EMBO/SourceData huggingface dataset:
Figure legend: " F) rpb-9 recruits Integrator at piRNA loci. Representative single-plan immunofluorescence images of Integrator (ints-6::GFP ) and PRDE-1 (prde-1::mCherry) localization in wild-type and rpb-9 (mj261) animals. Scale bar = 5 µm. G) Co-localization analysis of PRDE-1::mCHERRY and INTS-6::GFP foci in wild-type and rpb-9 (mj261) animals. Central bands represent the median, notches represent the confidence interval around the median, boxes represent the 25th and 75th percentiles and whiskers represent the lowest and highest values, excluding outliers. n (nuclei/genotype) &gt; 16. (Welch's t-test, p = 1.7e-17)."
NCBI gene IDs:
"GFP: 
mCherry: 
ints-6: 24104403
prde-1: 184750
rpb-9: 179178"
Figure legend: "(B) Proliferation of tumor tissue was determined by the percentage of Ki67-positive nuclei analyzed by flow cytometry. T: wt n=17, Casp-2-/- n=11, Raidd-/- n=10, Pidd1-/- n=8; NT: wt n=12, Casp-2-/- n=11, Raidd-/- n=7, Pidd1-/- n=5. N-numbers refer to biological replicates."
NCBI gene IDs:
"Casp-2: 12366
Raidd: 12905
Pidd1: 57913"
Figure legend: "(E) The number of binucleated hepatocytes per field was counted on H&amp;E stained paraffin sections of PBS treated wt and Pidd1-/- mice at t(0h) and at t(48h) after PBS or DEN treatment. N-numbers refer to biological replicates."
NCBI gene IDs:
"Pidd1: 57913"
Figure legend: "(G) Centriole number was quantified with respect to the number of nuclei per cell in wt and Pidd1-/- livers at the time points described in (E); n=3 biological replicates."
NCBI gene IDs:
"Pidd1: 57913"
Figure legend: "(A) Binucleation was assessed blinded in H&amp;E stained sections of murine non-tumor (NT) and tumor tissue (T) T: wt n=14, Casp-2-/- n=11, Raidd-/- n=10, Pidd1-/- n=10; NT: wt n=8, Casp-2-/- n=10, Raidd-/- n=8, Pidd1-/- n=9. N-numbers refer to biological replicates."
NCBI gene IDs:
"Casp-2: 12366
Raidd: 12905
Pidd1: 57913"
Figure legend: "Binucleation was assessed blinded in H&amp;E stained sections of murine non-tumor (NT) and tumor tissue (T) also shown in (B). T: wt n=14, Casp-2-/- n=11, Raidd-/- n=10, Pidd1-/- n=10; NT: wt n=8, Casp-2-/- n=10, Raidd-/- n=8, Pidd1-/- n=9. N-numbers refer to biological replicates."
NCBI gene IDs:
"Casp-2: 12366
Raidd: 12905
Pidd1: 57913"
Figure legend: "C, D (C) Representative histograms of nuclei stained for DNA, which were isolated from non-tumor and tumor tissue of wt and Casp2-/- mice. These animals are marked as red &quot;x&quot; in the quantification shown in (D) were the degree of polyploidy is reflected as percentage of octaploid nuclei (T: wt n=17, Casp-2-/- n=11, Raidd-/- n=10, Pidd1-/- n=8; NT: wt n=12, Casp-2-/- n=11, Raidd-/- n=7, Pidd1-/- n=5). N-numbers refer to biological replicates."
NCBI gene IDs:
"Casp-2: 12366
Casp2: 12366
Raidd: 12905
Pidd1: 57913"
Figure legend: "Copy number variations were determined using whole genome sequencing of 30 nuclei &quot;mini-bulks&quot; isolated from Casp2-/- or wt tumors (n=11 per genotype). Diploid and tetraploid pools of tumor cell nuclei were analyzed separately. A, B (A) Representative dot plots show the degree of aneuploidy and heterogeneity and are quantified in (B, empty symbols). Data are represented as median, statistical significance determined by one-way ANOVA with multiplicity correction (Sidak-Holm); * p≤0.05, ** p≤0.01. N-numbers refer to biological replicates."
NCBI gene IDs:
"Casp2: 12366"
Figure legend: "(B) mRNA expression analysis of the PIDDosome components in the TCGA Provisional LIHC data set across disease stages. Patients are divided based on the p53 mutation/deletion (mut/del) status. Statistical significance was determined using two-way ANOVA with Tukey's post-hoc analysis. The central band represents the median, the boxes indicate the 25th and 75th percentile, the whiskers are the 5th and 95th percentiles, statistical significance was defined as * p≤0.05, ** p≤0.01."
NCBI gene IDs:
"p53: 7157"
Figure legend: "(C) The same data set was analyzed for recurrence-free survival based on high or low expression of CASP2, RAIDD or PIDD1 divided at the median. Statistical significance was determined using a Log-rank test."
NCBI gene IDs:
"CASP2: 835
RAIDD: 8738
PIDD1: 55367"
Figure legend: "(B) E2F target genes expression was analyzed for correlation with expression of CASP2, RAIDD and PIDD1 using Spearman's correlation coefficient. The central band represents the median, the boxes indicate the 2nd and 3rd quartile, and the whiskers are 1.5 times the interquartile range (n=200 genes)."
NCBI gene IDs:
"CASP2: 835
RAIDD: 8738
PIDD1: 55367"
Figure legend: "Correlation (Pearson) of CASP2 mRNA with transcript levels of Ki67 in the TCGA data set."
NCBI gene IDs:
"CASP2: 835
Ki67: 4288"
Figure legend: "Correlation (Pearson) of RAIDD and PIDD1 mRNA with transcript levels of Ki67 in the TCGA data set."
NCBI gene IDs:
"RAIDD: 8738
Ki67: 4288
PIDD1: 55367"
Figure legend: "(A) siRNA knockdown of Tollip in SH-SY5Y cells was performed over 72 hours, with cells reverse transfected with siRNA oligos specific for Tollip (or mock) for 24 hours before a second transfection was performed for a further 48 hours. Knockdown was confirmed by western blotting."
NCBI gene IDs:
"Tollip: 54472"
Figure legend: "(B) After knockdown of Tollip, SH-SY5Y cells were treated with 5 μM antimycin A/10 μM oligomycin B (AO) or 25 μM Antimycin A (AA) alone for 2 hours, then fixed and stained for PDH E2/E3bp (green), TOM20 (red) and nuclei (blue). Images were captured using widefield immunofluorescence microscopy. Zoom insets represent 4x magnification and arrowheads indicate TOM20-positive MDVs."
NCBI gene IDs:
"Tollip: 54472"
Figure legend: "(F) Images captured using super-resolution radial fluctuations (SRRF) microscopy showing both TOM20 (arrowheads) and PDH (arrows) MDVs in SH-SY5Y cells after Tollip siRNA knockdown. Left side images are the first in each of the original widefield image stacks. Scale bar for zoom images is 0.5 μm."
NCBI gene IDs:
"Tollip: 54472"
Figure legend: "(A) TOM20-positive MDV formation was induced in SH-SY5Y by siRNA knockdown of Tollip. MDVs were defined as TOM20+ve/Cytochrome c (Cyt c)-ve via immunofluorescence microscopy, which indicated some colocalisation with Parkin (arrowheads)."
NCBI gene IDs:
"Tollip: 54472"
Figure legend: "(B) SH-SY5Y cells were transfected with GFP-Tollip for 24 hours, then treated with 5 μM antimycin A/10 μM oligomycin B (AO) or AO/100 μM bafilomycin A1 (BfnA1) for 2 hours prior to fixation and immunostaining. Antibodies specific to GFP (green), Parkin (red) and ubiquitin (blue) were used."
NCBI gene IDs:
"GFP: 
Tollip: 54472"
Figure legend: "C) GFP-Tollip/Parkin colocalisation was quantified from cells under steady state conditions or treated with AO and AO/BfnA1 by counting overall GFP puncta and GFP puncta positive for Parkin per cell, across 3-6 GFP-transfected cells/condition, per experiment (n = 3). Results are represented as a percentage of Tollip puncta positive for Parkin."
NCBI gene IDs:
"GFP: "
Figure legend: "(G) The percentage of GFP-Tollip puncta positive for Parkin was quantified from immunofluorescence images immunostained for GFP and Parkin from WT, R78A, and CUE mutant expressing cells across 3-6 GFP-transfected cells/ condition, per experiment (n = 3; *p=0.0162, **p=0.0034, ****p&lt;0.0001)."
NCBI gene IDs:
"GFP: "
Figure legend: "(H) The percentage of ubiquitin puncta positive for Tollip was quantitated from immunuofluorescence images immunostained for ubiquitin and GFP from WT, R78A, and CUE mutant expressing cells across 3-6 GFP-transfected cells/condition, per experiment (n = 3; *p=0.0382, **p=0.0068)."
NCBI gene IDs:
"GFP: "
Figure legend: "(I) The percentage of ubiquitin puncta positive for Parkin was quantitated from immunuofluorescence images immunostained for ubiquitin and Parkin from WT, R78A, and CUE mutant expressing cells across 3-6 GFP-transfected cells/condition, per experiment (n = 3; *p=0.0232, **p=0.0062)."
NCBI gene IDs:
"GFP: "
Figure legend: "(J) The percentage of GFP-Tollip/Parkin vesicles positive for ubiquitin were quantitated from immunofluorescence images immunostained for GFP, Parkin, and ubiquitin from WT, R78A, and CUE mutant expressing cells across 3-6 GFP-transfected cells/condition, per experiment (n = 3; **p=0.0070)."
NCBI gene IDs:
"GFP: "
Figure legend: "(A) HeLa cells expressing mycBioID-Tollip and HA-Parkin were either left untreated or treated with 5 μM antimycin A/10 μM oligomycin B (AO) or AO/100 μM bafilomycin A (BfnA1) for 6 hours in the presence of biotin. Cells were lysed and streptavidin pulldowns performed overnight to isolate biotinylated proteins. Proteins in whole cell extracts and pulldowns from each condition were then separated by SDS-PAGE and membranes probed with specific antibodies. Immunoblotting for Tom1 and mycBioID-Tollip were used as positive controls. Cells cultured in media lacking biotin were used as a negative control to assess background levels. Biotinylation of Parkin suggested Tollip specifically interacted with Parkin under these conditions."
NCBI gene IDs:
"Bio: 
myc: 
Tollip: 54472"
Figure legend: "(C) Hela cells co-expressing GFP-Tollip and HA-Parkin were either left untreated or treated with AO for 2 hours prior to lysis. Cell lysates were subjected to either a normal rabbit IgG IP or HA IP and western blot analysis was performed using antibodies against Parkin and GFP."
NCBI gene IDs:
"GFP: 
HA: 
Parkin: 5071
Tollip: 54472"
Figure legend: "(D) HeLa cells expressing mycBioID-Tollip containing the CUE domain mutation (CUEmut) and HA-Parkin were subjected to biotinylation and streptavidin pulldowns, followed by western blot analysis."
NCBI gene IDs:
"Bio: 
myc: 
Tollip: 54472"
Figure legend: "(E) HeLa wild-type (WT), Tom1 KO and ATG5 KO cells expressing mycBioID-Tollip and HA-Parkin underwent the same conditions as those above and immunoblotted for the indicated proteins."
NCBI gene IDs:
"Bio: 
myc: 
ATG5: 9474
Tollip: 54472
Tom1: 10043"
Figure legend: "(A) Cells were reverse transfected with Parkin or Tom1 siRNA oligos for 24 hours before a second transfection was performed for a further 48 hours, then fixed and stained with antibodies specific to TOM20 (green) and PDH E2/E3bp (red). Nuclei are labelled with Hoechst (blue). Zoom insets represent 5x magnification and arrowheads indicate TOM20-positive MDVs."
NCBI gene IDs:
"Parkin: 5071
Tom1: 10043"
Figure legend: "(E) Western blot analysis of lysates harvested from SH-SY5Y wild-type (empty vector) and CRISPR generated Parkin KO cells. Immunoblot analysis was performed using antibodies against Parkin and GAPDH."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(F) Immunofluorescence microscopy was performed on SH-SY5Y wild-type and Parkin KO cells either untreated or treated with AO for 2 hours. Cells were immunostained for TOM20 (red), PDH E2/E3bp (blue), and LAMP1 (green). Zoom insets represent 5x magnification. Circles indicate TOM20 MDVs positive for LAMP1 and arrowheads indicate TOM20 MDVs negative for LAMP1. Scale bar represents 10 µm."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(H) HeLa cells transiently transfected with HA-Parkin were subjected to mitochondrial stress by treatment with 25 μM antimycin A (AA) for 2 hours, then fixed and stained with antibodies specific to HA, PDH and TOM20. TOM20+ve/PDH-ve MDVs were quantified in cells that were either expressing or not expressing HA-Parkin (n = 12-14 cells per condition from 3 independent experiments)."
NCBI gene IDs:
"HA: 
Parkin: 5071"
Figure legend: "(I) Hela cells stably coexpressing BioID-Tollip and either HA-Parkin WT or Δ1-76 (ΔUBL) were incubated with and without biotin in the presence of AO for 6 hours prior to being subjected to cell lysis and streptavidin pulldowns. Western blot analysis was performed on lysate inputs and streptavidin pulldowns (Streptavidin PD) using antibodies against the indicated proteins or epitope tags."
NCBI gene IDs:
"Bio: 
HA: 
Parkin: 5071
Tollip: 54472"
Figure legend: "(A-B) siRNA knockdown of Tollip or Parkin in SH-SY5Y cells was performed over a 72 hour period, then 18 hours prior to treatment cells were transfected with GFP-2xFYVE to label endocytic membranes. Cells were treated with 25 μM antimycin A (AA) for 2 hours then fixed and immunostained with antibodies specific to PDH E2/E3bp (red) and TOM20 (blue). Arrowheads denote TOM20+ve/PDH-ve MDVs that colocalise with GFP-2xFYVE and arrows denote TOM20+ve/PDH-ve MDVs that do not."
NCBI gene IDs:
"FYVE: 
GFP: 
Parkin: 5071
Tollip: 54472"
Figure legend: "(E) siRNA knockdown of Parkin was performed in SH-SY5Y cells followed by 25 μM AA for 2 hours prior to fixation and immunostaining with antibodies specific to TOM20 (green), Tollip (red) and Cytochrome c (blue). We observed Tollip colocalisation with TOM20+ve/PDH-ve MDVs (denoted by arrowheads), which was still maintained following Parkin siRNA knockdown."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(F) SH-SY5Y cells were transfected with GFP-Tollip and treated with 5 μM antimycin A/10 μM oligomycin B (AO) or AO/100 μM bafilomycin A (BfnA1) for 2 hours prior to fixation and immunostaining with antibodies specific to GFP (green), Rab7a (red) and PDH E2/E3bp (blue). (G) Quantification of GFP-Tollip/Rab7a colocalisation using Pearson's correlation."
NCBI gene IDs:
"GFP: 
Tollip: 54472"
Figure legend: "(B) Quantitation of the prevalence of Tollip clusters in HEK293 WT or Tom1 KO cells treated with AO for 2 hours. The percentage of cells with vesicular clusters were quantified from an average of 50 cells for each condition from 5 independent experiments."
NCBI gene IDs:
"Tom1: 10043"
Figure legend: "(D-E) SH-SY5Y cells were transfected with either wild-type GFP-Tollip (WT), GFP-Tollip lacking its N-terminus (∆Nterm), or GFP-Tollip containing a CUE domain mutation (CUEmut) then treated with AO for 2 hours. Cells were fixed and immunostained with antibodies specific to GFP (green) and LAMP1 (red)."
NCBI gene IDs:
"GFP: 
Tollip: 54472"
Figure legend: "(F) The extent of colocalisation between GFP-Tollip and LAMP1 from untreated and AO treated SH-SY5Y cells were quantitated from immunofluorescence images and represented as a Pearson's correlation (2-3 cells per experiment, from 2 independent experiments). (G-I) The extent of colocalisation between GFP-Tollip and LAMP1 in Tom1 KO (G), ATG5 KO (H), and VPS35 KO (I) compared to wild-type (WT) HeLa cells was quantified from immunofluorescence images immunostained for GFP and LAMP1 and represented as a Pearson's correlation (2-3 cells per experiment, from 3 independent experiments). Western blot analysis of lysates harvested from wild-type (WT) alongside either Tom1 KO (G) or VPS35 KO (I) Hela cells was performed using antibodies specific to the indicated proteins."
NCBI gene IDs:
"ATG5: 9474
Tom1: 10043
VPS35: 55737"
Figure legend: "(A) A subset of TOM20+ve/PDH-ve MDVs are trafficked to the lysosome. siRNA knockdown of Tollip was conducted in SH-SY5Y cells over a 72 hours period prior to treatment with 5 μM antimycin A/10 μM oligomycin B (AO) or 25 μM antimycin A (AA) for 2 hours. Cells were then fixed and stained with antibodies specific to LAMP1 (green), PDH E2/E3bp (red) and TOM20 (blue). Arrows denote TOM20+ve/PDH-ve MDVs colocalising with LAMP1, whereas arrowheads denote MDVs that do not colocalise with LAMP1. (B) From immunofluorescence images, the total number of TOM20+ve/PDH-ve MDVs were counted as well as the number of TOM20 MDVs that colocalised with LAMP1 to calculate the % of TOM20 positive MDVs colocalising with LAMP1 per cell (n = 25-32 cells per condition from 3 independent experiments)."
NCBI gene IDs:
"Tollip: 54472"
Figure legend: "(C) siRNA knockdown was performed in SH-SY5Y cells, then 18 hours prior to fixation cells were transfected with GFP-Tollip wild-type (WT), ∆Nterm, CUEmut, or R78A. Cells were fixed and immunostained for PDH E2/E3bp (red) and TOM20 (blue). Arrowheads denote TOM20+ve/PDH-ve MDVs. (D) Quantification of TOM20 MDVs per cell was performed by eye (n = 11-14 cells per mutant from 2 independent experiments). Cells expressing a GFP-Tollip construct were identified using the GFP channel. Surrounding cells not expressing GFP were counted as the Tollip siRNA only population."
NCBI gene IDs:
"GFP: 
Tollip: 54472"
Figure legend: "A Generation of myeloid cells  genetically inactivated for Elp3. Elp3  mRNA and protein levels were assessed by Real-Time PCR  with extracts isolated from peritoneal macrophages of Elp3Control and Elp3∆Mye mice. mRNA levels in Elp3Control mice  were set to 1 and levels in other experimental conditions were relative to that after normalization with Gapdh  mRNA levels (n = 3 mice; mean +/- SD, Student T test, ***= p&lt; 0.001). An anti-Elp3 western blot  (WB) is also illustrated. The anti-Gapdh blot  is shown for normalization purposes."
NCBI gene IDs:
"Elp3: 74195
Gapdh: 14433"
Figure legend: "C and D Defective mTORC2  signaling upon Elp3  deficiency in myeloid cells.  Peritoneal macrophages from Elp3Control and Elp3∆Mye mice  were isolated and cultured ex-vivo. They were untreated or stimulated with a combination of LPS  (100 ng/ml) and IFNγ  (50 ng/ml) for the indicated periods of time  and the resulting cell extracts were subjected to WB  analyses."
NCBI gene IDs:
"Elp3: 74195"
Figure legend: "F mTORC2  activation by M1 polarization signals relies on Ctu2. Control and Ctu2-depleted bone marrow-derived macrophages  (BMDMs) (SiRNA-mediated depletions) were treated or not with IFNγ  (50 ng/ml) and LPS  (100 ng/ml) and the resulting cell extracts were subjected to WB  analyses."
NCBI gene IDs:
"Ctu2: 66965"
Figure legend: "C Elp3  deficiency in myeloid cells  exacerbates the decrease of colon  length upon DSS  administration (n = 7 mice; mean +/- SD, **= p&lt; 0.01)."
NCBI gene IDs:
"Elp3: 74195"
Figure legend: "E More severe histological  score in mice  lacking Elp3  in myeloid cells  upon DSS  administration. Representative intestinal crypts from the indicated genotypes are illustrated. The histological  score was established as described in methods (n = 5 mice  per genotype; mean +/- SD, Student T test, *= p&lt; 0.05)."
NCBI gene IDs:
"Elp3: 74195"
Figure legend: "F Increased infiltration of iNOS+/CD68+ cells upon DSS  administration in  Elp3∆Mye mice. The percentage of iNOS+ in CD68+ cells was established in both genotypes treated with DSS  (n = 7 mice  per genotype; mean +/- SD, Student T test, **= p&lt; 0.01). Anti-iNOS  and -CD68 immunofluorescence  analyses carried out in  intestinal crypts from both genotypes are illustrated."
NCBI gene IDs:
"Elp3: 74195"
Figure legend: "G Patients  suffering from  ulcerative colitis (UC) show reduced levels of both Elp1  and Elp3. The central band represents the mean value of relative expression  in the investigated cohort. Boxes represent 75th and 25th percentile. Whiskers represent maximum and minimum values before the upper and lower fence, respectively (**= p&lt; 0.01, ***= p&lt;0.001) (GSE9452-GEO DataSets, Definition of an ulcerative colitis  pre-inflammatory state)."
NCBI gene IDs:
"Elp1: 8518
Elp3: 55140"
Figure legend: "E Rictor  but not Raptor  deficiency impairs Elp3  expression. BMDMs  were transfected with the indicated siRNAs and the resulting cells were treated or not with  IL-4 (10 ng/ml)/IL-13  (10 ng/ml) for 24 hours. Cell extracts were subjected to WB  analyses."
NCBI gene IDs:
"Rictor: 78757
Raptor: 74370"
Figure legend: "Elp3    deficiency in myeloid cells impairs multiple signaling pathways triggered by  IL-4 (H, ,  IL-13  (H) or by both cytokines (H). Peritoneal macrophages isolated from the indicated mouse  genotypes were untreated or stimulated with IL-4 (10 ng/ml) (H, IL-13 (10 ng/ml) (H) or with both cytokines (H) for 8 hours (H) and the resulting cell extracts were subjected to WB analyses."
NCBI gene IDs:
"Elp3: 74195"
Figure legend: "J Elp3  deficiency in myeloid cells impairs multiple signaling pathways triggered by  IL-4 I and J) Peritoneal macrophages isolated from the indicated mouse  genotypes were untreated or stimulated with IL-4  (10 ng/ml) , I and J), or for the indicated periods of time  (I and J) and the resulting cell extracts were subjected to WB  analyses."
NCBI gene IDs:
"Elp3: 74195"
Figure legend: "L Elp3   promotes M2 macrophage polarization.  Peritoneal macrophages  isolated from the indicated mouse  genotypes were untreated or stimulated with  IL-4/IL-13 (10 ng/ml) for 24 hours and the resulting cell extracts were subjected to WB  analyses."
NCBI gene IDs:
"Elp3: 74195"
Figure legend: "B Defective induction of Pparγ  by  IL-4/IL-13 upon Elp3  deficiency. Cell extracts from  peritoneal macrophages of Elp3Control and Elp3∆Mye mice  treated or not with IL-4/IL-13 were subjected to WB  analyses."
NCBI gene IDs:
"Elp3: 74195"
Figure legend: "A The induction of Ric8b  expression by IL-4 relies on Elp3. BMDMs  from the indicated genotypes were treated or not with  IL-4 (10 ng/ml) up to 24 hours and the resulting cell extracts were subjected to WB  analyses."
NCBI gene IDs:
"Elp3: 74195"
Figure legend: "B Elp3  promotes Ric8B   mRNA translation. BMDMs  from Elp3Control and Elp3∆Mye mice  were treated by  IL-4  for 24 hours, followed by a treatment with 10 μg/ml puromycin  for 5 minutes. To detect newly synthesized Ric8b  proteins, a Puro-PLA  assay was conducted. Representative images detecting Ric8b (Red) and α-Tubulin+ microtubules  (green) in BMDMs  are illustrated. On the right, the graph shows a quantification of signals for Ric8b  in α-Tubulin+ areas. A random of six different areas were counted (6 technical replicates, mean +/- SD, Student's t-test, *= p&lt; 0.05)."
NCBI gene IDs:
"Elp3: 74195
Ric8B: 237422"
Figure legend: "C Ric8b  is a direct target of Elp3. BMDMs  from Elp3Control and Elp3∆Mye mice  were infected with a lentiviral GFP  construct (negative control), Flag-Ric8b  WT or with Flag-Ricb  MUT, as indicated and the resulting protein extracts were subjected to WB  analyses to assess Ric8b  and Elp3  protein levels. Gapdh  was used as a loading control."
NCBI gene IDs:
"Flag: 
GFP: 
Elp3: 74195
Ric8b: 237422
Ricb: 237422"
Figure legend: "D and E Ric8b  promotes  IL-4-dependent mTORC2  activation. Control or Ric8b-depleted BMDMs  were treated or not with IL-4 (10 ng/ml) for the indicated periods of time  and the resulting cell extracts were subjected to WB  analyses."
NCBI gene IDs:
"Ric8b: 237422"
Figure legend: "C Elp3  promotes mitochondrial  translation. BMDMs  from the indicated genotypes were treated or not with  IL-4/IL-13 (10 ng/ml) for the indicated hours and the resulting cell extracts were subjected to WB  analyses."
NCBI gene IDs:
"Elp3: 74195"
Figure legend: "D Elp3  expression in myeloid cells maintains the pool of tumor-associated macrophages (TAMs). The number of TAMs, defined as CD301+/F4/80+ cells among F4/80+ cells was quantified in  intestinal crypts from both Apc+/Min Elp3Control and Apc+/Min Elp3∆Mye mice  (n = 5 mice  per genotype; mean +/- SD, Student T test, *= p&lt; 0.05). Representative immunofluorescence  analyses are illustrated."
NCBI gene IDs:
"Apc: 11789
Elp3: 74195"
Figure legend: "Immunoblots (left) and quantifications normalized to control (right) of VPS16, VPS33A and VPS11 in lysates from fibroblasts transduced with a lentivirus to express VPS16 or control (empty vector)."
NCBI gene IDs:
"VPS16: 64601"
Figure legend: "Analysis of the early endosome marker EEA1 in fibroblasts transduced with control or VPS16-expressing lentivirus by confocal microscopy. (A) Representative confocal micrographs. Scale bar, 20 μm. (B) Quantification of EEA1-stained puncta number and intensities (ca 80 cells analyzed for each of n=3 biological replicates)."
NCBI gene IDs:
"VPS16: 64601"
Figure legend: "Confocal micrographs of fibroblasts transduced with control or VPS16-expressing lentivirus and labeled with LysoTracker. Scale bar, 20 μm. Quantification of LysoTracker-stained puncta number and intensities (ca 80 cells analyzed for each of n=3 biological replicates)."
NCBI gene IDs:
"VPS16: 64601"
Figure legend: "Myelination, as reported using the Tg(mbp:gfp-caax) transgenic, is significantly reduced in vps16 crispants. The yellow box indicates the region assessed in D. Scale bar 100 μm. Bar graphs represent data as mean ±SEM. Statistical comparisons by Mann-Whitney U tests (n=6). ** p &lt; 0.01."
NCBI gene IDs:
"gfp: 
vps16: 798985"