EMBO/SourceData huggingface dataset:
Figure legend: "(F) Wip1 prolongs the half-life of Smad4. HEK293T cells were transfected with Co siRNA or Wip1 siRNA and then treated with FGF2 along with cycloheximide (CHX, 100 ng/ml) for the indicated times and harvested for western blotting. An arrow indicates non-specific bands."
NCBI gene IDs:
"Wip1: 8493"
Figure legend: "(A-J) Embryos injected dorsally with wt Wip1 (1 ng), wt Smad4 (1 ng), Smad4(T277A) (1 ng) and Smad4 (T277E) (1 ng) as denoted were subjected to in situ hybridization against Chordin or Xbra at stage 10.25. Control, control embryo injected with LacZ mRNA only. Scale bar, 150 μm. (K) Quantification of the results from in situ hybridization analysis in (A-J). "
NCBI gene IDs:
"LacZ: 945006
Wip1: 443988///380383
Smad4: 4089"
Figure legend: "(L) Wip1-mediated neural induction is inhibited by Smad4 with a phosphorylatable or phospho-mimetic amino acid at the MAPK site. (-), no co-injection of wt or mutated Smad4."
NCBI gene IDs:
"Wip1: 443988///380383
Smad4: 4089"
Figure legend: "(M) MDA-MB231 and MDA-MB468 cells were transfected with wt Wip1 alone or with wt Smad4 or Smad4(T277A) and then subjected to CCK-8 assays to measure cell growth. Data are presented as the mean ± SEM (n=3 biological replicates). *P&lt;0.05 by unpaired Student's t-test."
NCBI gene IDs:
"Wip1: 443988///380383
Smad4: 4089"
Figure legend: "(N) Anchorage-independent colony-formation assays were performed in MDA-MB231 and MDA-MB468 cells transfected with Wip1 or negative control constructs. Scale bar, 100 μm. (O) Quantification of the assays shown in (N). The number of colonies larger than 50 μm in diameter was scored. Data are expressed as the mean ± SEM (n=3 biological replicates). *P&lt;0.05 by unpaired Student's t-test. "
NCBI gene IDs:
"Wip1: 443988///380383"
Figure legend: "(F) Graph reporting the volume of blood loss (µL) over 30 minutes following the tail clip. WT: wild-type littermates of F9-/- mice. The grey area represents the range of blood loss of F9-/- mice that received AAV-vectors expressing human FIX. Data are presented as mean±SD (n=3-4/group), and were analyzed in a 1-way ANOVA with Tukey's correction for multiple comparisons. **p&lt;0.01 Boxes represent 25%-75% quartiles, with the line indicating the median. Whiskers span min to max."
NCBI gene IDs:
"F9-/-: 14071
FIX: 2158"
Figure legend: " (B) Western blotting of WT and Drp1-KO MEFs with or without FCCP treatment (30 min) using the indicated antibodies. "
NCBI gene IDs:
"Drp1: 74006"
Figure legend: " (B) Western blotting of WT MEFs, Drp1-KO MEFs, and Drp1-KO MEFs carrying Drp1, all of which express L2-HA, using the indicated antibodies. The expression of L2-HA was induced for 16 h (0.1 µg/ml doxycycline). The asterisk indicates non-specific bands of anti-Oma1 antibodies. "
NCBI gene IDs:
"Drp1: 74006"
Figure legend: " (E) WT and Drp1-KO MEFs, both of which express L2-HA, were transduced with lentiviruses carrying either scramble or Oma1-targeted shRNAs. Whole-cell lysates were analyzed by Western blotting using the indicated antibodies. The asterisk indicates non-specific bands of anti-Oma1 antibodies. "
NCBI gene IDs:
"Drp1: 74006
Oma1: 67013"
Figure legend: "(A) The mitochondrial membrane potential was measured in WT and Drp1-KO MEFs using a membrane potential-dependent dye (MitoLite NIR) and flow cytometry."
NCBI gene IDs:
"Drp1: 74006"
Figure legend: " (B) Drp1-KO MEFs carrying Su9-GFP were treated with DMSO (control) or 10 nM antimycin A or 10 ng/ml oligomycin for 1 h and viewed by laser scanning confocal microscopy for 30 min with 10-s intervals in the presence of TMRE. The arrows indicate mitochondria that showed flickering. Three frames from the time-lapse analysis are shown (please also see Movie EV1-EV4). Scale bar, 10 µm. "
NCBI gene IDs:
"Drp1: 74006"
Figure legend: " (F) Drp1-KO MEFs were treated with DMSO or 10 nM antimycin A or 10 ng/ml oligomycin or 10 µM FCCP for 1 h. The mitochondrial membrane potential was analyzed using MitoLite NIR and flow cytometry. "
NCBI gene IDs:
"Drp1: 74006"
Figure legend: " (G) Drp1-KO MEFs expressing L2-HA (induced for 16 h) were treated with 10 nM antimycin A along with 10 µM FCCP. Western blotting was performed using the indicated antibodies. The asterisk indicates non-specific bands of anti-Oma1 antibodies. (H) Quantification of band intensity. Values are average ± SD (n = 3). "
NCBI gene IDs:
"Drp1: 74006"
Figure legend: " (I) Western blotting of Drp1-KO MEFs with or without 10 ng/ml oligomycin treatment. The asterisk indicates non-specific bands of anti-Oma1 antibodies. (J) Quantification of band intensity. Values are average ± SD (n = 3). "
NCBI gene IDs:
"Drp1: 74006"
Figure legend: " (K) WT MEFs carrying Su9-GFP were treated with DMSO or 10 ng/ml oligomycin for 1 h and viewed by laser scanning confocal microscopy for 30 min with 10-s intervals in the presence of TMRE. The arrows indicate mitochondria that showed flickering. Three frames from the time-lapse analysis are shown (please also see Movie EV1 and EV5). Scale bar, 10 µm. "
NCBI gene IDs:
"GFP: "
Figure legend: " (A) Western blotting of Drp1flox/floxOpa1flox/flox and Drp1Opa1-KO MEFs. The asterisk indicates non-specific bands of anti-Oma1 antibodies. (B) Quantification of band intensity. Values are average ± SD (n = 3). "
NCBI gene IDs:
"Drp1: 74006
Opa1: 74143"
Figure legend: " (C) Drp1flox/floxOpa1flox/flox MEFs and Drp1Opa1-KO MEFs were transduced with the indicated Opa1 constructs. The cells were observed using laser scanning confocal microscopy for 30 min with 10-s intervals in the presence of TMRE. The percentage of cells that exhibited flickering is shown. Values are average ± SD (n = 3 experiments). In each experiment, 48-62 cells were analyzed. "
NCBI gene IDs:
"Drp1: 74006
Opa1: 74143"
Figure legend: " (D) Drp1flox/floxOpa1flox/flox MEFs and Drp1Opa1-KO MEFs carrying the indicated Opa1 constructs were subjected to confocal immunofluorescence microscopy using anti-PDH antibodies. Scale bar, 10 µm. "
NCBI gene IDs:
"Drp1: 74006
Opa1: 74143"
Figure legend: " (G) Western blotting of Drp1flox/floxOpa1flox/flox MEFs and Drp1Opa1-KO MEFs, both of which carry the indicated Opa1 constructs. The asterisk indicates non-specific bands of anti-Oma1 antibodies. "
NCBI gene IDs:
"Drp1: 74006
Opa1: 74143"
Figure legend: " (A) Western blotting of WT MEFs and Drp1-KO MEFs, both of which carry shRNAs (Oma1 or scramble) and/or ectopic Mfn1. The asterisk indicates non-specific bands of anti-Oma1 antibodies. (B) Quantification of band intensity is shown. Values are average ± SD (n = 3). "
NCBI gene IDs:
"Drp1: 74006
Oma1: 67013"
Figure legend: " (C-F) WT MEFs (C and E) and Drp1-KO MEFs (D and F) were transduced with Su9-Eos, along with Oma1 shRNAs and ectopic Mfn1. Su9-Eos in the small region of mitochondria (indicated by the asterisks) was photoconverted using a 405-nm laser on confocal microscope. Within 1 s after photoconversion, images were obtained for both photoconverted and unconverted Su9-Eos signals. Images before the photoconversion were also taken to detect background signals. Scale bar, 10 µm. (E and F) To determine the connectivity of mitochondria, the area containing photoconverted Su9-Eos signals was divided by the area containing the photoconverted and unconverted Su9-Eos signals (total mitochondria). Values are average ± SD (n = 30 cells). "
NCBI gene IDs:
"Drp1: 74006
Oma1: 67013"
Figure legend: " WT which carry shRNAs (Oma1 or scramble) and ectopic Mfn1, were stained with TMRE. The percentage of cells that maintained the membrane potential is shown. Values are average ± SD (n = 3). 100-150 cells were analyzed in each experiment. "
NCBI gene IDs:
"Oma1: 67013"
Figure legend: " Drp1-KO MEFs which carry shRNAs (Oma1 or scramble) and ectopic Mfn1, were stained with TMRE. The arrows indicate cells that lost the mitochondrial membrane potential in (C). Scale bar, 10 µm. The percentage of cells that maintained the membrane potential is shown. Values are average ± SD (n = 3). 100-150 cells were analyzed in each experiment. "
NCBI gene IDs:
"Drp1: 74006
Oma1: 67013"
Figure legend: "(d) Self-association pattern of Beclin 1 in vivo. Both GFP- and AsRed-tagged full-length Beclin 1 are co-transfected into HEK 293T cells and their self-association is probed by co-IP using GFP antibody for immunoprecipitation, followed by western blot with anti-AsRed antibody."
NCBI gene IDs:
"Beclin 1: 114558"
Figure legend: "c) Pull-down assay to assess the competition between Beclin 1-Atg14L and Beclin 1-UVRAG complexes. Increasing amount of His6-tagged Beclin 1 CC domain was added to a mixture of Atg14L and UVRAG proteins corresponding to their respective CC region. The Beclin 1-Atg14L/UVRAG complexes were pulled down by Ni2+- nitrilotriacetic acid (NTA) agarose beads and checked by SDS gel."
NCBI gene IDs:
"Beclin 1: 114558"
Figure legend: "(c) Self-association pattern of wild-type, MutM and MutStab constructs of Beclin 1 in vivo. For each construct, both GFP- and Myc-tagged full-length Beclin 1 are co-transfected into HEK 293T cells and their self-association is probed by co-IP using GFP antibody for IP, followed by western blot with anti-Myc antibody."
NCBI gene IDs:
"Beclin 1: 114558"
Figure legend: "(a,b) Interaction of Beclin 1 wild-type and monomeric (MutM) mutants with Atg14L or UVRAG in cultured cells. HEK 293T cells were transfected with GFP-tagged Beclin 1 variant alone (a) or together with FLAG-UVRAG (b). The lysates were immunoprecipitated by GFP antibody, followed by western-blot analysis with anti-Atg14L antibody for detecting binding to endogenous Atg14L (a) or with anti-UVRAG antibody for detecting binding to the FLAG-tagged UVRAG protein (b)."
NCBI gene IDs:
"Beclin 1: 114558"
Figure legend: "(a, b) Interaction of MutStab mutants of Beclin 1 with Atg14L or UVRAG in vivo. HEK 293T cells were transfected with GFP-tagged Beclin 1 variant alone (b) or together with FLAG-UVRAG (b). The lysates were immunoprecipitated by GFP antibody, followed by western blot analysis with anti-Atg14L antibody for detecting binding to endogenous Atg14L (a) or with anti-UVRAG antibody for detecting binding to the FLAG-tagged UVRAG protein (b)."
NCBI gene IDs:
"Beclin 1: 114558"
Figure legend: "(a,b). Representative fluorescent images of HeLa cells co-tansfected with GFP-tagged Beclin 1 wild type, MutM L178A/L192A or MutStab E189L/A217L/E224L/A255L (green) and AsRed-Atg14L (red) (a) or FLAG-UVRAG (red) (b); Co-localization of AsRed-Atg14L with GFP-tagged Beclin 1 wild type or MutM is shown in discrete puncta."
NCBI gene IDs:
"Beclin 1: 114558"
Figure legend: "(c-e) Representative fluorescence images of HeLa cells co-transfected with Myc-Beclin 1 wild type, MutM L178A/L192A or MutStab E189L/A217L/E224L/A255L (blue), AsRed-Atg14L (red) and GFP-tagged Atg12 (c). The scale bar is 20 μM."
NCBI gene IDs:
"Beclin 1: 114558"
Figure legend: "(c-e) Representative fluorescence images of HeLa cells co-transfected with Myc-Beclin 1 wild type, MutM L178A/L192A or MutStab E189L/A217L/E224L/A255L (blue), AsRed-Atg14L (red) and GFP-tagged LC3 (d) and DFCP (e) (green). The scale bar is 20 μM."
NCBI gene IDs:
"Beclin 1: 114558"
Figure legend: "Phenotypic analysis of ScUba4 mutant yeast strains in response to rapamycin."
NCBI gene IDs:
"Uba4: 856511"
Figure legend: "V-SVZ whole-mount staining showing reduced CCN1 expression in Ccn1cKO mice 1 week after TAM treatment. Scale bar: 10 μm."
NCBI gene IDs:
"Ccn1: 16007"
Figure legend: "Densities (cells/mm2) of BrdU+ cells in the OB granule cell layer (GCL) 2 days after TAM treatment. n=4 (Ctrl) and 3 (Ccn1cKO), **p=0.0086. OB sections stained for BrdU (yellow) and nuclei (blue). Scale bar: 50 μm."
NCBI gene IDs:
"Ccn1: 16007"
Figure legend: "Densities (cells/mm2) of BrdU+ cells in the OB GCL labeled 24h after TMZ treatment. n=5 (Ctrl) and 6 (Ccn1cKO), *p= 0.0484. OB sections stained for BrdU (yellow) and nuclei (blue). Scale bar: 50 μm."
NCBI gene IDs:
"Ccn1: 16007"
Figure legend: "Densities (cells/mm2) of BrdU+ cells in the OB GCL of aged mice labeled 3 days after TMZ treatment. n=4 (Ctrl) and 3 (Ccn1cKO), n.s. not significant. Scale bar: 50 μm."
NCBI gene IDs:
"Ccn1: 16007"
Figure legend: "Densities (cells/mm2) of VCAM1+ B1 cells in the adult V-SVZ whole-mounts. n=4 (Ctrl + vehicle and Ccn1cKO + vehicle) and 3 (Ccn1cKO + erlotinib), **p=0.0021 (Ccn1cKO + vehicle vs Ccn1cKO + erlotinib), **p=0.0014 (Ccn1cKO + erlotinib vs Ctrl + vehicle), ****p&lt;0.0001."
NCBI gene IDs:
"Ccn1: 16007"
Figure legend: "Densities (units/mm2) of NSC units in the adult V-SVZ whole-mounts. n=4 (Ctrl + vehicle and Ccn1cKO + vehicle) and 3 (Ccn1cKO + erlotinib), *p=0.017, **p=0.0061, ***p=0.0002."
NCBI gene IDs:
"Ccn1: 16007"
Figure legend: "(A) Dually labeled D. discoideum amoebae producing MCS components fused to GFP, and either calnexin  (CnxA)-mCherry  (pAW012), P4C-mCherry  (pWS032), or AmtA-mCherry  were infected (MOI 5, 2 h) with mCerulean-producing  L. pneumophila JR32   (pNP99), fixed with 4 % PFA, and imaged by confocal fluorescence microscopy. Merged images are shown. Scale bars: 3 μm (insets: 1 μm)."
NCBI gene IDs:
"mCerulean: "
Figure legend: "(A) Dually labeled  D. discoideum Ax3  producing mCherry-Vap  (pSV048) and OSBP8-GFP  (pMIB89) or GFP-OSBP11  (pMIB39) were infected (MOI 5, 1-8 h) with mCerulean-producing  L. pneumophila JR32  (pNP99) and fixed with 4 % PFA. Merged images for the analyzed time points are shown. Scale bars: 3 μm (insets: 1 μm)."
NCBI gene IDs:
"mCerulean: "
Figure legend: "(A) D. discoideum  Ax3, or the ∆vap, ∆osbG, ∆osbH, or ∆osbK mutant strains producing GFP  (pDM317) or GFP  fusions of the MCS components were infected (MOI 1) with mCherry-producing  L. pneumophila JR32 (pNP102), and intracellular replication was assessed by relative fluorescence units (RFU). Mean and SEM of three independent biological replicates are shown (statistics refer to JR32  infected  D. discoideum Ax3   producing GFP; *P&lt;0.05; **P&lt;0.01; ***P&lt;0.001, Student`s t-test). To improve clarity, the different mutant strains are shown in separate graphs, each depicting the same data for Ax3/GFP."
NCBI gene IDs:
"GFP: 
mCherry: 
osbG: 
osbH: 
osbK: 
vap: "
Figure legend: "(B)  D. discoideum Ax3 producing CnxA-GFP  (pAW016), GFP-Sac1  (pLS037), GFP-Sac1_C383S (pSV015) or GFP-Sac1_ΔTMD (pSV034) were infected (MOI 1) with mCherry-producing  L. pneumophila JR32  (pNP102), and intracellular replication was assessed by relative fluorescence units (RFU). Mean and SEM of three independent biological replicates are shown (statistics refer to JR32  infected  D. discoideum Ax3 producing GFP-Sac1; ***P&lt;0.001, Student`s t-test)."
NCBI gene IDs:
"GFP: 
mCherry: 
Sac1: 
CnxA: 8617897"
Figure legend: "(C) RAW 264.7 macrophages  were treated with increasing concentrations of OSW-1 (0-100 nM, 1-60 h), infected (MOI 1) with GFP-producing L. pneumophila JR32 (pNT28), and intracellular replication was assessed by relative fluorescence units (RFU). Mean and SEM of three independent biological replicates are shown (statistics refer to infected cells treated with 0 nM OSW-1; *P&lt;0.05; ***P&lt;0.001, Student`s t-test)."
NCBI gene IDs:
"GFP: "
Figure legend: "(A) Dually labeled D. discoideum Ax3, ∆vap, ∆osbG, ∆osbH, ∆osbK or ∆sey1  mutants producing P4C-mCherry  (pWS032) and CnxA-GFP  (pAW016), or Ax3  producing P4C-mCherry  and either GFP-Sac1 (pLS037), GFP-Sac1_C383S (pSV015) or GFP-Sac1_ΔTMD (pSV034) were infected (MOI 5, 2-16 h) with mCerulean-producing L. pneumophila JR32 (pNP99) and fixed with 4 % PFA. Merged images for the analyzed  time points  are shown. Scale bars: 3 μm. (B) LCV  area was measured using ImageJ (n=100-200 per condition from 3 independent biological replicates). Means and SEM of single cells are shown (**P&lt;0.01; ***P&lt;0.001, Student`s t-test)."
NCBI gene IDs:
"GFP: 
mCerulean: 
osbG: 
osbH: 
osbK: 
sey1: 
vap: 
Sac1: 8618030"
Figure legend: "(A) Dually labeled D. discoideum Ax3, ∆vap, ∆osbG, ∆osbH, ∆osbK or ∆sey1  mutants producing P4C-mCherry  (pWS032) and GFP-Sac1  (pLS037) were infected (MOI 5, 2-16 h) with mCerulean-producing L. pneumophila JR32 (pNP99) and fixed with 4 % PFA. Merged images for the analyzed  time points are shown. Scale bars: 3 μm. (B, C) Imaging flow cytometry  (IFC) analysis of dually labeled D. discoideum Ax3, ∆vap, ∆osbG, ∆osbH, ∆osbK or ∆sey1 mutants producing P4C-mCherry  (pWS032) and either GFP-Sac1  (pLS037) or GFP-Sac1_ΔTMD (pSV034), infected (MOI 5, 2 h) with mPlum-producing L. pneumophila JR32 (pAW014). Data information (B, C, : Data represent mean and SEM of three independent biological replicates (*P&lt;0.05; **P&lt;0.01; ***P&lt;0.001, Student`s t-test)."
NCBI gene IDs:
"GFP: 
mCerulean: 
mPlum: 
osbG: 
osbH: 
osbK: 
sey1: 
vap: 
Sac1: 8618030"
Figure legend: "(D) Dually labeled  D. discoideum Ax3 producing GFP  fusions of MCS components and either mCherry-Sac1  (pSV044) or mCherry-Sac1_ΔTMD (pSV045) were infected (MOI 5, 2 h) with mCerulean-producing  L. pneumophila JR32  (pNP99) and fixed with 4 % PFA. Merged images for the analyzed  time points are shown. Scale bars: 3 μm. (E) IFC  analysis of dually labeled D. discoideum Ax3  producing GFP  fusions of MCS components and either mCherry-Sac1 (pSV044) or mCherry-Sac1_ΔTMD (pSV045), infected (MOI 5, 2 h) with mPlum-producing L. pneumophila JR32  (pAW014). Quantification of (B) P4C-mCherry  (C) Sac1-GFP  or (E) GFP  fusions of MCS components localizing  to LCVs  at 2 h p.i. Due to the lower resolution of IFC, \"LCVs\" designates the LCV  limiting membrane and tightly attached ER. Number of events per sample, n = 5000. Data information E): Data represent mean and SEM of three independent biological replicates (*P&lt;0.05; **P&lt;0.01; ***P&lt;0.001, Student`s t-test)."
NCBI gene IDs:
"mCerulean: 
mCherry: 
mPlum: 
Sac1: 8618030"
Figure legend: "(A) Dually labeled  D. discoideum Ax3 producing GFP-D4H* (pSV046) or P4C-GFP  (pWS034) and P4C-mCherry  (pWS032), CnxA-mCherry  (pAW012), or AmtA-mCherry  were infected (MOI 5, 15 - 120 min) with mCerulean-producing L. pneumophila JR32  (pNP99) and fixed with 4 % PFA. Merged images for the analyzed time points are shown. Scale bars: 3 μm. (B-C) The Pearson's correlation coefficient was generated using Coloc 2 from Fiji (ImageJ) and is shown for (B) AmtA-mCherry  with respect to P4C-GFP  or GFP-D4H* (n=100-150 per   time point), and (C) GFP-D4H* with respect to P4C-mCherry  or CnxA-mCherry  (n=100-150 each per time point). Data represent mean and SEM of three independent biological replicates (*P&lt;0.05, Student`s t-test)."
NCBI gene IDs:
"mCerulean: "
Figure legend: "(D) Single labeled D. discoideum Ax3 producing either CnxA-GFP  (pAW016) or P4C-GFP  (pWS034) were infected (MOI 5, 15-120 min) with mCherry-producing L. pneumophila JR32 (pNP102), fixed with 4 % PFA  and stained  with filipin. Merged images for the analyzed time points  are shown. Scale bars: 3 μm. (E) The Pearson's correlation coefficient was generated using Coloc 2 from Fiji (ImageJ) and is shown for filipin  with respect to CnxA-GFP  or P4C-GFP  (n=80-90 each per  time point). Data represent mean and SEM of the means of three independent biological replicates (***P&lt;0.001, Student`s t-test)."
NCBI gene IDs:
"mCherry: "
Figure legend: "(A) Dually labeled  D. discoideum Ax3  producing P4C-mCherry  (pWS032) and either CnxA-GFP  (pAW016), GFP-Sac1 (pLS037), or GFP-Sac1_ΔTMD (pSV034) were infected (MOI 5, 1-8 h) with mCerulean-producing L. pneumophila JR32, ΔlepB or ΔsidC (pNP99) and fixed with 4 % PFA. Merged images for the analyzed  time points are shown. Scale bars: 3 μm."
NCBI gene IDs:
"GFP: 
mCerulean: 
lepB: 66491661
Sac1: 8618030
sidC: 66491684"
Figure legend: "(C)  Imaging flow cytometry (IFC) analysis of dually labeled D. discoideum Ax3 producing P4C-mCherry  (pWS032) and either CnxA-GFP  (pAW016), GFP-Sac1 (pLS037), or GFP-Sac1_ΔTMD (pSV034), infected (MOI 5, 1-8 h) with mPlum-producing L. pneumophila JR32 (pAW014). Number of events per sample, n = 5000. Data represent mean and SEM of three independent biological replicates (*P&lt;0.05; **P&lt;0.01; ***P&lt;0.001, Student`s t-test)."
NCBI gene IDs:
"GFP: 
mPlum: 
Sac1: 8618030"
Figure legend: "(B) GALpr-Dfm1-BirA-Flag and GALpr-BirA-Flag levels were measured by western blotting with α -FLAG at 0 (uninduced) vs. 5 hours post-galactose induction (3 biological replicates; n=3)."
NCBI gene IDs:
"BirA: 
Flag: 
Dfm1: 852020
GAL: 855828"
Figure legend: "(C) Dfm1-BirA is still functional and able to degrade Hmg2-GFP. dfm1Δ+Hmg2-GFP strains containing DFM1-BIRA, empty vector, or BIRA only addbacks were grown to log phase and degradation was measured by CHX. After CHX addition, cells were lysed at the indicated times and analyzed by SDS-PAGE and immunoblotted for Hmg2-GFP with α-GFP."
NCBI gene IDs:
"BirA: 
BIRA: 
GFP: 
dfm1: 852020
Dfm1: 852020
DFM1: 852020
Hmg2: 851171"
Figure legend: "(D) Yeast strains expressing Dfm1-Bira and BirA only negative control were incubated with different amounts of biotin: 0, 0.1, and 1 mM. dfm1Δ+Hmg2-GFP. Microsomes were isolated from each strain and subjected to streptavidin pulldown (3 biological replicates; n=3). Flow-through and pull-down fractions were detected by western blotting for Dfm1-BirA with α-Flag and Cdc48 with α-Cdc48 antibodies."
NCBI gene IDs:
"Bira: 
BirA: 
GFP: 
Dfm1: 852020
dfm1: 852020
Hmg2: 851171"
Figure legend: "(A) Dfm1-GFP binding to Lcb2-RFP and Orm2-RFP were analyzed by co-IP. As negative control, cells not expressing Dfm1-GFP were used (3 biological replicates; n=3)."
NCBI gene IDs:
"GFP: 
Dfm1: 852020"
Figure legend: "(A) Indicated strains were spotted 5-fold dilutions on synthetic complete (SC) plates , and plates were incubated at room temperature, 30oC, and 37oC (3 biological replicates, 2 technical replicates; n=5). WT, dfm1∆, tsc3∆, and dfm1∆tsc3∆ were compared for growth in the dilution assay. Arrowhead indicates growth phenotype of tsc3∆ cells; open circle indicates growth phenotype of dfm1∆tsc3∆ cells. (B) dfm1∆tsc3∆ confers resistance to myrocin. WT, dfm1∆, tsc3∆, and dfm1∆tsc3∆ strains were grown to log-phase in YPD medium, and 5-fold serial dilutions of cultures were spotted on (SC) plates containing either drug vehicle alone, 1 µM of myriocin and 10 μM of PHS (3 biological replicates, 2 technical replicates; n=5). Arrowhead indicates growth phenotype of tsc3∆ cells; open circle indicates growth phenotype of dfm1∆tsc3∆ cells."
NCBI gene IDs:
"dfm1: 852020
tsc3: 852350"
Figure legend: "(D) Indicated strains were spotted 5-fold dilutions on SC plates in 3 biological replicates and 2 technical replicates (n=5), and plates were incubated at room temperature, 30oC, and 37oC (n=3). Upper panel: WT, orm1∆, tsc3∆, and orm1∆tsc3∆ were compared for growth by dilution assay. Middle panel: WT, orm2∆, tsc3∆, and orm2∆tsc3∆ were compared for growth by dilution assay. Bottom panel: WT, orm1∆, orm2∆, tsc3∆, and orm1∆orm2∆tsc3∆, were compared for growth by dilution assay. Upper panel: arrowhead indicates growth phenotype of tsc3∆ cells; open circle indicates growth phenotype of orm1∆tsc3∆ cells. Lower panel: arrowhead indicates growth phenotype of orm2∆ cells; open circle indicates growth phenotype of orm2∆tsc3∆ cells."
NCBI gene IDs:
"orm1: 852926
orm2: 851064
tsc3: 852350"
Figure legend: "(A) Indicated strains were spotted 5-fold dilutions on SC plates in 3 biological replicates and 2 technical replicates (n=5), and plates were incubated at room temperature, 30oC, and 37oC. Upper panel: WT, dfm1∆, orm1∆, and dfm1∆orm1∆ were compared for growth by dilution assay. Middle panel: WT, dfm1∆, orm2∆, and orm2∆tsc3∆ were compared for growth by dilution assay. Bottom panel: WT, dfm1∆, orm1∆, orm2∆, and orm2∆, and orm1∆orm2∆ were compared for growth by dilution assay. Upper, middle, and lower panel: gray arrowhead depicts growth phenotype of dfm1∆orm1∆, dfm1∆orm2∆, and orm1∆orm2∆ respectively. (B) dfm1∆orm1∆ confers resistance to myriocin and sensitivity to PHS. WT, dfm1∆, orm1∆, and dfm1∆orm1∆ strains were grown to log-phase in SC medium, and 5-fold serial dilutions of cultures were spotted on YPD plates containing either drug vehicle alone, 1 mM of myriocin and 10 μM of PHS with each condition performed in 3 biological replicates and 2 technical replicates (n=5). Plates were incubated at room temperature and photographed after 3 days. Open circle indicates growth phenotype of dfm1∆orm1∆ cells."
NCBI gene IDs:
"dfm1: 852020
orm1: 852926
orm2: 851064
tsc3: 852350"