EMBO/SourceData huggingface dataset:
Figure legend: "(E) Immunoblots for the precursor form and processed form of FTMT-GFP, endogenous FTMT, NCOA4, LC3, and Tom20 using the mitochondrial fractions of Huh7 cells expressing FTMT-GFP with or without digestion with proteinase K in the presence or absence of DFP. mtHSP70 was used as the loading control."
NCBI gene IDs:
"GFP: 
FTMT: 94033"
Figure legend: "(B) Immunofluorescence staining for the polarized mitochondria (red), Tom20 (blue), LC3 (blue), and FTMTD57A (green) using Huh7 cells expressing FTMTD57A. Boxed areas are enlarged on the right. The white puncta in overlaid pictures indicate the colocalization of the polarized mitochondria, Tom20 and FTMTD57A or the colocalization of the polarized mitochondria, FTMTD57A, and LC3. Scale bar: 10 μm, and 5 μm in enlarged images."
NCBI gene IDs:
"FTMT: 94033"
Figure legend: "(A) Immunoblots for FTMT, frataxin, mitoferrin, HSP60, FTH1 and TfR using the hepatic mitochondrial fraction lysate and whole liver lysate in control (C57BL/6J) mice and STAM mice treated with DFP (0, 0.0375, or 0.075 mg/g body weight) (n=6). The expression of FTMT, frataxin, mitoferrin, FTH1, and TfR were normalized to HSP60 or β-actin, respectively. The central horizontal bar and the error bards indicate mean ± SD. The Tukey's honestly significant test was used for statistical analysis. *: P&lt;0.05, **: P&lt;0.01. (B) The mean number of mitophagosome-like structures/100 μm2 from four randomly selected areas in the livers of DFP (0.075 mg/g body weight)-administered mice were compared between control and FTMT siRNA-treated groups for STAM mice (n=6) and DMBA + HFD mice (n=6). The central horizontal bar and the error bards indicate mean ± SD. Two sample t test was used for statistical analysis. NC: negative control siRNA, *: P&lt;0.05. "
NCBI gene IDs:
"FTMT: 94033"
Figure legend: "(C) Frozen liver sections of DFP (0.075 mg/g body weight)-administered mice (STAM mice and DMBA + HFD) with or without FTMT knockdown were stained with dihydroethidium. Red fluorescence indicates the ROS production. Scale bar: 100 μm. siNC: negative control siRNA."
NCBI gene IDs:
"FTMT: 94033"
Figure legend: "(D, E) STAM mice (D) were fed a high-fat diet without DFP treatment or orally administered with 0.075 mg/g body weight of DFP from the age of 4 weeks, injected with FTMT siRNA (10 μl/g body weight) or negative control siRNA through the tail vein every 2 weeks for 8 weeks prior to sacrifice, and followed until 16 weeks of age (n=6). DMBA + HFD mice (E) were fed a high-fat diet, treated with DFP and siRNA in the same manner with STAM mice, and followed until 30 weeks of age (n=6). The number and maximum size of liver tumors were compared among the three groups (control without DFP, negative control siRNA, and FTMT siRNA with DFP). The central horizontal bar and the error bards indicate mean ± SD. The Tukey's honestly significant test was used for statistical analysis. *: P&lt;0.05, **: P&lt;0.01. Representative liver images are shown in the upper panel. Scale bar: 1 cm."
NCBI gene IDs:
"FTMT: 94033"
Figure legend: "B Interaction  of Atg18 with retromer  subunits. Genomically tagged  yomCherry-fusions of each retromer  subunit were expressed in SEY6210 atg18∆, atg21∆, hsv2∆ cells, together with a plasmid expressing  Atg18HA3yEGFP. Cell lysates were subjected to immunoprecipitation  using RFP-Trap magnetic beads and analyzed by SDS-PAGE and Western blotting against the indicated proteins."
NCBI gene IDs:
"HA3: 
yEGFP: 
yomCherry: 
atg18: 850577
Atg18: 850577
atg21: 856004
hsv2: 853138"
Figure legend: "D Atg18-Vps35 interaction. Genomically tagged Vps35yomCherry was pulled down from lysates of SEY6210   WT or SEY6210 vps26∆ strains carrying genomically tagged Atg18HA3yEGFP. Adsorbed proteins were analyzed by  SDS-PAGE and Western blotting using the antibodies indicated in brackets. E Signals from the blots  in d were quantified on an infrared fluorescence scanner and normalized to the amount of  pulled-down Vps35yomCherry. n=3 independent experiments were analyzed using an unpaired Student's t-test. Bars represent the mean and errors bars the SEM. *** P &lt; 0.001."
NCBI gene IDs:
"HA3: 
yEGFP: 
yomCherry: 
Atg18: 850577
vps26: 853393
Vps35: 853287"
Figure legend: "F Atg18-Vps26 interaction. Genomically tagged Vps26yomCherry was pulled down from lysates of SEY6210  WT, SEY6210 vps35∆ or SEY6210 vps29∆ strains carrying genomically tagged  Atg18HA3yEGFP. Adsorbed proteins were analyzed as in D. G Proteins from F were quantified as in E. n=3 independent experiments were analyzed using an unpaired Student's t-test. Bars represent the mean and errors bars the SEM. *** p &lt; 0.001)."
NCBI gene IDs:
"HA3: 
yEGFP: 
yomCherry: 
Atg18: 850577
Vps26: 853393
vps29: 856403
vps35: 853287"
Figure legend: "A Vps17  labilizes the Atg18-Vps26 interaction. Wildtype or vps17∆ cells expressing ATG18HA3-yEGFP from a centromeric  plasmid were logarithmically grown in YPD. Genomically tagged Vps26yomCherry was  pulled down from whole-cell extracts and analyzed for associated Atg18HA3-yEGFP by SDS-PAGE  and Western blotting. Glucose-6-phosphate dehydrogenase (Zwf1) serves as a loading control. The intensity of the interacting Atg18HA3-yEGFP was quantified on a LICOR fluorescence imager and normalized to the amount of  Vps26yomCherry. Values of the wildtype interaction  were used as the reference and set to 1. n = 4 independent experiments were analyzed using an unpaired Student's t-test. Bars represent the mean and errors bars the SEM, ** p &lt; 0.01)"
NCBI gene IDs:
"HA3: 
yEGFP: 
yomCherry: 
ATG18: 850577
Vps26: 853393
Vps17: 854300
vps17: 854300"
Figure legend: "B Epistasis of ATG18  and retromer  genes concerning vacuolar morphology. The indicated cells were logarithmically grown in YPD medium, stained  with FM4-64 and  calcofluor white C Quantification of vacuole morphology. The number of vacuoles  per cell was measured in the cells from B. The graph shows the fractions of cells displaying the indicated numbers of  vacuolar vesicles (n = 3 biological experiments with at least 100 cells per condition and experiment were analyzed using an unpaired Student's t-test. Bars represent the mean and errors bars the SEM. ** p &lt; 0.01"
NCBI gene IDs:
"ATG18: 850577"
Figure legend: "C  Pull-down. Cells (SEY6210 atg18∆, atg21∆) expressing genomically tagged Vps26yomCherry  and the indicated Atg18HA3-yEGFP variants were logarithmically grown in SC-URA media.  Vps26yomCherry was pulled down from whole-cell extracts with RFP-trap magnetic beads and analyzed by  SDS-PAGE and Western blotting against the indicated proteins. Bands were quantified on a LICOR fluorescence imager. Signals of Atg18HA3yEGFP were normalized relative to those of Vps26yomCherry. Vps1 served as a loading control. n = 3 independent replicates. Data were subjected to an unpaired t-test. Bars represent the mean and errors bars the SEM, *** P &lt; 0.001)."
NCBI gene IDs:
"HA3: 
yEGFP: 
yomCherry: 
atg18: 850577
Atg18: 850577
atg21: 856004
Vps26: 853393"
Figure legend: "A, Effect of Atg18T56E on salt-induced vacuole fission. Cells expressing Atg18WTHA3-yEGFP or Atg18T56E-HA3-yEGFP from centromeric  plasmids in a SEY6210 atg18∆, atg21∆ strain were logarithmically grown in SD-URA medium. They were stained  and imaged before and after the induction of vacuole fission   by a short salt shock Calcofluor white-stained  cell walls are only represented in the merge (blue). Scale bar: 5 µm. B, Quantification of the number of vacuoles per cell from A, n = 3 biological experiments with at least 100 cells per condition were scored; bars represent the mean and error bars the SEM. C, Epistasis of atg18T56E over a vps17∆ mutation. The indicated variants of Atg18-HA3-yEGFP  were expressed from plasmids in a SEY6210 atg18∆, atg21∆, vps17∆ strain. Cells were logarithmically grown in SD-URA  and imaged Scale bar: 5 µm. D, Quantification of the experiments from C, n = 3 independent experiments with at least 100 cells per condition scored; bars represent the mean and error bars the SEM ."
NCBI gene IDs:
"HA3: 
yEGFP: 
Atg18: 850577
atg18: 850577
atg21: 856004
vps17: 854300"
Figure legend: "A  Colocalization of WIPI1  with Vps26A. The indicated  WIPI1mCherry variants and VPS26EGFP were expressed for 18 h in HK2  cells, from which endogenous WIPI1  had been deleted (WIPI1-KO). The cells were analyzed by confocal microscopy. Scale bars: 10 μm. Insets show enlargements of the outlined areas. B Colocalization  between WIPI1  variants and Vps26  was quantified in the cells from A using the Manders' colocalization  coefficient M2. The red line indicates the mean; n = 120 cells per condition, pooled from three independent experiments. P-values were calculated by t-test (analysis performed with 99% confidence ***p &lt; 0.0001). C Expression  levels of WIPI1mCherry  variants. Lysates (50 μg of protein per sample) from the cells in A were analyzed by  SDS-PAGE  and Western blot  against WIPI1  and tubulin."
NCBI gene IDs:
"EGFP: 
mCherry: 
VPS26: 9559
WIPI1: 55062"
Figure legend: "D Depletion of VPS35. HK2  cells expressing the indicated WIPI1eGFP variants were transfected with siRNA against VPS35  (VPS35  KD) or a control siRNA pool. Lysates (50 μg per sample) from the cells were analyzed by  SDS-PAGE and Western blot  against Vps35   and tubulin. E Blots  from D were quantified on a LICOR Odyssey fluorescence imager. n=3. Red lines indicate the means, n = 3 independent experiments, using a Welch's t-test statistical analysis. Bars represent the mean and error bars the SD."
NCBI gene IDs:
"eGFP: 
VPS35: 55737
WIPI1: 55062"
Figure legend: "A, Tf  recycling. WIPI1-KO cells were transfected with WIPI1WT-eGFP, WIPI1S69E-eGFP  or  WIPI1S69A-eGFP for 18h. Then, they were serum-starved  for 1 h, loaded with  Alexa Fluor 568-conjugated Tf, chased at 37°C for 1 h without labeled Tf, and analyzed by  confocal microscopy. Scale bar: 10 μm. White dashed lines delineate the circumference of the cells. B, Quantification of Tf-fluorescence in the cells from a that expressed WIPI1  variants. Total cell fluorescence was integrated and corrected for background fluorescence. Mean values ± SD are shown. n = 3 independent experiments with a total of 150 cells analyzed per condition. P values were calculated by unpaired Student's t-test. 99% confidence: *** = p &lt; 0.0001."
NCBI gene IDs:
"eGFP: 
WIPI1: 55062"
Figure legend: "ER Proliferation under UPR-Inducing Conditions(A) Determination of ER abundance in control and UPR-induced cells. Representative cells are shown. The UPR was induced in wild-type cells by addition of DTT. Ultrastructure of control cells and UPR-induced cells was analyzed using ImageJ. The lower images show traces of cortical ER (represented in magenta) and the nuclear envelope (NE, in blue). Vacuoles, nuclei, and mitochondria are indicated as V, N, and M, respectively.(B) Quantification of the ER proliferation during the UPR. UPR was induced and cells were collected for EM at the indicated time points. Length of the ER (as traced in [A]) was measured and divided by the area of the section. Data are plotted relative to time 0. Measurements for each time point correspond to the mean of 25 independent cell images.(C) Expression of HAC1i was induced by addition of 100 μM DOC for 3 h. ER was quantified as described above in (B)."
NCBI gene IDs:
"HAC1: 850513"
Figure legend: "(A) Wild-type cells transformed with a plasmid containing GFP-Atg8 were grown for 4 h in synthetic media with no drug, with UPR-inducing conditions (+DTT and +TM), or under nitrogen starvation conditions (N starv), and then harvested for protein preparation. Protein extracts were analyzed by Western blotting using antibodies against GFP (top panel) or Hac1 (bottom panel). Total protein concentration was measured by BCA protein assay. Same concentration of protein was loaded in each lane, and transfer efficiency was checked by Ponceau staining. The identities of the different bands are indicated."
NCBI gene IDs:
"Atg8: 852200"
Figure legend: "(B) Wild-type cells expressing GFP-Atg8 grown under the conditions described above were visualized by fluorescence microscopy."
NCBI gene IDs:
"Atg8: 852200"
Figure legend: "(C) GFP-Atg8 was detected in extracts from untreated hac1Δ cells or cells expressing HAC1i (+DOC) by Western blotting using antibodies against GFP."
NCBI gene IDs:
"Atg8: 852200
hac1: 850513
HAC1: 850513"
Figure legend: "(D) Western blot using antibodies against GFP of extracts from hac1Δ, ire1Δ, or vps4Δ pep4Δ cells expressing GFP-Atg8. Mutant cells were grown under regular conditions, UPR-inducing conditions (+DTT), or nitrogen starvation conditions (N starv)."
NCBI gene IDs:
"Atg8: 852200
hac1: 850513
ire1: 856478
pep4: 855949
vps4: 856303"
Figure legend: "Localization of GFP-Atg8 during UPR InductionSome of the DTT-treated cells shown in Figure 4B expressing GFP-Atg8 and Sec61-cherry (as an ER marker) were visualized using fluorescence microscopy. GFP-Atg8 localizes in close proximity to the ERAs detected by the ER marker."
NCBI gene IDs:
"Atg8: 852200"
Figure legend: "Atg8 and Other ATG Genes Are Necessary during UPR InductionSerial dilutions for wild-type, hac1Δ, atg1Δ, atg8Δ, atg9Δ, atg16Δ, and atg20Δ deletion cells and vps4Δ pep4Δ double deletion cells were grown on rich-media plates with no drug (YPD) or with different concentrations of tunicamycin (TM; 0.2 or 1.0 μg/ml). atg19Δ gave an identical result to the other autophagy genes shown here (unpublished data)."
NCBI gene IDs:
"atg1: 852695
atg16: 855194
atg20: 851445
atg8: 852200
atg9: 851406
hac1: 850513
pep4: 855949
vps4: 856303"
Figure legend: "(E) Genome browser images of ChIL-seq for H3K27ac and PolII-S5P and bulk tissue  RNA-seq data at the Alb locus in  liver tissues."
NCBI gene IDs:
"Alb: 11657"
Figure legend: "(B) The IGV tracks of H3K27ac ChIL-seq at identified tissue-specific enhancers of Rxra, Gnat3, Eps8, and a house-keeping gene of Actb  loci are shown with the replicates."
NCBI gene IDs:
"Actb: 11461
Eps8: 13860
Gnat3: 242851
Rxra: 20181"
Figure legend: "(F) Hnf4ɑ  binds to the SE at Alb  gene loci."
NCBI gene IDs:
"Alb: 11657"
Figure legend: "(E) The tissue-specific genes identified by PolII  S5P ChIL-seq. The IGV tracks of all replicates of  PolII S5P  ChIL-seq are shown at each specific gene (Trf, Myh6, and Meig for the liver,  heart, and testis, respectively). Actb is also shown as the ubiquitously expressed gene in the three tissues."
NCBI gene IDs:
"Actb: 11461
Meig: 104362
Myh6: 17888
Trf: 22041"
Figure legend: "(B) PolII  S5P  ChIL-seq signal of the marker genes of mature skeletal muscle (Acta1) and  macrophages (Cd68)."
NCBI gene IDs:
"Acta1: 11459
Cd68: 12514"
Figure legend: "(C) Expression, TSS level, and TR of genes. EEF1A1  is shown as a control housekeeping gene. The horizontal dotted line indicates the median level of all genes. Error bars indicate 95% confidence intervals for each estimate indicated by dots (N=1 for each)."
NCBI gene IDs:
"EEF1A1: 13627"
Figure legend: "(A) Quantification of cell death in 293 cells24 h after transfection with luciferase, p55/TNFR1, DRP-1 Δ73 or DAPk ΔCaM, and GFP. Graphs show the percentage of GFP-positive cells with altered cell morphology. (B) Photographs of GFP-positive cells cotransfected with luciferase (1), p55/TNFR1 (2), DRP-1 Δ73 (3), or DAPk ΔCaM (4)."
NCBI gene IDs:
"luciferase: 
DAPk: 23604
DRP-1: 10059
p55: 7132
TNFR1: 7132"
Figure legend: "(C) Photographs showing the overlay of GFP and phase-contrast images of 293 cells24 h after transfection with GFP and luciferase (1) or with GFP- DAPk (2 and 3); both a blebbing GFP-DAPk-expressing cell (2, arrows indicate blebs) and spread nontransfected cells are shown (3)."
NCBI gene IDs:
"luciferase: 
DAPk: 23604"
Figure legend: "(D) Hoechst staining (4-6) of GFP-positive 293 cells (1-3) 60 h after cotransfection with GFP and DAPk ΔCaM (1 and 4), DRP-1 Δ73 (2 and 5), or p55/TNFR1 (3 and 6). Arrows point to condensed nuclei resulting from DRP-1 Δ73 or DAPk ΔCaM transfections (4 and 5)."
NCBI gene IDs:
"DAPk: 23604
DRP-1: 10059
p55: 7132
TNFR1: 7132"
Figure legend: "(A) Scoring loss of mitochondrial membrane potential (ΔΨm). 293 cells expressing luciferase (black), DRP-1 Δ73 (pink), DAPk ΔCaM (purple), and Bax (green) were assayed for loss of mitochondrial membrane potential 24 h after transfection using flow cytometric analysis of TMRM fluorescence. The fraction of TMRM-negative cells calculated from three experiments is shown in the graph below. The small increase in TMRM fluorescence in the kinase-transfected cells is not statistically significant."
NCBI gene IDs:
"luciferase: 
Bax: 581
DAPk: 23604
DRP-1: 10059"
Figure legend: "(B) Scoring the release of cytochrome C from mitochondria. 293 cells cotransfected with luciferase (1 and 2), Bax (3 and 6), DRP-1 Δ73 (7 and 8), or DAPk ΔCaM (9 and 10) and GFP constructs were incubated for 24 h and immunostained using anti-cytochrome C antibodies. Cells were visualized for cytochrome C (left) or GFP (right) fluorescence. Bax-transfected spread (3 and 4) or blebbed (5 and 6) cells are shown. In fields that also contain nontransfected cells, arrows point to GFP-positive cytochrome C-stained cells."
NCBI gene IDs:
"luciferase: 
Bax: 581
DAPk: 23604
DRP-1: 10059"
Figure legend: "(C) Assessing the effects of Bcl-2 and Bcl-XL. 293 cells were cotransfected with luciferase, DRP-1 Δ73, DAPk ΔCaM, or Bax, and either Bcl-2 or Bcl-XL together with GFP. GFP-positive cells were visualized by fluorescent microscopy and scored for the appearance of cell death morphology 24 h after transfection. Total cell death refers to the sum of all morphological changes observed."
NCBI gene IDs:
"luciferase: 
Bax: 581
Bcl-2: 596
Bcl-XL: 598
DAPk: 23604
DRP-1: 10059"
Figure legend: "(A) Transmission electron micrographs of 293 cells transfected with luciferase (1) p55/TNFR1 (2a-2c), DRP-1 Δ73 (3a and 3b; part of fig. 3b is magnified on its right), and DAPk ΔCaM (4). The different stages of autophagic development are depicted as follows: immature autophagic vesicles (double arrow), mature autophagic vesicles and autolysosomes (black arrow), and residual bodies (dashed arrow). Empty vacuoles (white arrow) are also shown. Arrowheads show condensed and fragmented chromatin. m, mitochondria; g, Golgi apparatus. Bar, 1 μm."
NCBI gene IDs:
"luciferase: 
DAPk: 23604
DRP-1: 10059
p55: 7132
TNFR1: 7132"
Figure legend: "(B) Transmission electron micrographs of MCF-7 cells transfected with luciferase (1), p55/TNFR1 (2a-2c), DRP-1 Δ73 (3a and 3b), and DAPk ΔCaM (4). Immature autophagic vesicles (double arrow), autophagic vesicles (black arrow), and residual bodies (dashed arrow) are shown. Insets in B, 2b and 2c, correspond to empty vacuoles, whereas those in B, 3a and 4, correspond to autophagic vesicles. Arrowheads show condensed and fragmented chromatin. m, mitochondria; dm, darkened mitochondria; n, nucleus; g, Golgi apparatus; v, vacuoles; ly, lysosomes; er, endoplasmic reticulum."
NCBI gene IDs:
"luciferase: 
DAPk: 23604
DRP-1: 10059
p55: 7132
TNFR1: 7132"
Figure legend: "(A) Quantification of autophagy in 293 and MCF-7 cells. Graphs show the percentage of MDC-positive cells resulting from luciferase or DRP-1 Δ73 transfections (mean ± SD calculated from triplicates of 100 cells each; note that total cell number comprises transfected and nontransfected cells). These experiments were repeated three times with reproducible results."
NCBI gene IDs:
"luciferase: 
DRP-1: 10059"
Figure legend: "(B) Photographs of MDC-stained MCF-7 cells from the same experiment shown in A. Arrows point to MDC-positive cells. Transfections: luciferase (1a and 1b) and DRP-1 Δ73 (2a and 2b) at low (a) and high (b) magnifications."
NCBI gene IDs:
"luciferase: 
DRP-1: 10059"
Figure legend: "(A) Quantification of cell death-associated morphologies in 293 cells. Graphs show the percentage of cells harboring all spectrum of morphological changes occurring as a result of luciferase, p55/TNFR1, DRP-1 Δ73, or DAPk ΔCaM transfections in the presence or absence of the caspase inhibitors BD-fmk or z-VAD-fmk (100 μM; mean ± SD calculated from triplicates of 100 cells each). This experiment was repeated three times with reproducible results."
NCBI gene IDs:
"luciferase: 
DAPk: 23604
DRP-1: 10059
p55: 7132
TNFR1: 7132"
Figure legend: "(C) Graphs show the percentage of cells harboring the complete spectrum of death-associated morphological changes occurring as a result of cotransfections of luciferase, p55/TNFR1, DRP-1 Δ73, or DAPk ΔCaM with the caspase inhibitor crmA or control luciferase vector (mean ± SD calculated from triplicates of 100 cells each). Immunoblot shows the expression levels of transfected HA-tagged DAPk and DRP-1 Δ73, confirming that cotransfection with crmA did not alter expression of the death-inducing proteins."
NCBI gene IDs:
"luciferase: 
DAPk: 23604
DRP-1: 10059
p55: 7132
TNFR1: 7132"
Figure legend: "(D) Transmission electron micrographs of 293 cells transfected with p55/TNFR1 (1) or DRP-1 Δ73 (2a and 2b; parts of these figures are magnified at the right) and treated with the caspase inhibitor BD-fmk (100 μM). Immature autophagic vesicles (double arrow), autophagic vesicles (black arrow), and autolysosomes (white arrow) are shown. m, mitochondria; g, Golgi apparatus."
NCBI gene IDs:
"DRP-1: 10059
p55: 7132
TNFR1: 7132"
Figure legend: "(E) Western blots of cell lysates prepared from HeLa cells transfected with luciferase, p55/TNFR1, DRP-1 Δ73, or DAPk ΔCaM and GFP and incubated for 24 h. Blots were reacted with anti-PARP antibodies, anti-caspase-8 antibodies, anti-caspase-3 antibodies, anti-HA antibodies for DRP-1 Δ73 and DAPk ΔCaM detection, and anti-β-tubulin antibodies to quantitate protein loading."
NCBI gene IDs:
"luciferase: 
DAPk: 23604
DRP-1: 10059
p55: 7132
TNFR1: 7132"
Figure legend: "(A) 293 cells were cotransfected with p55/TNFR1 in combination with DAPk death domain fused to GFP or DRP-1 K42A and pEGFP-N1 vector. A control luciferase vector was also used. GFP-positive cells were visualized by fluorescent microscopy and scored for the appearance of membrane blebbing 24 h after transfection."
NCBI gene IDs:
"luciferase: 
DAPk: 23604
DRP-1: 10059
p55: 7132
TNFR1: 7132"
Figure legend: "(B) Photographs of the various categories of p55/TNFR1-transfected 293 cells: spread cells (1), blebbed cells (2), condensed cells (3), cells displaying a fragmented cytoplasm (4), and cells carrying fragmented nuclei within a noncondensed cytoplasm (5). (C) Quantification of each death morphology observed 24 h after transfection with GFP, p55/TNFR1, and either luciferase or DRP-1 K42A."
NCBI gene IDs:
"luciferase: 
DRP-1: 10059
p55: 7132
TNFR1: 7132"
Figure legend: "(A and B). Quantification of autophagy in MCF-7 cells. MCF-7 cells were transfected with luciferase or FLAG-DRP-1 K42A followed by steroid withdrawal (serum starvation plus 10−6 M tamoxifen treatment) (A) or by serum and amino acid starvation (B) (mean ± SD calculated from triplicates of 100 cells each). These experiments were repeated three times with reproducible results. Proteins extracted from the transfected cells were subjected to Western blot analysis with anti-FLAG and anti-β-tubulin antibodies."
NCBI gene IDs:
"luciferase: 
DRP-1: 10059"
Figure legend: "(C) Photographs of the MDC-stained steroid withdrawn MCF-7 cells taken from the same experiment shown in A. Transfections: luciferase (1a and 1b) and DRP-1 K42A (2a and 2b) at low (a) and high (b) magnifications."
NCBI gene IDs:
"luciferase: 
DRP-1: 10059"
Figure legend: "(E) DAPk antisense-transfected and control DHFR-transfected polyclonal populations of HeLa cells were incubated with hygromycin B (200 μg/ml) in the presence or absence of IFN-γ (1,000 U/ml) and BD-fmk (50 μM). Detection of autophagic vesicles was performed 2 d later using the MDC dye. Graphs represent mean ± SD of MDC-positive cells calculated from triplicates of 100 cells each."
NCBI gene IDs:
"DAPk: 23604
DHFR: 1719"