EMBO/SourceData huggingface dataset:
Figure legend: "(F) Representative images of GFP-positive HEK293  cells at day 7 post-transduction using 1x106 TU/cell of RGD4C.TPA.GFP   or RGD4C.AAVP.GFP   particles. Non-targeted (NT) particles were included as control. Data shown are representative of five independent experiments, performed each in triplicates. Scale bar, 100 μm."
NCBI gene IDs:
"GFP: "
Figure legend: "(A) Quantification of gene expression in HEK293  cells after transduction with 0.5x106, 1x106, and 2x106 TU/cell of RGD4C.TPA, RGD4C.AAVP  or non-targeted (NT) particles carrying Lucia.  Luciferase activity was measured at days 1 to 6 post-transduction. Data shown are representative of three independent experiments (n = 3), and are expressed as mean + SEM. One-way ANOVA with Tukey's HSD test was used for data analysis."
NCBI gene IDs:
"Lucia: "
Figure legend: "(F) Quantification of Lucia reporter  gene expression following transduction of human  primary SEBTA003 glioblastoma  and G26 glioblastoma-derived  neural stem cells  with 1x106 TU/cell. Data are expressed as mean + SEM of n = 3 independent experiments. One-way ANOVA with Tukey's HSD test was used for data analysis."
NCBI gene IDs:
"Lucia: "
Figure legend: "(G) 3D primary GBM001   tumor spheres subjected to transduction by increasing doses of TPA  and AAVP  encoding Lucia. Experiments were repeated three times and performed in triplicates. Data are shown as mean + SEM and are representative of one experiment. Independent t-test was used for data analysis."
NCBI gene IDs:
"Lucia: "
Figure legend: "(B) ELISA  quantification of TNFα production in media collected on days 3 to 5 post-transduction of human  primary GBM001 tumor spheres at 1x106 TU/cell of targeted (RGD4C) or non-targeted (NT) TPA  particles carrying native TNFα or recombinant TNFαIL2 sequences. Data are representative of one experiment and expressed as mean + SEM. Experiments were repeated twice in triplicates, one-way ANOVA with Tukey's HSD test was used for data analysis."
NCBI gene IDs:
"IL2: 3558
 TNFα: 7124
TNFα: 7124"
Figure legend: "(C) Biodistribution of gene delivery upon intravenous administration of 5x1010 TU of NT or RGD4C.TPA.TNFαIL2 to NOD/SCID mice  bearing subcutaneous human GBM001. Tumors and healthy organs were harvested at day 18 post-transduction and analysed using RT-qPCR to quantify the TNFαIL2  transcripts. Data shown are expressed as mean + SEM, from n = 3 mice. Two-way ANOVA was used for data analysis."
NCBI gene IDs:
"IL2: 3558
TNFα: 7124"
Figure legend: "(D) BLI  of Luc  showing representative mice with subcutaneous  GBM001 labelled with Luc gene, at day 18 post targeted TNFαIL2 cytokine treatment. (E) Analysis of tumor growth in representative mice, from D, using the tumor bioluminescence  data (total flux) and expressed as fold changes of tumor luminescence flux  at different time points compared to day 0."
NCBI gene IDs:
"Luc: 
IL2: 3558
TNFα: 7124"
Figure legend: "(B) Investigation of the TPA.IL15IgK in comparison to the native TPA.IL15   in  B16.F1  and CT26.CL25 tumor cells. The TPA  DNA constructs were transfected into tumor cells, then the bioactivity  of secreted  IL15   was assessed by evaluating the effects of media from transfected cells on the proliferation  of mouse CTLL-2. Data are representative of one experiment and expressed as mean + SEM. Experiments were repeated twice and performed in triplicates, one-way ANOVA with Tukey's HSD test was used for data analysis"
NCBI gene IDs:
"IgK: 243469
IL15: 3600"
Figure legend: "(C) Targeted (RGD4C) and non-targeted (NT) TPA  particles carrying  IL15IgK were produced and used to transduce B16.F1   or CT26.CL25 cells at 0.5x106 or 1x106 TU/cell. Then secreted IL15   was quantified by ELISA  in tumor cell media collected on day 5 post-transduction. RGD4C.TPA  without  IL15IgK (mock) was also included as control. Experiments were repeated twice and shown are the results from a representative experiment. Data are expressed as mean + SEM, one-way ANOVA with Tukey's HSD test was used for data analysis."
NCBI gene IDs:
"IgK: 243469
IL15: 3600"
Figure legend: "(D) Evaluation of CTLL-2 proliferation  in the presence of media collected from  B16.F1 or CT26.CL25  tumor cells after transduction with TPA  particles carrying IL15IgK. Cells treated with a recombinant IL2  cytokine were included as a positive control. Data are representative of one experiment, expressed as mean + SEM and shown as change in CTLL-2 number relative to treatment initiation day. Experiments were repeated twice and in triplicates, one-way ANOVA with Tukey's HSD test was used to analyse the data."
NCBI gene IDs:
"IgK: 243469
IL15: 3600"
Figure legend: "(A) Tumor-bearing BALB/c mice  with established subcutaneous CT26.CL25 tumors  were intravenously injected with a single dose, 5x1010 TU/mouse, of targeted (RGD4C) or non-targeted (NT) TPA.IL15IgK. Gene delivery was evaluated by quantifying the IL15IgK mRNA expression  in tumors  and healthy tissues at day 5 post TPA  administration. Data are representative of one experiment, n = 3, and expressed as mean + SEM. Two-way ANOVA test was used for data analysis."
NCBI gene IDs:
"IgK: 243469
IL15: 3600"
Figure legend: "(B) Safety of dose escalation regimens assessed at day 5 following TPA  delivery, by evaluating the serum  levels of LDH  from n = 2 mice/TPA  dose of targeted (RGD4C) or non-targeted (NT) TPA.IL15IgK. Serums  from untreated mice  were also analysed."
NCBI gene IDs:
"IgK: 243469
IL15: 3600"
Figure legend: "(C) Representative tumor-bearing mice  showing bioluminescence  imaging  of luciferase  on days 0 and 5 post administration with 5x1010 TU of RGD4C.TPA.IL15IgK (RGD4C) or non-targeted (NT) particles. The CT26.CL25 tumor cells stably express a luciferase Luc  reporter gene. Untreated mice  were also included as controls (CTRL)."
NCBI gene IDs:
"Luc: 
luciferase: 
IgK: 243469
IL15: 3600"
Figure legend: "(A) The immune profile of CT26.CL25  tumors was investigated using  RT-qPCR at day 5 after TPA.IL15IgK administration. A panel of immunological mRNA transcripts were selected for analysis and included CD8a  and CD8b  as markers for CD8+ T cell  population; NKp46  for NK  cell population. Markers for cytotoxic cell-killing by CD8+ T cells (GZMa, GZMb) and by NK  cells (Prf1) were also analysed. Expression  of TBX21  was evaluated as a marker for the Th1 response mediated by interferon gamma  (IFN-γ), and FoxP3  for  Treg  cells. Data shown are representative of n = 5 mice  and expressed as mean + SEM. Non-parametric Mann-Whitney test was used for GZMb  and TBX2 data analysis, and independent t-test to analyse data of the other markers."
NCBI gene IDs:
"CD8a: 12525
CD8b: 12526
FoxP3: 20371
GZMa: 14938
GZMb: 14939
IgK: 243469
IL15: 3600
NKp46: 17086
Prf1: 18646
TBX2: 57765
TBX21: 57765"
Figure legend: "(B) TPA  particles encoding IL12 were used to treat immunocompetent BALB/c mice  bearing subcutaneous CT26.CL25 tumors labelled with a Luc  reporter gene. Representative tumor-bearing mice  at day 5 post-treatment with targeted RGD4C.TPA.IL12  (RGD4C) or non-targeted TPA.IL12  (NT)."
NCBI gene IDs:
"Luc: 
IL12: 16160"
Figure legend: "(C) Analysis of total flux change in tumors, n = 4 mice, after IL12 immunotherapy. The central band represents the median of the data. The boxes upper and lower lines represent quartile 3 and quartile 1 of the data, respectively. The whiskers represent the maximum and minimum outliers of the data. Non-parametric Mann-Whitney test was used for data analysis."
NCBI gene IDs:
"IL12: 16160"
Figure legend: "(E) Serial quantification of  IL12 in media of B16.F10 cells treated with RGD4C.TPA.IL12 or controls. Data are representative of one experiment, n = 3 biological repeats, and shown as mean + SD Experiments were repeated three times. One-way ANOVA with Tukey's HSD test was used for data analysis."
NCBI gene IDs:
"IL12: 16160"
Figure legend: "(F) RGD4C.TPA.IL12  immunotherapy of subcutaneous  B16.F10 tumors in C57BL/6 mice  (n = 4). Data are shown as mean + SEM independent t-test was used for data analysis. Tumor volume changes are shown over time."
NCBI gene IDs:
"IL12: 16160"
Figure legend: "(B) Western blot analysis of lysates and media from wt and mutant N9 cells (N9 wt /mu) using antibody anti-murine TREM2 (clone 5F4), which is raised against the murine TREM2 extracellular domain. sTREM2, soluble TREM2* Indicate unspecific bands. Anti-calnexin antibody was used as loading control."
NCBI gene IDs:
"TREM2: 83433"
Figure legend: "(D) Western blot of BMDM derived from wt and Trem2 knockout (ko) animals using antibody 5F4."
NCBI gene IDs:
"Trem2: 83433"
Figure legend: "(E) Phagocytosis of fAβ42 by BMDM from wt and Trem2 ko animals in the presence or absence of 2D8, or the non-binding control antibody 6687. (n = 3, +/- SEM; 2 way ANOVA, interaction P=0.0005, genotype P&lt;0.0001, treatment P&lt;0.0001; post hoc tests wt vs. ko for the following conditions: fAβ42 P=0.0021, fAβ42-2D8 1 µg/ml P&lt;0.0001, fAβ42-2D8 5 µg/ml P&lt;0.0001, fAβ42-2D8 10 µg/ml P&lt;0.0001, fAβ42/6687 10 µg/ml P=0.0007)(F) Quantification of relative fAβ42uptake to lowest antibody concentration used."
NCBI gene IDs:
"Trem2: 83433"
Figure legend: "(G) Phagocytosis of fAβ42 by BMDM from wt and Trem2 ko animals in the presence or absence of mAb11, or an isotype control antibody (IC). (n = 4, +/- SEM; 2 way ANOVA, interaction P=0.0223, genotype P&lt;0.0001, treatment P&lt;0.0001; post hoc tests wt vs. ko for the following conditions: fAβ42-mAb11 1 µg/ml P=0.0391, fAβ42-mAb11 5 µg/ml P=0.0069, fAβ42-mAb11 10 µg/ml P&lt;0.0001, fAβ42-mAb11 20 µg/ml P=0.0001, fAβ42-mAb11 50 µg/ml P&lt;0.0001).(H) Quantification of relative fAβ42 uptake to lowest antibody concentration used."
NCBI gene IDs:
"Trem2: 83433"
Figure legend: "(I) Recombinant mousesTREM2 does not rescue fAβ42 uptake in Trem2-deficient BMDM. Increasing amounts of sTREM2 were added to the media of wt or Trem2 ko BMDM in the presence or absence of mAb11 (10 µg/ml)."
NCBI gene IDs:
"Trem2: 83433"
Figure legend: "(K) Phagocytosis of fAβ42 by primary microglia from wt and Trem2 ko animals in the presence or absence of mAb11, or an isotype control antibody (IC). (n = 5, +/- SEM; 2 way ANOVA, interaction P=0.4797, genotype P&lt;0.0001, treatment P&lt;0.0001; post hoc tests wt vs. ko for the following conditions: fAβ42-mAb11 5 µg/ml P=0.0449, fAβ42-mAb11 10 µg/ml P=0.0370, fAβ42-mAb11 20 µg/ml P=0.0299, fAβ42-mAb11 50 µg/ml P=0.0120).(L) Quantification of relative fAβ42uptake to lowest antibody concentration used."
NCBI gene IDs:
"Trem2: 83433"
Figure legend: "(A) Representative histograms for Fcγ-receptors-PE (FcγR-PE) expression levels as used for quantification. Stacked histograms for log PE fluorescence intensity of wt and Trem2 ko BMDM are shown for the respective FcγR (I, IIB/III and IV).(B) Relative quantification of cell surface levels of FcγR molecules. Absolute number of cell surface FcγR-PE molecules was determined by the BD QuantiBRITE® method (see methods section for details) and normalized to expression levels of the respective wt control. (n=4, +/- SEM, t test, two-tailed; wt vs. ko: FcγRI-PE P=0.0008, FcγRIIB/III-PE P=0.0033, FcγRIV-PE P=0.7001)."
NCBI gene IDs:
"Trem2: 83433"
Figure legend: "(C) mRNA levels of FcγR are increased in Trem2 ko BMDM. Fold changes of the respective FcγR (I, IIB, III, IV) mRNA levels in Trem2 ko BMDM were determined by quantitative real-time PCR. (n=6, +/- SEM; one-sample t test, two-tailed; wt vs. ko: FcγRI P=0.0118, FcγRIIB P=0.0006, FcγRIII P=0.0004, FcγRIV P=0.0284)"
NCBI gene IDs:
"FcγRI: 14129
FcγRIIB: 14130
FcγRIII: 14131
FcγRIV: 246256
Trem2: 83433"
Figure legend: "(D) Phosphorylated Syk (P-Syk) and total Syk (T-Syk) levels were determined by western blotting in lysates from wt and Trem2 ko BMDM after 1 h treatment with Aβ alone, together with antibody 2D8 (Aβ-2D8), or an isotype control (Aβ-IC). Actin was used as a loading control.(E) Quantification of P-Syk normalized to T-Syk. (n = 4, +/- SEM; 2 way ANOVA, interaction P=0.0490, genotype P=0.0898, treatment P&lt;0.0001. Bonferroni-corrected pair-wise post hoc tests, ** P =0.0075 vs. wt)."
NCBI gene IDs:
"Trem2: 83433"
Figure legend: "(A) BMDM from wt or Trem2 ko mice were cultured on APP/PS1micebrain cryosections incubated with or without mAb11 (1 µg/ml) or an isotype control (IC; 1 µg/ml) for 24 h. Sections were then probed with methoxy-X04. Scale bar, 500 µm.(B) The amyloid plaque load was quantified from the entire sagittal section. Sections incubated with medium (no cell) were set as baseline. (n = 6, +/- SEM; 2 way ANOVA, interaction P&lt;0.0001, genotype P&lt;0.0001, treatment P&lt;0.0001; Tukey's multiple comparisons tests; wt vs. ko for the following conditions: no antibody P=0.0304, IC P=0.0049, mAb11 P=0.0212; wt : IC vs. wt : mAb11 P=0.0008; ko : IC vs. ko : mAb11 P=0.0001)."
NCBI gene IDs:
"APP: 351
PS1: 5663
Trem2: 83433"
Figure legend: "(C, D) Equal numbers of wt and Trem2 ko BMDM were added and cell numbers were analyzed after termination of experiments by quantifying the CD68 positive cells on top of the sections. (n = 4, +/-SEM; t-test; n.s., nonsignificant, P=0.5004). Scale bar, 200 µm."
NCBI gene IDs:
"Trem2: 83433"
Figure legend: "(A) Cryosections from unfixed brain of 6-months old APP/PS1mice were pre-incubated with increasing concentrations of mAb11 (0.001, 0.01, 0.1, 1, 5 µg/ml). BMDM from wt or Trem2 ko mice were added for 24 h. Sections were stained with methoxy-X04. Scale bar, 500 µm.(B) Methoxy-X04 signals were quantified from the entire sagittal section. (n = 5, +/- SEM; 2 way ANOVA, interaction P=0.0082, genotype P&lt;0.0001, treatment P&lt;0.0001. Fisher's LSD post hoc comparisons; * show statistics between wt and ko under the same experimental condition. # in black show wt compares to no antibody stimulation; # in grey show ko compares to no antibody stimulation; wt vs. ko for the following conditions: no antibody P=0.0053, mAb11 0.001 µg/ml P=0.0003, mAb11 0.01 µg/ml P&lt;0.0001, mAb11 0.1 µg/ml P=0.0001, mAb11 1 µg/ml P=0.0007, mAb11 5 µg/ml P=0.0011; Following conditions compare to wt / no antibody: wt / mAb11 0.01 µg/ml P=0.0166, wt / mAb11 0.1 µg/ml P=0.0002, wt / mAb11 1 µg/ml P&lt;0.0001, wt / mAb11 5 µg/ml P&lt;0.0001; Following conditions compare to ko / no antibody: ko / mAb11 0.1 µg/ml P=0.0099, ko / mAb11 1 µg/ml P&lt;0.0001, ko / mAb11 5 µg/ml P&lt;0.0001."
NCBI gene IDs:
"APP: 351
PS1: 5663
Trem2: 83433"
Figure legend: "C, DNA content profiles of BAT1 and bat1Δ cells from asynchronous cultures, in SMM medium. Where indicated, exogenous amino acids were added at 1mM final concentration. On the x-axis of the histograms is fluorescence per cell, while on the y-axis is the cell number. Peaks corresponding to cells in G1 with unreplicated (1N) and cells in G2 and M phases with fully replicated (2N) DNA are indicated. The percentage of cells with G1 DNA content (%G1) from 3 independent measurements is shown in each case (mean and sd)."
NCBI gene IDs:
"BAT1: 856615
bat1: 856615"
Figure legend: "B, Immunoblots of total cell extracts from asynchronous BAT1 and bat1Δ cells, from four independent experiments. The signal from Pgk1 (α-Pgk1) is shown on the blot at the bottom, and from phosphorylated Rps6 (α-Rps6-P) is on the blot above, indicated for two exposures (2 min, top; 20 sec, middle)."
NCBI gene IDs:
"BAT1: 856615
bat1: 856615"
Figure legend: "D, Exogenous addition of valine leads to sustained activation of TORC1 and phosphorylation of Rps6 in cells lacking Bat1. Wild type (BAT1+) and bat1∆ (two independent isolates, #4, and #5) strains were grown overnight in minimal (SMM) medium, diluted to 1E+06 cells/mL in fresh SMM media containing the indicated amino acid (at 1mM), and harvested when they reached 5E+06 cells/mL. The levels of phosphorylated Rps6 (α-Rps6-P) and Pgk1 (α-Pgk1) are shown in immunoblots from total cell extracts in each case. The relative levels of Rps6-P/Pgk1 are shown in each case at the bottom. The boxplot graphs were generated with R language functions. Each box is drawn from the first to the third quartile, with a horizontal line drawn in the middle to denote the median. The whiskers show the interquartile range (IQR), and they were drawn at 1.5xIQR. The replicates were all biological ones."
NCBI gene IDs:
"bat1: 856615
Bat1: 856615
BAT1: 856615"
Figure legend: "A‐F′ Confocal fluorescent images of wild‐type (A, C, E) and mtm‐3(tm4475) (B, D, F) embryos at the 1.5‐fold stage stained by DAPI (A-F) and anti‐SQST‐1 (A′, B′), anti‐SEPA‐1 (C′, D′) or anti‐LGG‐1 (E′, F′) antibodies. Scale bars: 5 μm."
NCBI gene IDs:
"mtm‐3: 175490"
Figure legend: "G Western blot analysis of LGG‐1‐I and LGG‐1-II (lipidated) in wild type, epg‐6, and mtm‐3."
NCBI gene IDs:
"epg‐6: 189705
mtm‐3: 175490"
Figure legend: "H mtm‐3 and epg‐6 mutant L1 larvae have shortened mean and maximum life span in the absence of food. At least 300 animals were scored each day."
NCBI gene IDs:
"epg‐6: 189705
mtm‐3: 175490"
Figure legend: "A-C Fluorescent images of wild‐type embryos (1.5‐fold stage) expressing GFP::MTM‐3 (A), GFP::MTM‐3(C459S) (B), or GFP::MTM‐3(C459S, del PH‐G) (C)."
NCBI gene IDs:
"MTM‐3: 175490"
Figure legend: "D‐G″ Confocal fluorescent images of wild‐type (D‐D″), mtm‐3 (E‐E″), atg‐2 (F‐F″), and vps‐34 (G‐G″) embryos at the 200‐cell stage expressing GFP::MTM‐3(C459S) and stained by anti‐LGG‐1 antibody. Insets show magnified views. Arrows indicate overlapping GFP and LGG‐1 puncta. Scale bars: 5 μm."
NCBI gene IDs:
"atg‐2: 180949
mtm‐3: 175490
vps‐34: 172280"
Figure legend: "H, I Number of GFP::MTM‐3(C459S)‐positive puncta and co‐localization of GFP::MTM‐3(C459S)‐ and LGG‐1‐positive puncta in various strains [mtm‐3(tm4475), atg‐2(bp576), lgg‐1(bp500), vps‐34(h797)]. At least 10 (I) and 15 (H) embryos were scored per strain. Data are shown as mean ± SD. Data from different mutant backgrounds were compared with wild type. **P 0.0001; N.S.: not statistically different."
NCBI gene IDs:
"atg‐2: 180949
lgg‐1: 174050
mtm‐3: 175490
vps‐34: 172280"
Figure legend: "J MTM‐3 but not MTM‐3(C459S) exhibits phosphatase activity toward PtdIns3P and PtdIns(3,5)P2 in vitro."
NCBI gene IDs:
"MTM‐3: 175490"
Figure legend: "J-L TEM analysis of embryos in wild type (I) and mtm‐3(tm4475) (J, K). Double‐membrane autophagosomes (arrows) were observed in mtm‐3 but not wild‐type embryos. Scale bars: 500 nm."
NCBI gene IDs:
"mtm‐3: 175490"
Figure legend: "A-H Fluorescent images of embryos at the 4‐fold stage in the indicated strains expressing ATG‐18::GFP (A-D), ATG‐18(FKKG)::GFP (E, F), or ATG‐18(FTTG)::GFP (G, H)."
NCBI gene IDs:
"ATG‐18: 179246"
Figure legend: "I Confocal fluorescent images of 4‐fold mtm‐3 embryos expressing ATG‐18::GFP (I′) and stained by DAPI (I) and anti‐LGG‐1 (I″) antibody. Insets show magnified views. Arrows indicate ATG‐18 puncta labeled by anti‐LGG‐1 antibody. Scale bars: 5 μm."
NCBI gene IDs:
"ATG‐18: 179246
mtm‐3: 175490"
Figure legend: "A Relative  mRNA expression levels of  H2A.B in  L1236, L428, HDLM2 HL cell lines and Germinal centre B lymphocytes (GC) compared to the Ramos B lymphocyte cell line. The results are presented as the mean ± SD of three biological replicates."
NCBI gene IDs:
"H2A.B: 474381///83740///474382"
Figure legend: "E H2A.B interacts with RPA194 in live cells. Western blot analysis was performed to detect  RPA194  in the BioID  samples from L1236  cells (left panel), and L428  cells (right panel). The samples were prepared using  pull-down with streptavidin beads from the cell lysate of the empty vector, BirA*-H2A.B  and H2A.B-BirA* transduced cells, which were preincubated with 50 µM biotin  for 24 h. The positive control was loaded as 1% input."
NCBI gene IDs:
"BirA: 948469
H2A.B: 474381///83740///474382"
Figure legend: "B Cell proliferation assay in the presence (shNTC) or during depletion of H2A.B (shH2A.B). The results are presented as mean ± SD for five biological replicates. The significance of the difference was determined by Student's t test and denoted as ns (not significant); **, p &lt; 0.01; ***, p&lt;0.001."
NCBI gene IDs:
"H2A.B: 474381///83740///474382"
Figure legend: "E Genome browser screen shots of gene examples (RPs RPLP1 and RPL23A, and HDAC5 and TAF10) that contain H2A.B at their promoters identified by the CUT&amp;RUN peak calling and whose expression  decreased significantly following H2A.B  knockdown in the RNA-seq  analysis. Green and purple indicates L1236 and  L428cells, respectively."
NCBI gene IDs:
"H2A.B: 474381///83740///474382
HDAC5: 10014
RPL23A: 6147
RPLP1: 6176
TAF10: 6881"
Figure legend: "B Differential exon usage of the CD44 gene. C.  Differential exon usage of the RPL17 gene. "
NCBI gene IDs:
"CD44: 960
RPL17: 6139"
Figure legend: "D, E Two examples show increased accessibility at the promoter peak (NXF1) (D) and decreased accessibility at the peak across the intron-exon boundary (KDM4A) (E), respectively."
NCBI gene IDs:
"KDM4A: 9682
NXF1: 10482"
Figure legend: "MITOL-KO MEFs was vulnerable to ER stress. Control MEFs (MITOLF/F) and MITOL-KO MEFs (MITOL-/-) were treated with DMSO as control, 0.8 µM thapsigargin (Tg), 0.7 µg/mL tunicamycin (Tu) or 1.2 µg/mL brefeldin A (Br) for 24 hours. All experiments using Tu below were performed at concentration of 0.7 µg/mL. The relative cell viability shows a ratio between the survival of MEFs in the absence and presence of ER stress inducers. Viable cells were detected by cell viability assay using cell counting kit-8."
NCBI gene IDs:
"MITOL: 69104"
Figure legend: "MITOL KO increased ER stress-induced apoptosis. MEFs were treated with indicated ER stress inducers at same concentration as Figure 1A for 18 hours and stained with Annexin V-FITC for the detection of apoptosis using flow cytometry."
NCBI gene IDs:
"MITOL: 69104"
Figure legend: "MITOL re-expression in MITOL-KO MEFs rescued ER stress vulnerability. MEFs were transfected with MITOL-coding vector (WT), MITOL C65/68S-coding vector (CS), or empty vector (Vec) 24 hours prior to Tu treatment for 18 hours, followed by immunoblotting with indicated antibodies. Cleaved caspase-3 (cC3) and cleaved PARP (cPARP) were used as apoptosis markers."
NCBI gene IDs:
"MITOL: 69104"
Figure legend: "MITOL KO enhanced ER stress-induced Bax translocation and cytochrome c release. Mitochondria or cytosol fraction was isolated from MEFs treated with Tu for 18 hours, followed by immunoblotting with indicated antibodies."
NCBI gene IDs:
"MITOL: 69104"
Figure legend: "MITOL KO induced excessive mitochondrial depolarization by ER stress. MEFs transfected with indicated vectors were treated with Tu for 18 hours and then stained with TMRM, followed by flow cytometric analysis."
NCBI gene IDs:
"MITOL: 69104"
Figure legend: "IRE1α inhibition compensated MITOL-KO MEFs for vulnerability to ER stress. MEFs were transfected with scramble or siIRE1α (#1, #2). After 24 hours, these MEFs were exposed with Tu for 24 hours , followed by immunoblotting with indicated antibodies. Error bars represent SD (n=3)."
NCBI gene IDs:
"IRE1α: 78943
MITOL: 69104"
Figure legend: "MITOL KO did not affect the autophosphorylation of IRE1α. MEFs were exposed with Tu for indicated periods and phosphorylated IRE1α was detected by immunoblotting after Phos-tag SDS-PAGE."
NCBI gene IDs:
"MITOL: 69104"
Figure legend: "MITOL KO enhanced RIDD and xbp1 splicing. MEFs were incubated with Tu for 4 hours. Expression levels of various UPR associated genes were determined by qRT-PCR"
NCBI gene IDs:
"MITOL: 69104
xbp1: 22433"
Figure legend: "MITOL KO enhanced RIDD and xbp1 splicing. MEFs were incubated with Tu for 4 hours. MEFs were transfected with either miR-17 or miR-34 luciferase reporter vector 24 hours prior to Tu treatment for 4 hours, followed by luciferase reporter assay (F). Error bars represent SD (n=3)."
NCBI gene IDs:
"luciferase: 
MITOL: 69104
miR-17: 723905
miR-34: 723848
xbp1: 22433"
Figure legend: "IRE1α-mediated JNK phosphorylation was prolonged by MITOL KO. MEFs were incubated with Tu for indicated periods and phosphorylated JNK was detected by immunoblotting with indicated antibodies. Error bars represent SD (n=3)."
NCBI gene IDs:
"MITOL: 69104"
Figure legend: "JNK inhibition reduced ER stress-induced apoptosis of MITOL-KO MEFs. MEFs were treated with 20 µM JNK inhibitor-II (JNK inh) 2 hours prior to Tu treatment for 24 hours, followed by immunoblotting with indicated antibodies. Error bars represent SD (n=3)."
NCBI gene IDs:
"MITOL: 69104"