EMBO/SourceData huggingface dataset:
Figure legend: "(a,b) Primary NCMs from WT and Hace1−/− newborn pups stably transfected with WT HACE1 and C876S-mutant HACE1, were transiently transfected with a tandem tagged mRFP-GFP-LC3 reporter (tfLC3) plasmid, followed by 8 h treatment with MG132 or MG132 plus Baf in the last 4 h, and were subjected to confocal microscopy. DMSO treatment only was used in the control group. (a,c) Representative confocal micrographs of images used for quantification of the percentage of yellow dots in b and d. At least 10 images from each group were used for the calculation; error bars represent s.e.m., P-value as indicated (one-way ANAVO). Scale bars, 10 μm. Autophagosomes show both GFP and mRFP-LC3 signals (yellow) while autolysosomes exhibit mRFP-L3 signals only (red)."
NCBI gene IDs:
"Hace1: 209462
HACE1: 209462
LC3: Q91VR7///Q9CQV6///67443///66734
LC3: 67443///66734"
Figure legend: "(c,d) WT and Hace1−/− MEF, as well as Hace1−/− MEF stably transfected with WT HACE1 and C876S-mutant HACE1, were transiently transfected with a tandem tagged mRFP-GFP-LC3 reporter (tfLC3) plasmid, followed by 8 h treatment with MG132 or MG132 plus Baf in the last 4 h, and were subjected to confocal microscopy. DMSO treatment only was used in the control group. (a,c) Representative confocal micrographs of images used for quantification of the percentage of yellow dots in b and d. At least 10 images from each group were used for the calculation; error bars represent s.e.m., P-value as indicated (one-way ANAVO). Scale bars, 10 μm. Autophagosomes show both GFP and mRFP-LC3 signals (yellow) while autolysosomes exhibit mRFP-L3 signals only (red)."
NCBI gene IDs:
"Hace1: 209462
HACE1: 209462
LC3: 67443///66734"
Figure legend: "(a,b) Hace1−/− MEF cells were stably transfected with HA-tagged WT HACE1 (HA-HACE1) and empty vector MSCV. (a) Immunoblot for HA shows stable expression of HA-tagged HACE1 in HA-HACE1MEF cell lysate. (b) HA-HACE1MEF and control MSCVMEF cell lysates were subjected to Co-IP with anti-HA antibody and coomassie blue staining shows a couple of distinct bands only detected in HA-HACE1MEFIP pull-down as indicated by red arrows."
NCBI gene IDs:
"MSCV: 
HACE1: 209462"
Figure legend: "(c-f) Identification of HACE1 interacting proteins by MS analysis of Co-IP products. (c) Hierarchical clustering (heat) map demonstrating the clustering of proteins based on their expression intensities in HA-HACE1MEF and control MSCVMEFHA-IP pull-down products. To the left of the heat map, selected annotations found to be enriched in the protein clusters are shown. n=5 for HA-HACE1 group and n=4 for control MSCV group. (d) Pie chart shows enriched representative HACE1-interacting proteins according to molecular function by GO term. (e) Selected HACE1-interacting proteins identified by HA-IP MS were evaluated by western blot with the indicated antibodies (IB). HA-HACE1 denotes HA-IP pull-down from HA-HACE1MEF; MSCV denotes HA-IP pull-down from control MSCVMEF; and input indicates HA-HACE1MEF lysate before IP. (f) HA-HACE1MEF and control MSCVMEF lysates were subjected to co-IP with an anti-Unc-45b antibody and the pull-down were analysed by western blot with an anti-HA antibody."
NCBI gene IDs:
"MSCV: 
HACE1: 209462"
Figure legend: "(g,h) HA-IP pull-down products from HA-HACE1MEF (HA-HACE1) and Hace1 KO MSCVMEF (MSCV) immortalized in HA beads were further subjected to Co-Co-IP with WT mouseheart lysates, and the pull-down products were analysed by western blot using the indicated antibodies. HACE1 and those proteins with which it interacts were still detectable (g). There were also increased ubiquitinated proteins in the Co-Co-IPheart tissues (h)."
NCBI gene IDs:
"MSCV: 
HACE1: 209462"
Figure legend: "(a-c) Representative western blots and (d) quantification show increased accumulation of some of the HACE1-interacting proteins in the Hace1−/− sTAC myocardium. n=3 mice per group, error bars represent s.e.m., P-value between KO and WT sTAC as indicated (one-way analysis of variance). Gapdh was used as a loading control."
NCBI gene IDs:
"HACE1: 209462
Hace1: 209462"
Figure legend: " C mRNA expression in female Lin-Sca1+ cells, differentiated in the presence of 100 nM Rosi or vehicle for 8 days, as determined by qRT-PCR (n=3) t-test Cited4-/- vs. Cited4+/+ (Rosi) *P=0.013 (Ucp1), **P=0.004 (Cpt1b), *P=0.026 (Dio2)"
NCBI gene IDs:
"Cited4: 56222
Cpt1b: 12895
Dio2: 13371
Ucp1: 22227"
Figure legend: " G mRNA expression in primary SVF cells from human female subcutaneous fat transfected with the indicated siRNA prior to differentiation in the presence of 100 nM Rosi for 9 days, as determined by qRT-PCR (n=3) ***P=0.0002 (CITED4), **P=0.002 (UCP1), *P=0.02 (UCP1), *P=0.035/0.026 (PPARG), ***P=0.0006 (SLC2A4), **P=0.002 (ADIPOQ) in one-way ANOVA with Tukey posttests (vs. siCtrl)"
NCBI gene IDs:
"ADIPOQ: 9370
CITED4: 163732
PPARG: 5468
SLC2A4: 6517
UCP1: 7350"
Figure legend: " A-C Quantitative fluorescence microscopy of LipidTOX- and DAPI-stained female Cited4F/F Lin-Sca1+ progenitor cells transfected with Cre or control mRNA prior to differentiation in the presence of 100 nM Rosi for 8 days (n=5). **P=0.002 in t-test (Cre vs. Ctrl). Scale bar is 10 µm "
NCBI gene IDs:
"Cited4: 56222"
Figure legend: " D, E Ucp1 expression in female Cited4F/F Lin-Sca1+ progenitor cells transfected with Cre or control mRNA prior to differentiation in the presence of 100 nM Rosi for 8 days, as determined by Western blot with VCP as loading control (n=3) "
NCBI gene IDs:
"Cited4: 56222"
Figure legend: " A, B mRNA expression in scWAT of mice fed a diet with 0.0075% Rosi or control diet for 2.5 weeks, determined by qRT-PCR t-test Cited4-/- vs. Cited4+/+ (Rosi), (A) n=5/5/6/6, **P=0.003 (Ucp1), **P=0.008 (Cidea), **P=0.007 (Cyc1), *P=0.048 (Ndufb3), (B) n=5/4/5/5, *P=0.022 (Ucp1), *P=0.037 (Cidea)"
NCBI gene IDs:
"Cidea: 12683
Cited4: 56222
Cyc1: 66445
Ndufb3: 66495
Ucp1: 22227"
Figure legend: " C, D Ucp1 expression in scWAT of mice treated as in A, as determined by Western blot with VCP as loading control t-test Cited4-/- vs. Cited4+/+ (Rosi), females: n=5/5/6/6, *P=0.011, males: n=5/4/5/5"
NCBI gene IDs:
"Cited4: 56222"
Figure legend: " E mRNA expression in scWAT of female mice treated with  CL-316,243 (CL) (1 mg/kg/day via Alzet minipumps) or vehicle for 10 days (n=5/7/13, t-test Cited4-/- vs. Cited4+/+ (CL)) "
NCBI gene IDs:
"Cited4: 56222"
Figure legend: " F mRNA expression in scWAT of female mice  exposed to 5°C or 23°C for 2 weeks (n=5/10/6, t-test Cited4-/- vs. Cited4+/+ (5°C)) "
NCBI gene IDs:
"Cited4: 56222"
Figure legend: " C Oxygen consumption rate of female mice fed a diet with 0.0075% Rosi for 3.5 weeks and injected with 1 mg/kg CL-316,243 (CL) at the indicated time point, as determined by indirect calorimetry (n=9/10). *P=0.013 (-1 h), *P=0.045 (3 h), *P=0.015 (5 h), *P=0.016 (6 h), *P=0.019 (8 h), *P=0.046 (10 h) in repeated measures 2x2 ANOVA with Holm-Sidak posttests (Cited4-/- vs. Cited4+/+) "
NCBI gene IDs:
"Cited4: 56222"
Figure legend: " D Maximal CL-induced oxygen consumption rate of female mice shown in (C) adjusted for body weight by ANCOVA. Averages of VO2 throughout 3-8 hours post CL injection were calculated for each mouse (n=9/10). *P=0.049 in ANCOVA with Bonferroni posttest (Cited4-/- vs. Cited4+/+) "
NCBI gene IDs:
"Cited4: 56222"
Figure legend: " E Oxygen consumption rate of male mice treated as in (A), determined as in (C) (n=9/10). ANCOVA with Bonferroni posttest (Cited4-/- vs. Cited4+/+) "
NCBI gene IDs:
"Cited4: 56222"
Figure legend: " F Oxygen consumption rate of male mice treated as in (C), determined as in (C) (n=9/10). *P=0.044 (9 h), *P=0.013 (12 h) in repeated measures 2x2 ANOVA with Holm-Sidak posttests (Cited4-/- vs. Cited4+/+) "
NCBI gene IDs:
"Cited4: 56222"
Figure legend: " G Maximal CL-induced oxygen consumption rate of male mice shown in (F) and calculated as in (D) (n=9/10). ANCOVA with Bonferroni posttest (Cited4-/- vs. Cited4+/+) "
NCBI gene IDs:
"Cited4: 56222"
Figure legend: " A, B mRNA expression in scWAT of mice fed a high-fat diet (HFD) for 11 weeks followed by 5 weeks of HFD with 0.0075% Rosi (qRT-PCR). t-test Cited4-/- vs. Cited4+/+, (A) n=8/7, *P=0.029 (Ucp1), **P=0.009 (Elovl3), **P=0.006 (Cpt1b), **P=0.004 (Cyc1), *P=0.016 (Ndufb3), **P=0.003 (Cd36), **P=0.009 (Gyk), (B) n=7/8, *P=0.026 (Pck1) "
NCBI gene IDs:
"Cd36: 12491
Cited4: 56222
Cpt1b: 12895
Cyc1: 66445
Elovl3: 12686
Gyk: 14933
Ndufb3: 66495
Pck1: 18534
Ucp1: 22227"
Figure legend: " E, F Blood glucose during insulin tolerance test (ITT) with 1 U insulin per kg body mass on female mice after 12 weeks of HFD (n=8) (E) or 16 weeks of HFD and 4 weeks of HFD+Rosi (n=7) (F), expressed as % of the 0-time point value. **P=0.003 in repeated measures 2x2 ANOVA with Holm-Sidak posttests (Cited4-/- vs. Cited4+/+). G Area under the curve (AUC)  of blood glucose during the ITT (0-120 min) in (E,F). 2x2 ANOVA with Holm-Sidak posttests (After Rosi vs. Before Rosi) "
NCBI gene IDs:
"Cited4: 56222"
Figure legend: " H, I Blood glucose during  
insulin tolerance test (ITT) on male mice as in (E,F), n=8 (H), n=7/8 (I). Repeated measures 2x2 ANOVA with Holm-Sidak posttests (Cited4-/- vs. Cited4+/+). J Area under the curve (AUC) of blood glucose during the ITT in (H,J). **P=0.001, ***P=0.00006 in 2x2 ANOVA with Holm-Sidak posttests (After Rosi vs. Before Rosi) "
NCBI gene IDs:
"Cited4: 56222"
Figure legend: "C. qRT-PCR data showing induction of each gene in the iniBAC operon in WT Mtb cultured in low iron and in the virR mutant strain cultured in high iron, expressed as fold change relative to WT Mtb cultured in iron sufficient conditions. RNA extracted from biological triplicates was analyzed. The data are presented as means +/- SEM. **P≤ 0.01 ***P ≤ 0.001 (Student's t-test)."
NCBI gene IDs:
"iniB: 886518
virR: 886362"
Figure legend: "E. Protein and lipid content in vesicle preparations isolated from the same number of WT and Msm overexpressing iniACMtb (Msm iniACMtb). Three independent cultures were analyzed. Data are presented as mean ± SEM *P≤ 0.05; *** P≤ 0.001 (Student's t-test)."
NCBI gene IDs:
"iniA: 886510"
Figure legend: "H. The graph shows the avarage of nanoparticle size distribution in three independent vesicle preparations derived from WT (black) and Msm iniACMtb (grey)."
NCBI gene IDs:
"iniA: 886510"
Figure legend: "C. Protein in vesicle isolates derived from three independent cultures of Mtb WT and iniA::hyg mutant grown in low (LI) or high iron (HI) MM with or without 50 ng·mL-1 INH. Data are presented as mean ± SEM *P ≤ 0.05. ***P≤ 0.001 (Student's t-test)"
NCBI gene IDs:
"iniA: 886510"
Figure legend: "D. Lipid in vesicle isolates derived from three independent cultures of Mtb WT and iniA::hyg mutant cultured in low (LI) or high iron (HI) MM with or without 50 ng·mL-1 INH. Data are presented as mean ± SD *P ≤ 0.05 (Student's t-test)"
NCBI gene IDs:
"iniA: 886510"
Figure legend: "B. Mycobactin synthesized by Mtb WT and iniA::hyg grown in low iron conditions. Data are presented as the mean of mycobactin extracted from two independent cultures."
NCBI gene IDs:
"iniA: 886510"
Figure legend: "C. The Mtb siderophore synthesis mutant (ST142) was cultured in low iron MM (medium) plain or supplemented with MEV preparations derived from equal number of Mtb WT, iniA::hyg and complemented strains grown in low iron MM. ST142 growth was determined based on the number of viable cells detected by the resazurine cell viability assay. MEV obtained from three independent cultures were tested."
NCBI gene IDs:
"iniA: 886510"
Figure legend: "A. Representative Immunodot-blot of bacterial antigens associated with EVs isolated from the culture supernatants of THP-1 cells infected with Mtb WT, iniA:hyg and complemented strains versus uninfected cells (UI). Anti-MEV specific antiserum was used for detection. The decreasing black bar indicates that increasing dilutions were spotted onto the membrane. The experiment was repeated three times with independent cultures."
NCBI gene IDs:
"iniA: 886510"
Figure legend: "B. Number of nanoparticles per mL determined by Zeta View NTA in three EV preparations derived from the culture supernatans of THP-1 cells infected with Mtb WT, iniA:hyg and iniA::hyg complemented strains."
NCBI gene IDs:
"iniA: 886510"
Figure legend: "C. Representative Western blot of total EVs isolated from the CSF of THP-1 cells infected with Mtb WT, iniA::hyg and complemented strains versus uninfected cells (UI) detecting the exosome marker CD9. The experiment was repeated twice with similar results."
NCBI gene IDs:
"iniA: 886510"
Figure legend: "A Confocal laser scanning microscopy analyses in cells treated with BafA1. Total HA-ATZNNN (red) or HA-ATZNNN polymers (magenta) in LAMP1-positive endolysosome (green) in WT MEF. (C) Same as (A) in Cnx-KO MEF. (D) Same as (A) in WT MEF exposed to kifunensine (KIF). (E) Same as (A) in WT MEF exposed to Castanospermine (CST). (F) Same as (A) in sCNX MEF. (G) Same as (A) in Uggt1-KO MEF. "
NCBI gene IDs:
"Cnx: 12330
sCNX: 12330
Uggt1: 320011"
Figure legend: "(J) Halo-ATZNNN in Uggt1-KO MEF mock-transfected (empty pcDNA3 plasmid). (K, L) (K) Same as (J), with a plasmid for expression of active or (L) inactive UGGT1. (M) Quantification of Halo-ATZNNN-positive endolysosomes (mean, n=22, 10, 15 cells for panels J-L, respectively). One-way ANOVA and Dunnett's multiple comparison test, ns P&gt;0.05, **** P&lt;0.0001). "
NCBI gene IDs:
"Uggt1: 320011
UGGT1: 320011"
Figure legend: "(C) Co-immunoprecipitation of ATZXXX (Bait, lower panel) with CNX (upper panel) and BiP (middle panel). Protein content in the total cell extracts (TCE) is shown. (D) Quantification of (C) for CNX association (n=3). Unpaired two-tailed t-test, ** P&lt;0.01*** P&lt;0.001, **** P&lt;0.0001. (E) Quantification of (C) for BiP association (n=3 for ATZNNN and ATZQQN; n=4 for ATZQNQ and ATZQQQ). Unpaired two-tailed t-test, * P&lt;0.005, ** P&lt;0.01, *** P&lt;0.001, **** P&lt;0.0001. "
NCBI gene IDs:
"ATZ: 20703"
Figure legend: "(C) NSI mice  homozygous for the Fah  knockout displayed a lethal neonatal phenotype (left). Fah  expression  was detected in the livers  of homozygous NSI mice  with Fah  knockout and Fah  intact NSI mice  by  Western blotting (right). Cropped blots  are shown"
NCBI gene IDs:
"Fah: 14085"
Figure legend: "(F) Representative PCR amplification of MYC, TP53R249S, KRASG12D, NRASG12D, CTNNB1S45F, BRAFV600E, AXIN1G652S, IL6, PIK3CAE542K and CSF1RY969C in the genomic DNA of dissected primary tumors harvested from NSIF mice  transplanted with OC-PHHs  (Tumor) and their corresponding overexpression vector plasmids as positive controls (OCs)"
NCBI gene IDs:
"AXIN1: 8312
BRAF: 673
CSF1R: 1436
CTNNB1: 1499
IL6: 3569
KRAS: 3845
MYC: 4609
NRAS: 4893
PIK3CA: 5290
TP53: 7157"
Figure legend: "(B) Genomic DNA of colonies that were derived from single cells of iHCC1-1 and iHCC2-1 tumor samples were extracted for PCR amplification of MYC, TP53R249S, and KRASG12D"
NCBI gene IDs:
"KRAS: 3845
MYC: 4609
TP53: 7157"
Figure legend: "(B) Volcano plot of  RNA-seq data showing genes with differential expression  (1,591 upregulated and 2,243 downregulated genes, fold change≥2 and P value≤0.05) in iHCC cells compared to PHHs. TP53, KRAS, MYC, MUC1, and AFP  were highly expressed in  iHCC  cells, whereas hepatocyte  signature markers, including FOXA2, FOXA3, ATF5, HNF4A, and ALB  were highly expressed in PHHs"
NCBI gene IDs:
"AFP: 174
ALB: 213
ATF5: 22809
FOXA2: 3170
FOXA3: 3171
HNF4A: 3172
KRAS: 3845
MUC1: 4582
MYC: 4609
TP53: 7157"
Figure legend: "HeLa  cells were transfected with a WT or mutant Parkin  plasmid (FLAG), shown in blue, along with reporters for either PA  or DAG  shown in green. DMSO  or 10 µM CCCP  was added for the indicated periods of time. Mitochondria  were visualized via anti-Tom20 staining  (red). (A) PA  accumulated on Parkin-positive mitochondria  after 1 hour of 10uM CCCP  treatment, with a more dramatic increase by 3hr and 18 hr. Scale bar = 25 µM, and zoom is 9x. (B) Quantification of imaging experiments shown in A and B. Bars represent mean with SEM from three biological independent experiments; two-way ANOVA analysis was performed for statistical analysis (***P&lt;0.0001). (C) DAG  (diacylglycerol) accumulated on Parkin-positive mitochondria  after 5.5 hr of 10uM CCCP  treatment. Arrowheads and arrows point to the DAGR  concentration at the Golgi  and mitochondria, respectively. Scale bar = 25 µM, and zoom is 9x."
NCBI gene IDs:
"FLAG: 
Parkin: 5071"
Figure legend: "(B) HEK-293T  cells were transfected with Parkin-FLAG  and DAGR-YFP  followed by CCCP  treatment for indicated times. Mitochondrial  and cytosolic  fractions were purified and analyzed by Western blots by indicated antibodies. Citrate synthetase  and α-tubulin were used as a mitochondrial  and cytosolic  marker, respectively. Note that PLD2  and Parkin  levels were elevated in the mitochondrial  fraction in response to CCCP  treatment."
NCBI gene IDs:
"FLAG: 
YFP: 
Parkin: 5071"
Figure legend: "(C) Hela  cells were co-transfected with mCherry-Parkin  and the PA  reporter, followed by CCCP  treatment alone or with a PLD2  inhibitor VU 0364739 (3 µM) for 5.5 hrs. Line scan analysis (Image J software) corresponding to the line drawn in the images indicate colocalization  between the PA  reporter (green) and mitochondria  (red). Note that VU 0364739 suppressed mitochondrial PA  accumulation. Scale bar = 10 µM. (D) Quantification of the numbers of cells with the PA  reporter positive mitochondria  shown in (C). Asterisks indicate statistical significance (***P&lt;0.001, Student's t-test) from three biological independent experiments. The bars indicate mean± SEM."
NCBI gene IDs:
"mCherry: 
Parkin: 5071"
Figure legend: "(E) Hela  cells were transfected with a lipin1  siRNA, followed by the DAG  reporter and mCherry-Parkin, treated with CCCP  (10 µM) for 9 hrs and then subject to image analysis. Scale bar = 25 um, and zoom is 4x. Lipin 1 KD reduced mitochondrial DAGR, but not Golgi-DAGR, accumulation (arrowheads) (F) The numbers of cells with DAG-reporter positive mitochondria  shown in (E) and in Lipin-1 knockdown cells transfected with siRNA-resistant wildtype (WT) and catalytically dead (CD; D712E;D714E) mutant cDNA. Note that Lipin1  KD reduced mitochondrial DAG  accumulation, which can be significantly restored by the re-expression of WT, but not CD mutant, Lipin-1. The graph shows the means with SEM (error bars) from three biological independent experiments. Asterisks indicate statistical significance by one-way ANOVA (**P&lt; 0.01, ***P&lt;0.001)."
NCBI gene IDs:
"mCherry: 
Lipin 1: 23175
Lipin-1: 23175
Lipin-1: 14245
lipin1: 14245
Lipin1: 23175
Parkin: 5071"
Figure legend: "(A-B) Hela  cells were transfected with a Lipin1  or control (cKD) siRNA followed by a GFP-Parkin  expression plasmid. Transfected cells were treated with CCCP  at 10 µM for 18 hrs, and subject to immuno-staining. (B) Quantification of Parkin-positive cells in (A) that have lost a majority of mitochondria  (marked by TOM20, arrows). Note that mitochondrial  clearance is reduced in Lipin-1  knockdown cells (arrowheads in (A)). Scale bar = 25 µM."
NCBI gene IDs:
"GFP: 
Lipin-1: 23175
Lipin1: 23175
Parkin: 5071"
Figure legend: "(C). Control or lipin1  knockdown Hela  cells stably expressing parkin-mCherry  were treated with DMSO  or CCCP  (10 µM for 18 hrs) and Bafilomycin A1  (1μM, lysosomal inhibitor) treatment, followed by immunoblotting  with indicated antibodies and quantified by the Image J. software. Note that lipin1  silencing suppressed CCCP-induced mitochondrial  protein degradation. Lipin-1-mediated mitochondrial DAG  production is required for mitophagosome  production."
NCBI gene IDs:
"mCherry: 
Lipin-1: 23175
lipin1: 23175
parkin: 5071"
Figure legend: "(D-F). Hela  cells were transfected with control or a Lipin1  siRNA followed by the expression plasmids of GFP-Parkin  and RFP-DAGR. Transfected cells were treated with DMSO or CCCP  at 10 µM for 9 hr, with or without further incubation with 1,2-Dipalmitoyl-sn-glycerol  (DPG) at 100 µM, as indicated. Autophagosome formation was assessed by an LC3  antibody (pseudocolored in white in single-channel and blue in the overlay images). Arrows point to DAGR concentration at the Golgi  under basal conditions. The number (E) and size (F, arbitrary unit) of LC3 vesicles  were quantified. n=4 biological replicates. The bars indicates mean± SEM. Asterisks indicate statistical significance by one-way ANOVA (*P&lt; 0.05, **P&lt;0.01). Scale bar = 25 µM and zoom is 5x. Note that both the number and size of LC3-vesicles  in Lipin-1 knockdown cells were much smaller than those in WT cells, and these defects were corrected by DPG  treatment."
NCBI gene IDs:
"GFP: 
RFP: 
Lipin-1: 23175
Lipin1: 23175
Parkin: 5071"
Figure legend: "(A) E3 ligase-deficient Parkin  mutants (T240R and T415N) have no effect on PA  accumulation (green) on depolarized, Parkin-positive mitochondria. The expression of WT and Parkin  mutants were determined by Immunoblotting. Scale bar = 25 µM, and zoom is 3x. (B) DAG  accumulation depends upon intact Parkin E3 ligase  activity. Scale bar = 25µm, and zoom is 3x. (C) Quantification of imaging experiments shown in (A) and (B). Bars represent mean with SEM; two-way ANOVA analysis was performed for statistical analysis(***P&lt;0.001). n=3 biological replicates."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(D) Hela  cells were transfected with control or optineurin- and NDP52- siRNAs and expression plasmids of FLAG-Parkin  and YFP-DAGR. These cells were treated with DMSO  or 10 µM CCCP  for 5.5 hrs, as indicated. Note that OPTN/NDP52  double knockdown prevented mitochondrial YFP-DAGR accumulation. (Scale bar = 25 µM and zoom is 3x) (E) Hela OPTN/NDP52  knockdown cells were transfected with a siRNA-resistant wildtype or ubiquitin-binding deficient E478G OPTN  mutant, as indicated. The percentage of cells with mitochondrial YFP-DAGR following CCCP  treatment was quantified. Asterisks indicate statistical significance by one-way ANOVA (**P&lt; 0.01, ***P&lt;0.001) from three biological independent experiments. The bars indicate mean± SEM. Bottom panel: Expression of OPTN, OPTN  E478 and NDP52  was determined by immunoblotting."
NCBI gene IDs:
"FLAG: 
YFP: 
NDP52: 10241
optineurin: 10133
OPTN: 10133
Parkin: 5071"
Figure legend: "(F-G) Hela OPTN/NDP52  knockdown cells were incubated with 1,2-Dipalmitoyl-sn-glycerol (DPG) followed by CCCP  treatment for 18 hrs. Mitophagy  efficiency was assessed by TOM20 staining  and quantified in (G) (n = 2 biological replicates). Note that DPG  significantly restored mitophagy  in OPTN/NDP52  knockdown cells. Scale bar = 10 µM."
NCBI gene IDs:
"NDP52: 10241
OPTN: 10133"
Figure legend: "(C). Cytosolic  and mitochondrial  fractions purified from control and OPTN/NDP52  knockdown cells treated with CCCP  were immunoblotted  with indicated antibodies. Note that mitochondrial EndoB1  levels were reduced in OPTN/NDP52  knockdown cells"
NCBI gene IDs:
"NDP52: 10241
OPTN: 10133"
Figure legend: "(D-E) Hela  cells were transfected with an EndoB1  siRNA, followed by the expression plasmids for mCherry-Parkin  and YFP-DAGR, and CCCP  treatment (10 µM) for 9 hrs. Cells with mitochondrial YFP-DAGR were quantified in (E) (*P&lt;0.05, Student's t-test, n=3 biological replicates). Scale bar = 25 µM and zoom is 5x. Note that knockdown of EndoB1  suppressed mitochondrial DAG  production."
NCBI gene IDs:
"mCherry: 
YFP: 
Parkin: 5071
EndoB1: 51100"
Figure legend: "(A, B) The  Mouse macrophage J774A.1 cell line was transfected with control siRNA or siRNA against IKKβ (A) or  IKKα  (B). 72 h post-transfection, the cells were co-stimulated for 60 min without (-) or with (+) 100 ng/ml LPS  and/or 5 μM nigericin. Cell lysates (10 μg) were denatured in SDS, subjected to SDS-PAGE  and  immunoblotted with the antibodies indicated. Similar results were obtained in three (A) or two (B) independent experiments."
NCBI gene IDs:
"IKKα: 12675
IKKβ: 16150"
Figure legend: "(C, D) As in (A, B) except that BMDM from  IKKβ-LysM-Cre (flox/flox) (IKKβ (fl/fl)) or WT control mice were co-stimulated without (-) or with (+) 100 ng/ml LPS  and/or 4 mM ATP (C) or with 100 ng/ml  LPS and/or 5 μM nigericin (D). Similar results were obtained in two independent experiments."
NCBI gene IDs:
"LysM: 
Cre: 2777477
IKKβ: 16150"