes MidgutLen_HS MidgutLen_HY PH3Cells_HS PH3Cells_HY	7 DGRP lines DGRP_356 DGRP_362 DGRP_370 DGRP_502 DGRP_765 DGRP_853 DGRP_911	Download
Raw dataset #3	2 phenotypes ECArea_HS ECArea_HY	7 DGRP lines DGRP_356 DGRP_362 DGRP_370 DGRP_502 DGRP_765 DGRP_853 DGRP_911	Download