EMBO/SourceData huggingface dataset:
Figure legend: "(a) HeLa cells transfected for 24 h with GFP-Atg16L1 (green) were incubated with CellMask Orange plasma membrane stain for 5 min at 37 °C, after which they were imaged immediately (in an incubated chamber at 37 °C). A time series after fusion of a CellMask Orange vesicle (red) with a GFP-Atg16L1 vesicle (green) is shown. Scale bar, 5 μm. A higher-magnification image showing co-localization (yellow) of GFP-Atg16L1 vesicle (green) with CellMask Orange-positive vesicle (red), indicated by arrows, is also shown in the top and bottom panels."
NCBI gene IDs:
"Atg16L1: 55054"
Figure legend: "(b, c) HeLa cells transfected with control, clathrin heavy chain, AP1 or AP2 siRNA for 72 h were subsequently transfected with GFP-Atg16L1 (green) together with the siRNA for the next 24 h. The cells were then incubated for 15 min with Alexa Fluor-555-conjugated cholera toxin subunit B (red) at 4 °C, followed by further incubation for 10 min at 37 °C, after which the cells were fixed for confocal analysis (b). The co-localization (yellow) of GFP-Atg16L1 (green) with cholera toxin (red) in control or clathrin heavy-chain knockdown is shown and is quantified in the graphs in c. n = 25 cells. Three asterisks, P = 0.0002 for clathrin heavy-chain knockdown, and P 0.0001 for AP2 knockdown. All error bars represent s.e.m. Scale bar, 5 μm."
NCBI gene IDs:
"Atg16L1: 55054
clathrin heavy chain: 1213
clathrin heavy-chain: 1213"
Figure legend: "(a) HeLa cells transfected with two rounds of control, clathrin heavy chain or AP2 siRNA for 4 days were collected for immunoprecipitation (IP) with anti-Atg16L1 antibody. Western blot for total lysate (bottom) and IP (top) were performed with anti-Atg16L1 and anti-clathrin antibodies. Note the decrease in Atg16L1-clathrin interaction with AP2 knockdown. The graph shows quantification of the Atg16L1-clathrin or Atg16L1-AP2 with knockdown of control, clathrin heavy chain or AP2 from two independent experiments."
NCBI gene IDs:
"clathrin heavy chain: 1213"
Figure legend: "(b) HeLa cells transfected for 24 h with Flag-tagged wild-type Atg16L1, GFP-PLC(PH) together with empty vector (control) or dominant-negative dynamin II mutant (K44A dynamin; DN-Dyn) were fixed and analysed by confocal microscopy. Note the co-localization of Atg16L1 with PLC(PH) at the plasma membrane; this is quantified in the graph at the right. Asterisk, P 0.01. n = 20 cells. Scale bars, 5 μm. DAPI, 4′,6-diamidino-2-phenylindole."
NCBI gene IDs:
"Atg16L1: 55054
dynamin II: 1785
PLC(PH): 5333"
Figure legend: "  (D) Survival of WT, PI3Kγ null (left) and liver-specific PI3Kγ knockout mice (PI3Kγ floxtg/tg x AlbCre(tg)/tg, middle) or systemic application of the PI3Kγ inhibitor, AS605240 (right) in a model of polymicrobial sepsis induced by peritoneal contamination with a human stool suspension. Animal numbers: B6: 86 (%male: 52, %female: 48), B6-Pi3kcgko/ko: 59 (%male: 51, %female 49), B6-Pi3kcgflox/flox x AlbCre(tg)/tg: 25 (%male: 68, %female 32), FVB/N Vehicle: 25 (%male: 44, %female 56), FVB/N AS: 43 (%male: 44, %female 56)  "
NCBI gene IDs:
"Alb: 11657
Cre: 2777477
Pi3kcg: 30955
PI3Kγ: 30955"
Figure legend: "(b) Correlation analyses of RNA expression levels of uPA (PLAU gene), PAI-1 (SERPINE1 gene), and the neutrophil marker gene FPR1, and overall survival of breast cancer patients (stages 0 and 1) with high and low PLAU or SERPINE1 gene expression levels (cut-off z≥ 2.0) in the METABRIC breast cancer cohort."
NCBI gene IDs:
"FPR1: 14293
PLAU: 18792
uPA: 18792
PAI-1: 18787
SERPINE1: 18787"
Figure legend: "a, b, Representative images of GFP-LC3 puncta (autophagosomes) in skeletal (vastus lateralis) (a) and cardiac muscle (b) from GFP-LC3 transgenic mice at serial time points after exercise. Scale bar, 20 µm. c, Quantification of data (mean ± s.e.m. of 10 tissue sections) in a and b. **P  0.01, ***P  0.001 (one-way ANOVA)."
NCBI gene IDs:
"LC3: 67443///66734"
Figure legend: "a, Analysis of BCL2 phosphorylation (detected by anti-BCL2 immunoprecipitation and autoradiography of 32P-labelled cells) and beclin 1 co-immunoprecipitation with BCL2 in wild-type (WT) or BCL2 AAA MEFs grown in normal media or subjected to 4 h Earle's balanced salt solution (EBSS) starvation. p-BCL2, phospho-BCL2."
NCBI gene IDs:
"BCL2: 12043"
Figure legend: "c, Representative images of GFP-LC3 puncta (autophagosomes) in skeletal and cardiac muscle of GFP-LC3 wild-type and GFP-LC3BCL2 AAA mice before exercise, after 80 min exercise, or after 75% of maximal exercise capacity. Scale bar, 20 µm. d, Quantification of data (mean ± s.d. of 4 mice per experimental group) in c."
NCBI gene IDs:
"BCL2: 12043"
Figure legend: "A Quantification of the number of OCTμDsRed2μpositive/TOM20μnegative vesicles in cells expressing GFP, GFPμparkinWT, GFPμparkinR42P, GFPμparkinK211N, or GFPμparkinC431F, treated with or without antimycin A (anti A) as in (C); both the total number (white bars) and the number colocalizing with GFPμparkin (gray bars) are indicated. Bars represent the mean ± s.e.m. Pμvalues are given first for GFPμ/GFPμparkinμpositive vesicles, then for total vesicle number (n = 49-68 cells in 2-3 experiments); ns, not significant; **P &lt; 0.01; ***P &lt; 0.001)."
NCBI gene IDs:
"parkin: 5071"
Figure legend: "C HeLa cells expressing various GFP-parkin mutant contructs (green), pOCT-DsRed2 (red) and CFP-Drp1K38E were treated with 50 µM antimycin A for 2 h, then fixed and immunostained against TOM20. Arrows indicate matrix-positive/TOM20-negative structures colocalizing with GFP-parkin. Scale bars, 30 µm."
NCBI gene IDs:
"Drp1: 10059
parkin: 5071"
Figure legend: "A Representative immunoblot of whole‐cell lysates from U2OS:GFP and U2OS:GFP‐parkin cells transfected with non‐targeting siRNA or siRNA targeting Drp1 (siDrp1)."
NCBI gene IDs:
"Drp1: 10059
parkin: 5071"
Figure legend: "B U2OS:GFP−parkin cells transfected with siRNA targeting Drp1 were treated with DMSO (upper panels) or 25 μM antimycin A (anti A, lower panels) for 90 min, then fixed and immunostained against PDH (red) and TOM20 (blue). PDHE2/E3 bp−positive/TOM20−negative MDVs colocalizing with GFP−parkin (arrows) or not (circles) are indicated. Scale bars, 20 μm (first panels on left) and 2 μm."
NCBI gene IDs:
"Drp1: 10059
parkin: 5071"
Figure legend: "C Quantification of PDH−positive/TOM20−negative vesicles in U2OS:GFP and U2OS:GFP−parkin cells transfected with the indicated siRNA, treated with DMSO or antimycin A (anti A) as in (B); both the total number (white bars) and the number colocalizing with GFP−parkin (gray bars) are indicated. Bars represent the mean ± s.e.m. P−values are given first for GFP−/GFP−parkin−positive vesicles, then for total vesicle number (n = 48-85 cells in 2-3 experiments); ns, not significant; ***P &lt; 0.001)."
NCBI gene IDs:
"parkin: 5071"
Figure legend: "E Quantification of the distance between the centres of GFP−parkin−negative (black bar) or −positive (gray bar) vesicles and the edge of the nearest mitochondrial tubule for the vesicles quantified in antimycin A−treated U2OS:GFP−parkin cells transfected with siDrp1 in (C). Error bars represent the mean ± s.e.m.; *P &lt; 0.05 (obtained by Student's t−test)."
NCBI gene IDs:
"Drp1: 10059
parkin: 5071"
Figure legend: "F U2OS:GFP‐parkin cells transfected with siRNA targeting Drp1 (siDrp1) were treated with 25 μM antimycin A for 90 min prior to fixation. Samples were immunostained against TOM20 (blue) and the indicated mitochondrial marker (red). TOM20‐negative MDVs containing the specified cargo and colocalizing with GFP‐parkin (arrows) or not (circles) are indicated. Arrowheads show lack of colocalization between GFP‐parkin and the indicated mitochondrial marker. Scale bars, 20 μm (first two columns of panels) and 2 μm (remaining columns of panels)."
NCBI gene IDs:
"Drp1: 10059"
Figure legend: "G Quantification of TOM20−negative structures that stained positively for the indicated cargo in U2OS:GFP (GFP) and U2OS:GFP−parkin (GFP−parkin) cells, transfected with siRNA targeting Drp1, treated with antimycin A (anti A); both the total number (white bars) and the number colocalizing with GFP−parkin (gray bars) are indicated. Error bars represent the mean ± s.e.m. P−values are given first for GFP−/GFP−parkin−positive vesicles, then for total vesicle number (n = 24-59 cells in two experiments; ns, not significant; ***P &lt; 0.001)."
NCBI gene IDs:
"Drp1: 10059
parkin: 5071"
Figure legend: "AHeLa cells, transfected with siRNA targeting Drp1 and GFP‐parkin (green), were treated with 25 μM antimycin A for 90 min following a 30‐min pretreatment with 50 nM bafilomycin A1, then fixed and immunostained against PDH E2/E3 bp (red) and TOM20 (blue). PDH E2/E3 bp‐positive/TOM20‐negative MDVs colocalizing with GFP‐parkin (arrows) or not (circles) are indicated. Scale bar, 30 μm."
NCBI gene IDs:
"Drp1: 10059"
Figure legend: "CHeLa cells, transfected with GFP‐parkin (green) and siRNA targeting Drp1 and Atg5, were treated with 25 μM antimycin A for 90 min, then fixed, immunostained for PDH (red) and TOM20 (blue), and counterstained for Hoescht (gray). PDH E2/E3bp bp‐positive/TOM20‐negative MDVs colocalizing with GFP‐parkin (arrows) or not (circles) are indicated. Scale bars, 20 μm."
NCBI gene IDs:
"Atg5: 9474
Drp1: 10059"
Figure legend: "A Representative immunoblot of whole‐cell lysates from HeLa cells transfected with non‐targeting siRNA or siRNA targeting PINK1 (siPINK1), treated with 10 μM CCCP for 6 h in order to stabilize the PINK1 full‐length band."
NCBI gene IDs:
"PINK1: 65018"
Figure legend: "B HeLa cells transfected with GFP−parkin (green) and siRNA targeting PINK1 (siPINK1) or non−targeting control (ctrl siRNA), were treated with 25 μM antimycin A for 90 min, then fixed and immunostained for PDH E2/E3 bp (red) and TOM20 (blue). PDH E2/E3 bp−positive/TOM20−negative MDVs colocalizing with GFP−parkin (arrows) or not (circles) are indicated. Arrowheads indicate parkin−positive MDVs adjacent to mitochondria, possibly budding. Scale bar, 20 μm."
NCBI gene IDs:
"PINK1: 65018"
Figure legend: "A Representative immunoblot of whole‐cell lysates from U2OS:GFP and GFP‐parkin cells treated with DMSO, 25 μM antimycin A (anti A), 25 μM antimycin A with 10 μM oligomycin (anti A + oligo), or 20 μM CCCP for the indicated time period."
NCBI gene IDs:
"parkin: 5071"
Figure legend: "C Quantification of mitochondrial clearance in U2OS:GFP−parkin cells treated as in (A), fixed and immunostained for TOM20. Data are shown as percentage of cells containing mitochondria, by TOM20 staining, visualized by fluorescence microscopy. Error bars represent the mean ± s.e.m. (n = 3 experiments, with at least 85 cells quantified per condition, per experiment)."
NCBI gene IDs:
"parkin: 5071"
Figure legend: "C Imaging of the PI4P probe GFP-2xPHOsh2 in wild type and cho1∆ cells. Images show average intensity projections of deconvolved z-stacks in which black and white pixels were inverted."
NCBI gene IDs:
"cho1: 856748"
Figure legend: "D Scatter dot plot showing PI4P levels at the plasma membrane (see experimental procedure for details of the quantification) in wild type and cho1∆ cells. Values are means ± SD, n &gt; 100 cells, observed over 3 experiments. Mann-Whitney tests were performed."
NCBI gene IDs:
"cho1: 856748"
Figure legend: "E Ratio of PI4P average fluorescence intensity in the bud versus mother cell in the cho1∆ mutant. Values are means ± SD, n &gt; 100 cells, observed over 3 experiments. A value &gt; 1 indicates enrichment of the fluorescence in the bud."
NCBI gene IDs:
"cho1: 856748"
Figure legend: "F Images of Bem1-GFP in cho1∆ 9xMyc-AID-stt4 cells after 30 min treatment with or without 0.5 mM auxin. Images are average intensity projections of deconvolved z-stacks."
NCBI gene IDs:
"Myc: 
cho1: 856748
stt4: 851014"
Figure legend: "G Frequency of cells with polarized Bem1-GFP signal or Bem1-GFP in puncta in cho1∆ 9xMyc-AID-stt4 cells treated with or without auxin as shown in F. Values are means ± SD, n &gt; 100 cells in each of 6 independent experiments. Paired Student's t-tests were performed."
NCBI gene IDs:
"Myc: 
cho1: 856748
stt4: 851014"
Figure legend: "H Images of Bem1-GFP (cyan) and Cdc24-mCherry (red) signals in cho1∆ 9xMyc-AID-stt4 cells with or without auxin. Images display maximum intensity projections of z-stacks."
NCBI gene IDs:
"Myc: 
cho1: 856748"
Figure legend: "I Maximum intensity projections of z-stacks displaying Bem1-GFP in the mutants indicated. Bem1-GFP was imaged in mss4-102 cho1∆ cells after shifting to the restrictive temperature for 30 minutes."
NCBI gene IDs:
"cho1: 856748
mss4: 851789"
Figure legend: "D Ten-fold serial dilutions of cells and subsequent colony formation on the indicated plates, where expression of wild type GALp-CDC42 is either induced in the presence of Gal or repressed in Dex. Note how mutation of the wild type Cdc42 (KKSKK) to MMSMM is lethal (see blue box), whereas appending the Bem1 BC-1 motif to this cdc42 mutant restores viability (red box)."
NCBI gene IDs:
"GALp: 
Bem1: 852499
cdc42: 850930
Cdc42: 850930
CDC42: 850930"
Figure legend: "E Representative images of the mEOS-cdc42 mutants signal (cyan) after inducing the expression of GAL1p-CDC42 in the presence of Gal or repressing it in the presence of Dex. The cells in the blue and red boxes correspond to the cells in the blue and red box in panel (D). Images are average fluorescence intensity projections in which black and white pixels have been inverted."
NCBI gene IDs:
"CDC42: 850930
GAL1p: 852308"
Figure legend: "C Representative images of the indicated bem1 mutants tagged with GFP at the BEM1 locus. The inverted fluorescence images are average intensity projections."
NCBI gene IDs:
"GFP: 
BEM1: 852499
bem1: 852499"
Figure legend: "F DIC images of the indicated bem1 and cdc24 mutants showing the increased morphological defects ensuing from loss of lipid tethering in the bem1 and cdc24 mutants."
NCBI gene IDs:
"bem1: 852499
cdc24: 851190"
Figure legend: "B Global average MSD curves of mEOS-Cdc42 in the strains indicated at the Pole (P) and Non-Pole (NP) of cells. Trajectories longer than 6 frames were analyzed. Number of trajectories analyzed: BEM1 (n = 11 cells: Non Pole: 1814 tracks; Pole: 706); bem1 bc-14E px (n = 10 cells: Non Pole: 1793 tracks; Pole: 908); bem1 bc-14E (n = 13 cells: Non Pole: 1714 tracks; Pole: 975). Error bars display s.e.m. C D coefficients of mEOS-Cdc42 in the strains indicated (in box-plots displaying the median (line), the 25-75 percentiles (box) and the mean (cross)), which were compared using a non-parametric, two-tailed Mann-Whitney rank sum test. "
NCBI gene IDs:
"BEM1: 852499
bem1: 852499"
Figure legend: "C (Upper) Schematic diagram of dox-inducible shRNA system for MATR3  knockdown and MATR3  rescue in AML12  cells. (Lower)  Western blotting  detected the expression level of MATR3  after 3 days of Dox  treatment (+Dox) and followed by 3 days of Dox  removal (±Dox) in AML12  cells. Rep, replicate."
NCBI gene IDs:
"MATR3: 17184"
Figure legend: "D (Upper) Representative cross-section images showing distribution of histone  modifications  upon Ctrl and MATR3  knock down (+Dox). (Lower) Quantify the distribution pattern of histone  modifications by Standard Deviation of Pixel Intensity in cell nuclei. For H3K9me3, n=102 (Ctrl) or 84 (+Dox); for H3K9me2, n=100 (Ctrl) or 101 (+Dox); for H3K27me3, n=98 (Ctrl) or 98 (+Dox); for H3K27ac, n=117 (Ctrl) or 124 (+Dox); for H3K27me3, n=98 (Ctrl) or 98 (+Dox); for H3K4me3, n=107 (Ctrl) or 97 (+Dox). Each point represents one cell. The P values were calculated using unpaired two-tailed Student's t test; ns, not significant, *p&lt;0.05, ****p&lt;0.0001. Error bars indicate mean ± s.e.m."
NCBI gene IDs:
"MATR3: 17184"
Figure legend: "G (Left) Representative cross-section images showing relative distribution between AS L1  RNA with MATR3  and with histone  modification marks (H3K27me3, H3K9me3 and H3K27ac) in AML12  cells. Probes for RNA FISH were designed towards the consensus sequence of antisense L1_Mus1 RNAs. (Right) Line charts showing pixel intensity of each channel on the ROIs. Scale bars, 5μm. r, coefficient of correlation."
NCBI gene IDs:
"L1: 107980437"
Figure legend: "H Normalized average density of the marks (top) and heatmaps(bottom) for the two groups of L1  loci. The two groups are antisense L1  RNAs or sense L1  RNAs that interacted  with MATR3. L1  loci with RIP (MATR3  -IgG) count number &gt;= 10 of antisense RNA were identified as MATR3-associated antisense L1, and the same cutoff for MATR3-associated sense L1."
NCBI gene IDs:
"L1: 107980437"
Figure legend: "A (Left) The representative cross-section image showing nuclear  distribution of MATR3  and H3K27me3 before and after 12h treating with antisense L1  ASOs in AML12  cells. (Right) Line charts showing pixel intensity of each channel on the ROIs. r, coefficient of correlation. Scale bars, 5μm."
NCBI gene IDs:
"L1: 107980437"
Figure legend: "C (Left) The representative cross-section image showing nuclear  distribution of H3K27me3 and AS  L1  RNA before and after MATR3  knockdown (Dox  treatment for 3d) in AML12  cells. (Right) The normal distribution curve for the AS  L1  pixel intensity. Scale bars, 5μm."
NCBI gene IDs:
"L1: 107980437
MATR3: 17184"
Figure legend: "E Representative images showing nuclear colocalization  of AS L1  RNAs with wild-type and truncated GFP-MATR3  proteins in AML12  cells. Scale bars, 5μm."
NCBI gene IDs:
"GFP: 
L1: 107980437
MATR3: 17184"
Figure legend: "G Representative cross-section images showing nuclear localization  of  H3K27me3 upon Ctrl, MATR3  knockdown and exogenous GFP-MATR3  (WT/△ZF1/△ZF2/△RRM1/△RRM2) overexpression in AML12  cells. Scale bars, 5μm."
NCBI gene IDs:
"GFP: 
MATR3: 17184"
Figure legend: "H Representative images of  droplet formation assays by GFP-MATR3  with different concentration (0nM, 5nM, 50nM, 200nM, 500nM) of AS L1  RNAs. GFP-MATR3  protein concentration, 3 μM. NaCl  concentration, 50mM. Scale bars, 5μm."
NCBI gene IDs:
"L1: 107980437"
Figure legend: "E Snapshot of an example region, showing Hi-C, H3K27me3 ChIP-seq and AS L1  in MATR3 RIP-seq in Ctrl and/or shMatr3 samples, using HiCExplorer. The values on the y-axis for Hi-C contact and O/E heatmap are iced normalized read counts at 100kb resolution. The values on the y-axis for ChIP-seq and RIP-seq  are average reads per million of mapped reads (RPM)."
NCBI gene IDs:
"L1: 107980437
Matr3: 17184"
Figure legend: "A Representative Western blot  on chromatin  fractionation experiments of Ctrl and shMatr3 cells. Each fraction was loaded with same number of cells. GAPDH, histone H3,  Lamin A/C were used as positive controls for S1, S2  and S3, S4, respectively."
NCBI gene IDs:
"Matr3: 17184"
Figure legend: "B Genome browser view of the SAMMY-Seq  and H3K27me3 ChIP-seq in Ctrl and shMatr3 (replicate 1 and 2 merged) cells at a representative region. Gray boxes under each SAMMY-seq track showing the SAMMY-seq  domains. The shadows showing the shMatr3 loss SAMMY-seq  domains."
NCBI gene IDs:
"Matr3: 17184"
Figure legend: "H Average MATR3 RIP-seq sense and antisense signal at L1  loci around H3K27me3 domains (groups as in F) with 200kb upstream and downstream flanking regions from AML12  cells."
NCBI gene IDs:
"L1: 107980437"
Figure legend: "C MATR3  knockdown and GFP-tagged WT/S85C/F115C MATR3  protein replacement in N2A  cells. The efficiency of endogenous MATR3  knockdown and exogenous GFP-MATR3  (WT/S85C/F115C) over-expression as detected by western blotting. Representative of two independent replicates with similar results."
NCBI gene IDs:
"GFP: 
MATR3: 17184"
Figure legend: "G Representative cross-section images showing nuclear localization  of H3K27me3 upon Ctrl, MATR3  knockdown and exogenous MATR3  (WT/S85C/F115C) overexpression in N2A  cells. Scale bars, 5μm. H Standard deviation of H3K27me3 pixel intensity upon Ctrl (n=93), MATR3  knock down (n=100), GFP-MATR3  (WT) rescue (n=104), GFP-MATR3  (S85C) rescue (n=82) and GFP-MATR3  (F115C) rescue (n=120). The P values were calculated using unpaired two-tailed Student's t test; ns, not significant, *p&lt;0.05, ****p&lt;0.0001. Error bars indicate mean ± s.e.m."
NCBI gene IDs:
"GFP: 
MATR3: 17184"
Figure legend: "(A) survival curves of MyD88 flies injected with different doses of A. fumigatus conidia (c/f: conidia injected per fly; error bars represent mean ± SD of the survival of biological triplicates of 20 flies each)."
NCBI gene IDs:
"MyD88: 35956"
Figure legend: "(B) fungal loads of single MyD88 mutant and wild-type flies (50 conidia injected per fly)."
NCBI gene IDs:
"MyD88: 35956"
Figure legend: "(C-D) GFP-labeled A. fumigatus (50 conidia per fly) injected in wild-type (C) or MyD88 mutant (D) flies form hyphae in the thorax of the flies (arrows). Scale bars 50 μm."
NCBI gene IDs:
"GFP: 
MyD88: 35956"
Figure legend: "(E) expression level of Drosomycin induced by different doses of injected A. fumigatus conidia measured by RT-qPCR; M. luteus (OD=10) represents the positive control (pooled data of n=3 experiments, biological replicates)."
NCBI gene IDs:
"Drosomycin: 38419"
Figure legend: "Hayan flies are susceptible to A. fumigatus. Survival (F), of Hayan mutant flies; Hayan 0h vs. 120h, (error bars represent mean ± SD of the survival of biological triplicates of 20 flies each)."
NCBI gene IDs:
"Hayan: 32831"
Figure legend: "time course of fungal loads of single Hayan mutant flies (500 conidia per fly) (G), and fungal load upon death (500 conidia per fly) (H) of Hayan mutant flies; Hayan 0h vs. 120h, (error bars represent mean ± SD of the survival of biological triplicates of 20 flies each)."
NCBI gene IDs:
"Hayan: 32831"
Figure legend: "(A) survival of MyD88 flies injected with ∆pptA and wild-type (Af) A. fumigatus conidia (error bars represent mean ± SD of the survival of biological triplicates of 20 flies each)."
NCBI gene IDs:
"pptA: 3513464
MyD88: 35956"
Figure legend: "(B) fungal loads of single flies after the injection of 500 ∆pptA conidia."
NCBI gene IDs:
"pptA: 3513464"
Figure legend: "(E) dose response of MyD88 flies after ∆gliP (gliotoxin) mutant or wild-type [∆akuB] A. fumigatus infection; error bars represent mean ± SD of the survival of biological triplicates of 20 flies each; wild-type flies are used as a control for the dose of 250 conidia. (F-H) dose response of MyD88 and wild-type flies after gliotoxin (F), fumagillin (G), and helvolic acid (H) injection at the indicated concentrations (20 flies per condition)."
NCBI gene IDs:
"akuB: 
gliotoxin: 3508164
gliP: 3508164
MyD88: 35956"
Figure legend: "(A) survival of MyD88 or wild-type flies to 250 injected ∆aspf1 (restrictocin mutant) or wild-type [∆akuB] A. fumigatus conidia (20 flies per condition); MyD88: ∆aspf1 vs. ∆akuB (***p=0.0007). (B) survival of MyD88 flies after the injection of different concentrations of restrictocin (R) (20 flies per condition ). (C-D) survival of antibiotics-treated (C) and axenic (D) MyD88 mutant flies after restrictocin injection (20 flies per condition)."
NCBI gene IDs:
"akuB: 
aspf1: 3505541
MyD88: 35956"
Figure legend: "(E-F) ribosomal RNA cleavage measurement after restrictocin or PBS injection in wild-type (E) and MyD88 (F) flies; the arrowheads show the position of the 28S RNA-derived α-sarcin fragments whereas arrows on the right show its electrophoretic band position."
NCBI gene IDs:
"α-sarcin: 
MyD88: 35956"
Figure legend: "(A-B) survival (A) and fungal load (B) of Bom∆55C (55C) deficient flies compared to wild-type and MyD88 after injection of 250 conidia (error bars represent mean ± SD of the survival of biological triplicates of 20 flies each); ****p &lt; 0.0001. (B): the fungal burden does not increase in Bom∆55C-deficient flies; wt 0h vs. 48h, **p=0.001; 55C 0h vs. 48h, **p=0.007; pooled data of n=3 experiments, biological replicates."
NCBI gene IDs:
"Bom: 37102///50207///49802///37101///50206///50209///37099///37100
MyD88: 35956"
Figure legend: "(C-D) rescue of the sensitivity of Bom∆55C flies to verruculogen (C) or to restrictocin (D) by the transgenic expression of individual 55C locus genes (caption in D also applies to (C)). 55C flies vs. BomS1, *p=0.0495, vs. BomS6 *p=0.011 for verruculogen assay (C); 55C flies vs. BomBc1 or BomS3, ****p&lt;0.0001, 55C flies vs. BomS6, **p=0.0028 for restrictocin assay (D) (20 flies per condition)."
NCBI gene IDs:
"BomBc1: 37099
BomS1: 37100
BomS3: 50209
BomS6: 50206"