EMBO/SourceData huggingface dataset:
Figure legend: "esgts midguts expressing GFP alone (control), or expressing Notch Intra Cellular Domain (NICD), and NICD + OvoB. In closeups (right), DAPI is shown in purple for improved contrast; the arrow highlights a cell with intermediate phenotype."
NCBI gene IDs:
"GFP: 
NICD: 31293
Notch Intra Cellular Domain: 31293
OvoB: 31429"
Figure legend: "esgtsF/O midguts expressing GFP alone (control), or expressing RasV12, and RasV12 + svb-RNAi (top panels). Bottom panels show esgts midguts expressing GFP alone (control), or expressing EGFR-DN, and EGFR-DN + OvoB. Samples were stained for GFP (green). The graph shows quantification of the number of GFP-positive cells in esgts midguts expressing GFP alone (ctrl), or expressing EGFR-DN, EGFR-DN + OvoB, and EGFR-DN + svb-RNAi. The Y axis is plotted as log(10)."
NCBI gene IDs:
"GFP: 
EGFR: 37455
OvoB: 31429
svb: 31429
Ras: 43873"
Figure legend: "esgts midguts expressing GFP alone (control), or expressing ArmS10, ArmS10 + svb-RNAi, ArmS10 + OvoB ,TCF-DN, and TCF-DN + OvoB. Samples were stained for GFP (green). The graph shows quantification of the number of GFP-positive cells in esgts midguts expressing GFP alone (ctrl), or expressing TCF-DN, TCF-DN + OvoB, and TCF-DN + svb-RNAi. The Y axis is plotted as log(10)."
NCBI gene IDs:
"GFP: 
Arm: 31151
OvoB: 31429
svb: 31429
TCF: 43769"
Figure legend: "esgts midguts expressing GFP alone (control), or expressing SvbREP. Samples were stained for GFP (green) and Prospero (red). Closeups correspond to boxed regions, with DAPI shown in purple and GFP-positive cells outlined in yellow."
NCBI gene IDs:
"GFP: 
Svb: 31429"
Figure legend: "esgts-F/O midguts expressing GFP alone (control), or expressing SvbREP. Samples were stained for GFP (green) and cleaved DCP1 (red). E' shows quantification of the number of GFP-positive cells in esgts guts expressing GFP alone (ctrl), or DIAP, SvbREP, and SvbREP + DIAP."
NCBI gene IDs:
"GFP: 
DIAP: 39753
Svb: 31429"
Figure legend: "esgts midguts expressing GFP alone (control), or expressing Notch-RNAi, Notch-RNAi + svb-RNAi, and Notch-RNAi + SvbREP. Samples were stained for GFP (green) and Prospero (red). The graph shows quantification of the number of GFP-positive cells."
NCBI gene IDs:
"GFP: 
Notch: 31293
svb: 31429
Svb: 31429"
Figure legend: "esgts midguts expressing GFP alone (control), or expressing STAT-RNAi, STAT-RNAi + svb-RNAi and STAT-RNAi + SvbREP. Samples were stained for GFP (green) and Prospero (red). The graph shows quantification of the number of GFP-positive cells."
NCBI gene IDs:
"GFP: 
svb: 31429
Svb: 31429
STAT: 42428"
Figure legend: "Cross sections of control MyoIAts midguts (expressing GFP and mCherry-RNAi), or expressing svb-RNAi, SvbACT, and Pri. Samples were stained for F-actin (white), GFP (green) and Tsp2a (yellow)."
NCBI gene IDs:
"mCherry: 
GFP: 
MyoIA: 43811
svb: 31429
Svb: 31429
Pri: 47191"
Figure legend: "MyoIAts midguts expressing GFP alone (control), or expressing SvbACT. Samples were stained for GFP (green), Scribble (yellow), ß-catenin (purple) and DAPI (Blue). A' pictures display cross sections of the regions shown in A."
NCBI gene IDs:
"GFP: 
Svb: 31429"
Figure legend: "MyoIAts midguts expressing GFP alone (control), or expressing SvbACT. Samples were stained for GFP (green) and PH3 (red). The graph plots number of mitotic PH3-positive cells per midgut of MyoIAts guts expressing GFP alone (ctrl), or expressing SvbACT , and SvbREP + pri."
NCBI gene IDs:
"GFP: 
Svb: 31429
pri: 47191"
Figure legend: "Top: Immunoblot analysis of CIC in WT, Drosha_KO, Dicer_KO and Ago2&amp;1_KO mESCs. TUBULIN was used as a loading control. Blot is a representative image of three biological replicates. Bottom: Bar graph showing quantification of CIC intensity, normalized to TUBULIN and relative to the WT sample in three biological replicates. Data information: Bar graph in Fig 2F shows mean intensity of CIC signal ± SD normalized to TUBULIN. Values are relative to WT, which was set to 1. P-values were calculated using a student's t-test comparing each value to the WT. *p-value&lt;0.05."
NCBI gene IDs:
"Ago2: 239528
Dicer: 192119
Drosha: 14000"
Figure legend: "MA plot of the DGE analysis in miR-290-295_KO mESCs. Data information: In A, significant genes in MA plot were determined using an adjusted p-value of 0.1."
NCBI gene IDs:
"miR-290: 102465789///100049710"
Figure legend: "F, G. Integrated data for Tfap4 gene shows multiple lines of evidence for its regulation by miR-290-295. In addition to the data shown and described in Fig 1D, E, a second AGO2-binding dataset, based on cross-linking immunoprecipitation and sequencing (CLIP-seq), has been integrated. Response elements for miR-290-295 cluster members are denoted in red and labeled."
NCBI gene IDs:
"miR-290: 102465789///100049710
Tfap4: 83383"
Figure legend: "Top: Immunoblot analysis of TFAP4 in WT, Drosha_KO, Dicer_KO, Ago2&amp;1_KO and miR-290-295_KO mESCs. LAMINB1 was used as a loading control. Blot is a representative image of three biological replicates. Bottom: Bar graph showing quantification of CIC intensity, normalized to LAMINB1 and relative to the WT sample in three biological replicates. Data information: In H bar graphs show mean intensity of TFAP4 signal ± SD normalized to LAMINB1 Values are relative to WT or the negative control mimic, which was set to 1. P-values were calculated using a student's t-test comparing each value to the WT. *p-value&lt;0.05, **p-value&lt;0.01, ****p-value&lt;0.0001."
NCBI gene IDs:
"Ago2: 239528
Dicer: 192119
Drosha: 14000
miR-290: 102465789///100049710"
Figure legend: "Top: Immunoblot analysis of TFAP4 after transfection of miRNA mimics (miR-291a-5p, miR-291a-3p and miR-291a-5p+miR-291a-3p combined) in miR-290-295_KO mESCs. Immunoblots were stained with Coomassie blue dye as a loading control. Blot is a representative image of three biological replicates. Bottom: Bar graph showing quantification of TFAP4 intensity, normalized to Coomassie and relative to the WT sample in three biological replicates. Data information: In I, bar graphs show mean intensity of TFAP4 signal ± SD normalized to Coomassie. Values are relative to WT or the negative control mimic, which was set to 1. P-values were calculated using a student's t-test comparing each value to the WT. *p-value&lt;0.05, **p-value&lt;0.01, ****p-value&lt;0.0001."
NCBI gene IDs:
"miR-290: 102465789///100049710
miR-291a-3p: 100049715
miR-291a-5p: 100049715"
Figure legend: "Top: Mature sequences of 5p and 3p miRNAs of the miR-290-295 family and the mature sequence of the human miR-302c-3p. Colors indicate identical seed sequences. Bottom: AGO2 CLIP-seq shows a peak at the miR-302c-3p binding site on human TFAP4."
NCBI gene IDs:
"miR-302c-3p: 442895
TFAP4: 7023"
Figure legend: "Immunoblot validation of siPOOL-mediated knock down of Tfap4. TFAP4 levels were compared between untreated WT versus miR-290-295_KO cells treated with a negative control and a Tfap4-targeted siPOOL. Immunoblots were stained with Coomassie blue dye as a loading control. Blot is a representative image of two biological replicates."
NCBI gene IDs:
"miR-290: 102465789///100049710
Tfap4: 83383"
Figure legend: "Scatterplot of DEG in miR-290-295_KO control versus siPOOL-Tfap4. SiPOOL experiments were performed in miR-290-295_KO cells and DE was assessed relative to a negative control siPOOL transfection. Only genes that are statistically significantly differentially expressed in miR-290-295_KO are shown. Genes predicted to be targeted by miR-290-295 are marked in blue. Genes are defined as rescued (orange) if the log2FoldChange-ratio between miR-290-295_KO control and siPOOL-Tfap4 is in the range [-2, -1/2]. Tfap4 is marked by a red dot."
NCBI gene IDs:
"miR-290: 102465789///100049710
Tfap4: 83383"
Figure legend: "Representative images of NANOG (red) and OCT4 (green) immunofluorescence staining in WT, Drosha_KO and Drosha &amp; Tfap4_KO mESCs. Scale bar = 20 μm. Quantification of NANOG fluorescence signal intensity in WT, Drosha_KO and Drosha &amp; Tfap4_KO mESCs show no significant rescue of NANOG intensity in Drosha &amp; Tfap4_KO Data information: In E, box plots show nuclear intensity of NANOG in ~300 cells per genotype. P-values were generated using ordinary one-way ANOVA. ****p-value&lt;0.0001. In panel E, the box plot's central band represents the median relative intensity for each genotype. The boxes represent the interquartile range and the whiskers represent the maximum and minimum relative intensity values. "
NCBI gene IDs:
"Drosha: 14000
Tfap4: 83383"
Figure legend: "Dose-dependent viability assays of BRCA2-proficient (+BRCA2) or -deficient (-BRCA2) human DLD1 cells treated with drugs at the indicated concentrations for six days."
NCBI gene IDs:
"BRCA2: 675"
Figure legend: "Human spheroids established from BRCA2-proficient (+BRCA2) or -deficient (-BRCA2) DLD1 cells, were incubated with 1.25 µM olaparib or 0.5 µM chlorambucil over the indicated period of time."
NCBI gene IDs:
"BRCA2: 675"
Figure legend: "Dose-dependent viability assays of BRCA1-proficient (+BRCA1) or -deficient (-BRCA1) human RPE1-hTERT cells treated with drugs at the indicated concentrations for six days."
NCBI gene IDs:
"BRCA1: 672"
Figure legend: "Dose-dependent viability assays of BRCA1-proficient (+BRCA1) or -deficient (-BRCA1) TP53-deleted cells treated with drugs at the indicated concentrations for six days."
NCBI gene IDs:
"BRCA1: 12189
TP53: 27223"
Figure legend: "Dose-dependent viability assays of Brca1+/+ and Brca1-/- mouse mammary tumour-derived cell lines treated with drugs at the indicated concentrations for six days."
NCBI gene IDs:
"Brca1: 12189"
Figure legend: "Dose-dependent viability assays of BRCA2-deficient (Capan-1) or -proficient (MIA PaCa-2) human pancreatic carcinoma-derived cells treated with drugs at the indicated concentrations for six days."
NCBI gene IDs:
"BRCA2: 675"
Figure legend: "Dose-dependent viability assays of BRCA2-deficient (PEO1) or -proficient (C4-2) human ovarian tumour-derived cells treated with drugs at the indicated concentrations for six days."
NCBI gene IDs:
"BRCA2: 675"
Figure legend: "BRCA2-deficient (PEO1) or -proficient (C4-2) human ovarian tumour-derived cells were infected with lentiviruses expressing control or CHD4 shRNAs, followed by selection with puromycin for 72 hours. Dose-dependent viability assays were performed on cells treated with drugs at the indicated concentrations for six days."
NCBI gene IDs:
"BRCA2: 675
CHD4: 1108"
Figure legend: "BRCA2-proficient (+BRCA2) or -deficient (-BRCA2) human DLD1 cells were incubated with 1 µM chlorambucil (Chl). Whole cell extracts prepared at the indicated time points during treatment were immunoblotted as shown. GAPDH was used as a loading control."
NCBI gene IDs:
"BRCA2: 675"
Figure legend: "Quantification of chromosome aberrations and chromatid/chromosome break frequencies in BRCA2-proficient (+BRCA2) or -deficient (-BRCA2) human DLD1 cells incubated with 1 μM chlorambucil or 1 µM cisplatin for 72 h. Data were obtained from three independent experiments and normalised to untreated controls. A minimum of 60 Giemsa-stained metaphases were analysed for each sample. Cis, cisplatin; Chl, chlorambucil."
NCBI gene IDs:
"BRCA2: 675"
Figure legend: "Nude mice (nu/nu) were injected subcutaneously with 5 x 106 human DLD1 cells, BRCA2-proficient (A) or BRCA2-deficient (B). Tumour-bearing mice were treated with 3 mg/kg daily chlorambucil administered intraperitoneally (i.p.) for a total of ten days. Tumour weight was determined on the indicated days after initiation of the treatment."
NCBI gene IDs:
"BRCA2: 675"
Figure legend: "PDTCs derived from breast cancer samples as previously described (Bruna et al, 2016) were treated with chlorambucil at the indicated doses. Cell survival is represented relative to DMSO control. AB521, ER-negative tumour, no BRCA1 alteration; STG201, tumour with BRCA1 promoter methylation and loss of BRCA1 expression; VHIO179, tumour with BRCA1 germline mutation and MAD2L2 inactivating mutation (olaparib-resistant)"
NCBI gene IDs:
"BRCA1: 672
MAD2L2: 10459"
Figure legend: "CB17/SCID mice were injected intramuscularly with 5 x 106 human BRCA2-deficient HCT116 cells. Tumour-bearing mice were treated on the indicated days with chlorambucil or cisplatin administered intraperitoneally (i.p.), or talazoparib administered orally (o.s.) Tumour volume was measured on the indicated days after treatment initiation and was expressed relative to tumour volume at the beginning of treatment (day 1). Scale bar, 40 µm. Each experimental group included n = 5 mice. Error bars represent SEM. Tumour sections were assessed at the end of each treatment using immunohistochemistry of γH2AX staining."
NCBI gene IDs:
"BRCA2: 675"
Figure legend: "HeLa cells were co-transfected with Myc empty vector (Myc), Myc-tagged FUNDC1 (F1-Myc) or Myc-tagged FUNDC1-ΔLIR mutant (ΔLIR-Myc) and Mito-OM-cherry, which localizes to the mitochondrial outer membrane, and immunostained with fluorescent anti-p62 and anti-Myc antibodies. Scale bar=10 μm."
NCBI gene IDs:
"Mito-OM-cherry: 
F1: 139341
FUNDC1: 139341
Myc: 4609"
Figure legend: "HeLa cells were co-transfected with Myc, F1-Myc or ΔLIR-Myc and Mito-OM-cherry and immunostained with anti-Ubiquitin (Ub) and anti-Myc antibodies. Scale bar=10 µm."
NCBI gene IDs:
"Mito-OM-cherry: 
F1: 139341
Myc: 4609"
Figure legend: "Fractionation analysis of HeLa cells transfected with Myc, F1-Myc or ΔLIR-Myc. The loading controls (L.C.) were α-Tubulin for total cell lysate (TCL) and cytosolic fraction (Cyto), and HSP60 for mitochondrial fraction (Mito)."
NCBI gene IDs:
"F1: 139341
Myc: 4609"
Figure legend: "HeLa cells transfected with Myc or Myc/His6 double-tagged F1-Myc-His were lysed and precipitated with Ni-NTA beads. Samples were then subjected to SDS-PAGE. The differential band (upper arrow) was isolated and subjected to mass spectral analysis. The identified proteins with a score higher than 50 are listed."
NCBI gene IDs:
"His: 
His6: 
F1: 139341
Myc: 4609"
Figure legend: "Co-IP of endogenous HSC70 with F1-Myc or ΔLIR-Myc. α-Myc, anti-Myc antibody"
NCBI gene IDs:
"F1: 139341
Myc: 4609"
Figure legend: "Co-IP analysis of endogenous FUNDC1 with Flag-HSP70 or Flag-HSC70. α-Flag, anti-Flag antibody. Flag，empty vector."
NCBI gene IDs:
"Flag: 
HSP70: 3306
HSC70: 10963"
Figure legend: "HeLa cells were co-transfected with Myc, F1-Myc or ΔLIR-Myc and Mito-OM-cherry and immunostained with anti-HSC70 and anti-Myc antibodies. Scale bar=10 µm."
NCBI gene IDs:
"Mito-OM-cherry: 
F1: 139341
Myc: 4609"
Figure legend: "Fractionation analysis of HeLa cells transfected with Myc or F1-Myc."
NCBI gene IDs:
"F1: 139341
Myc: 4609"
Figure legend: "HeLa cells were co-transfected with Ub-R-GFP and Myc or F1-Myc and immunostained with fluorescent anti-Myc and anti-GFP (α-GFP) antibodies. The α-GFP signals in F1-Myc transfected cells were lowered to avoid the overexposure of the mitochondrially localized R-GFP, making such signals of the equally distributed R-GFP invisible. Green arrowheads show the mitochondrially localized R-GFP proteins, which were more abundant than the equally distributed R-GFP and showed stronger R-GFP fluorescence, white arrowheads show the mitochondrially localized R-GFP proteins without stronger R-GFP fluorescence, although abundant. Scale bar=10 µm."
NCBI gene IDs:
"R-GFP: 
F1: 139341
Myc: 4609
Ub: 7316///7314"
Figure legend: "Fractionation analysis of HeLa cells co-transfected with Ub-R-GFP and Myc or F1-Myc."
NCBI gene IDs:
"R-GFP: 
F1: 139341
Myc: 4609
Ub: 7316///7314"
Figure legend: "HeLa cells were co-transfected with Ub-R-GFP and F1-Myc. Mitochondria were isolated and then treated with or without proteinase K (Pro.K), or proteinase K in combination with digitonin or Triton X-100 (TX-100). Samples were then subjected to Immunoblot analysis. HSP60, TIM23 and TOM20 are representatives of mitochondrial matrix-, mitochondrial inner membrane- and mitochondrial outer membrane-localized proteins, respectively."
NCBI gene IDs:
"R-GFP: 
F1: 139341
Myc: 4609
Ub: 7316///7314"
Figure legend: "Fractionation analysis of HeLa cells stably transfected with control (Ctrl) shRNA vector or HSC70 shRNA and transiently co-transfected with Ub-R-GFP, Flag or Flag-HSC70 (shRNA-resistant) and Myc, or F1-Myc, as indicated."
NCBI gene IDs:
"Flag: 
R-GFP: 
F1: 139341
Myc: 4609
HSC70: 10963
Ub: 7316///7314"
Figure legend: "Fractionation analysis of the HeLa cells transfected with Ub-R-GFP and treated with DMSO (control vehicle) or 10 μM MG132 for 4 hours."
NCBI gene IDs:
"R-GFP: 
Ub: 7316///7314"
Figure legend: "Proteinase K protection analysis of the mitochondria isolated from the HeLa cells transfected with Ub-R-GFP and treated with MG132."
NCBI gene IDs:
"R-GFP: 
Ub: 7316///7314"
Figure legend: "Proteinase K protection analysis of the mitochondria isolated from HeLa cells co-transfected with Ub-R-GFP and Ctrl, TOM20, TOM22 or TOM70 shRNA and treated with MG132."
NCBI gene IDs:
"R-GFP: 
TOM20: 9804
TOM22: 56993
TOM70: 9868
Ub: 7316///7314"
Figure legend: "Fractionation analysis of HeLa cells stably transfected with Ctrl or LONP1 shRNA and transiently co-transfected with Ub-R-GFP and Myc or LONP1 (shRNA-resistant) and then treated with DMSO or MG132."
NCBI gene IDs:
"R-GFP: 
LONP1: 9361
Myc: 4609
Ub: 7316///7314"
Figure legend: "Fractionation analysis of HeLa cells stably transfected with Ctrl shRNA, F1 shRNA, or F1 shRNA together with shRNA-resistant F1-Myc or ΔLIR-Myc, and transiently transfected with Ub-R-GFP and then treated with DMSO or MG132."
NCBI gene IDs:
"R-GFP: 
F1: 139341
Myc: 4609
Ub: 7316///7314"
Figure legend: "Fractionation analysis of HeLa cells stably transfected with Ctrl or HSC70 shRNA and transiently co-transfected with Ub-R-GFP and Flag or shRNA-resistant Flag-HSC70 and then treated with DMSO or MG132."
NCBI gene IDs:
"Flag: 
R-GFP: 
HSC70: 10963
Ub: 7316///7314"
Figure legend: "Fractionation analysis of HeLa cells stably transfected with Ctrl or HSP70 shRNA and transiently co-transfected with Ub-R-GFP and Flag or shRNA-resistant Flag-HSP70 and then treated with DMSO or MG132."
NCBI gene IDs:
"Flag: 
R-GFP: 
HSP70: 3306
Ub: 7316///7314"
Figure legend: "Mitochondria were isolated from the untransfected cells, cytosols were isolated from the cells transfected with GFP or Ub-R-GFP and treated with DMSO or MG132 for 8 hours, the isolated mitochondria and cytosols were then subjected to in vitro protein import analysis."
NCBI gene IDs:
"GFP: 
R-GFP: 
Ub: 7316///7314"
Figure legend: "Mitochondria isolated from the untransfected cells were resuspended in the cytosol isolated from the cells transfected with Ub-R-GFP and incubated at RT for I hour, the mitochondria were then isolated from the in vitro system, then treated with or without proteinase K and subjected to immunoblot analysis."
NCBI gene IDs:
"R-GFP: 
Ub: 7316///7314"
Figure legend: "Mitochondria were isolated from the cells transfected with ctrl shRNA, F1 shRNA or F1 shRNA together with F1-Myc, cytosols were isolated from the cells transfected with Ub-R-GFP, the isolated mitochondria and cytosols were then subjected to in vitro protein import analysis."
NCBI gene IDs:
"R-GFP: 
F1: 139341
Myc: 4609
Ub: 7316///7314"
Figure legend: "Cytosol isolated from the cells transfected with Ub-R-GFP were mixed with the cytosols isolated from the cells transfected with ctrl shRNA, HSC70 shRNA or HSC70 shRNA together with Flag-HSC70, mitochondria were isolated from the untransfected cells, the isolated mitochondria and cytosol mixtures were then subjected to in vitro protein import analysis."
NCBI gene IDs:
"Flag: 
R-GFP: 
HSC70: 10963
Ub: 7316///7314"
Figure legend: "Immunoblot analysis of the HeLa cells transfected with or without HA-Bcl-xL and treated with DMSO or MG132 for 6 hours."
NCBI gene IDs:
"HA: 
Bcl-xL: 572"
Figure legend: "Ni2+-NTA precipitation of HeLa cells transfected with indicated vectors. S13A-Myc-His, Myc/His6 double-tagged FUNDC1-S13A mutant."
NCBI gene IDs:
"His: 
His6: 
FUNDC1: 139341
Myc: 4609"
Figure legend: "HeLa cells were transfected with GFP-p62, treated with DMSO or 10 μM MG132 for 8 hours and then immunostained with anti-Ub and anti-γ-Tubulin antibodies. Note that the aggresome (blue arrowhead), rather than the MAPAs (white arrowheads), colocalizes with γ-Tubulin. Scale bar=10 µm."
NCBI gene IDs:
"GFP: 
p62: 8878"
Figure legend: "D, E. HeLa cells were transfected with Ctrl, TOM20, TOM22 or TOM70 shRNA vectors including nuclear localized GFP (N-GFP) expressing elements, then treated with MG132 and immunostained with the indicated antibodies. Scale bar=10 µm. Quantification is show in (E)."
NCBI gene IDs:
"GFP: 
TOM20: 9804
TOM22: 56993
TOM70: 9868"
Figure legend: "F, G. HeLa cells were transfected with GFP or GFP-Bcl-xL, then treated with MG132 and immunostained with anti-p62 antibodies. Scale bar=10 µm. Quantification is show in (G)."
NCBI gene IDs:
"GFP: 
Bcl-xL: 572"
Figure legend: "H, I. HeLa cells were stably transfected with Ctrl or LONP1 shRNA, treated with MG132 and immunostained with the indicated antibodies. Scale bar=10 µm. Quantification is show in (I)."
NCBI gene IDs:
"LONP1: 9361"
Figure legend: "csCLEM analysis of cells transfected with GFP-p62 and treated with MG132. Red arrowheads show the dark red fluorescent beads used to correlate the images from light microscopy (LM) and transmission electron microscopy (TEM). The blue arrowhead shows a MAPA observed under LM and TEM."
NCBI gene IDs:
"GFP: 
p62: 8878"
Figure legend: "Immunoblot analysis of the TX-100-soluble and -insoluble fractions of HeLa cells transfected with Ub-R-GFP and treated with MG132 as indicated."
NCBI gene IDs:
"R-GFP: 
Ub: 7316///7314"
Figure legend: "HeLa cells were co-transfected with Mito-OM-cherry and Mito-MTX-GFP, then treated with DMSO or MG132 and immunostained with anti-p62 antibody. Note the colocalization of a p62 punctum with a structure that is positive for Mito-OM-cherry but not for Mito-MTX-GFP (white arrowheads) in MG132-treated cells. Scale bar=10 µm."
NCBI gene IDs:
"Mito-MTX-GFP: 
Mito-OM-cherry: "
Figure legend: "HeLa cells were transfected with Mito-MTX-GFP, then treated with DMSO or MG132 and immunostained with anti-p62 and anti-TIM23 antibodies. Note the colocalization of a p62 punctum with a structure that is positive for TIM3 but not for Mito-MTX-GFP (white arrowhead) in MG132-treated cells. Scale bar=10 µm."
NCBI gene IDs:
"Mito-MTX-GFP: "
Figure legend: "HeLa cells were co-transfected with Mito-MTX-GFP and OTC-Myc or OTC-Δ-Myc, treated with DMSO or MG132 and immunostained with anti-Myc and anti-p62 antibodies. Note that the p62-labled MAPAs were colocalized with OTC-∆ (red arrowheads), but not with OTC (white arrowheads) in the MG132 treated cells. Scale bar=10 µm."
NCBI gene IDs:
"Mito-MTX-GFP: 
Myc: 4609
OTC: 5009"
Figure legend: "Time-lapse analysis of live HeLa cells transfected with OTC-Δ-GFP and Mito-MTX-DsRed and treated with MG132. White arrowheads show a OTC-Δ-GFP-positive Mito-MTX-DsRed-negative structure that eventually segregated from the mitochondrial network."
NCBI gene IDs:
"GFP: 
Mito-MTX-DsRed: 
OTC: "
Figure legend: "Immunoblot analysis of the MG132-induced deposition of FUNDC1, TIM23 and p62 in HeLa cells transfected with Ctrl or DLP1 shRNA."
NCBI gene IDs:
"DLP1: 10059"
Figure legend: "C, D. Immunoblot analysis of the MG132-induced deposition of FUNDC1 in cells transfected with ctrl shRNA, FIS1 shRNA or FIS1 shRNA together with shRNA-resistant Flag-FIS1. Quantification is shown in (D)."
NCBI gene IDs:
"Flag: 
FIS1: 51024"
Figure legend: "E, F. HeLa cells were stably transfected with Ctrl or FIS1 shRNA, treated with MG132 and immunostained with indicated antibodies. Scale bar=10 µm. Quantification is shown in (F)."
NCBI gene IDs:
"FIS1: 51024"
Figure legend: "G, H. Fractionation analysis of HeLa cells stably transfected with Ctrl or FIS1 shRNA, then transiently co-transfected with Ub-R-GFP and Flag or Flag-FIS1 and treated with DMSO or MG132. Quantification is shown in (H)."
NCBI gene IDs:
"Flag: 
R-GFP: 
FIS1: 51024
Ub: 7316///7314"
Figure legend: "HeLa cells were transfected with GFP-LC3, treated with DMSO or 10 μM MG132 for 8 hours and immunostained with anti-p62 antibody. Scale bar=10 µm."
NCBI gene IDs:
"GFP: 
LC3: 440738///81631///84557"