EMBO/SourceData huggingface dataset:
Figure legend: "NADPH/NADP ratios of GR cells transfected with NTC, IDH2 siRNA#1, and siRNA#2 (left: T24GR, right: UMUC3GR). The data are shown as the means ± SDs (n=3, biological replicates) and were analyzed by Student's t test. ** p&lt;0.01."
NCBI gene IDs:
"IDH2: 3418"
Figure legend: "E: Western blot analysis of PITRM1 in primary fibroblasts (left) and skeletal muscle (right) of controls (CTR) and subject II-2. Densitometric quantification using the Genetools software is shown below the blots. In blue is PITRM1WT and in red PITRM1R183Q."
NCBI gene IDs:
"PITRM1: 10531"
Figure legend: "F: proteolytic activity on two fluorescent oligopeptides (AnaSpec), reported at the bottom of each histogram, by 6-His tagged PITRM1WT and PITRM1R183Q proteins expressed in E. coli and affinity-purified by Ni-agarose chromatography. Values are expressed as arbitrary units per sec per µg of protein (a.u. s-1µg-1). Experiments were performed in duplicate."
NCBI gene IDs:
"PITRM1: 10531"
Figure legend: "G: degradation rate of Aβ1-42 by purified 6-His tagged PITRM1WT and PITRM1R183Q proteins. Quantification of these experiments is displayed below the blots. Experiments were performed in duplicate."
NCBI gene IDs:
"PITRM1: 10531"
Figure legend: "A: cell growth in glucose (GLU) and galactose (GAL). C29V, C47V, TpLV: immortalized fibroblast cell lines from control individuals; PITRM1V: immortalized fibroblasts from subject II-2, carrying the PITRM1R183Q mutation. pLKO.1: empty vector; sh38: shRNA38; sh41: shRNA41. Each cell line was measured six times. Error bars indicate ±SD. Statistic analysis was by two-way ANOVA post-hoc Bonferroni test ***p&lt;0.001."
NCBI gene IDs:
"PITRM1: 10531"
Figure legend: "C: co-localization of PITRM1 (red) with TOM20 (T20, green) in human fibroblast cells from a control (CTR) and subject II-2. Note that the intensity of PITRM1 immunofluorescence is much lower in II-2 cells than in CTR cells (see main text for further details). Nuclei are stained in blue by DAPI. A white bar corresponds to 10 µM."
NCBI gene IDs:
"PITRM1: 10531"
Figure legend: "A: oxidative growth. W303-1Bcym1Δ strains harbouring the wild-type CYM1 allele (CYM1wt), the cym1R163Q mutant allele or the empty vector were serially diluted from 107 to 104 cells/ml. Five microliters of each dilution were spotted on SC agar plates without uracil, supplemented with 2% glucose, 2% glycerol or 2% ethanol. Plates were incubated at 37°C for 3-7 days."
NCBI gene IDs:
"CYM1: 852041"
Figure legend: "B: oxygen consumption rate (OCR). Cells grown at 37°C SC medium without uracil were supplemented with 0.5% glucose. Values were normalized to the OCR of the CYM1wt strain (49 nmol O2 min−1 mg−1) and represented as the mean of at least three values ± SD. Statistical analysis was by unpaired, two-tail Student's t test: ***p&lt;0.001."
NCBI gene IDs:
"CYM1: 852041"
Figure legend: "D: respiratory chain complex activities. Biochemical activities of Succinate Quinone DCPIP Reductase, SQDR (CII), NADH-cytochrome c oxidoreductase activity NCCR (CIII), and cytochrome c oxidase (CIV) were measured on a mitochondrial-enriched fraction from cells grown at 37°C as in panel B. Values were normalized to that of CYM1wt strain and represented as the mean of three independent experiments ± SD. Statistical analysis was by unpaired, two-tail Student's t test: **p&lt;0.01; ***p&lt;0.001."
NCBI gene IDs:
"CYM1: 852041"
Figure legend: "E: Western-blot using an anti-HA monoclonal antibody visualizing the CYM1wt and cym1R163Q recombinant proteins both fused in frame with the HA epitope on the C-terminus. Western-blot analysis on total protein extract. Total protein extracts were obtained by strains expressing HA-tagged CYM1wt and cym1R163Q. PGK was used as a loading control and signals were normalized to the wt. The quantification was performed on 5 independent blots.F: prolonged exposure of a Western-blot containing the CYM1wt and cym1R163Q recombinant proteins reveals the presence of a band corresponding to a degradation product in the cym1R163Q lanes (arrow)."
NCBI gene IDs:
"CYM1: 852041"
Figure legend: "A: Western-blot analysis of Pitrm1 protein in brain, muscle and liver of two 4-mo male Pitrm1+/- mice and two Pitrm1+/+ littermates. Densitometric analysis is reported in the histograms below the blots. Pitrm1+/+ is in blue, Pitrm1+/- in red. Error bars indicate ±SD"
NCBI gene IDs:
"Pitrm1: 69617"
Figure legend: "B: representative hindlimb-clasping phenomenon is shown in a 4 mo Pitrm1+/- male mouse, consisting in strong adduction of the hindlimbs when the animal is suspended by the tail; a littermate Pitrm1+/+ control displays the normal reflex, consisting in wide abduction of the limbs. All examined Pitrm1+/- animals displayed this abnormal reflex from 2 months of age."
NCBI gene IDs:
"Pitrm1: 69617"
Figure legend: "C: rotarod test. Blue and red lines refer to Pitrm1+/+ (n=9) and Pitrm1+/- (n=7) 4 mo animals, respectively. Error bars indicate ±SD. Statistical analysis was by unpaired, two-tail Student's t test. *p&lt;0.05; ** p&lt;0.01."
NCBI gene IDs:
"Pitrm1: 69617"
Figure legend: "B: morphological analysis of an AD subject and of Pitrm1+/- and Pitrm1+/+ mouse brains. TF: Thioflavin T (thalamus); CR: Congo-red (brain cortex); PL: polarised light (same sections as those stained with CR); Aβ1-42 immunostaining (pons); Ub: ubiquitin immunohistochemistry shown as brownish staining (brain cortex). The white bar indicates 20 µm."
NCBI gene IDs:
"Pitrm1: 69617"
Figure legend: "A: upper panel: import of Aβ1-42 into mitochondria; lower panel: relative quantification from two independent experiments. Values of Aβ1-42 signal were normalized to HSP60 signal and the resulting value at 5 min without trypsin was arbitrarily chosen as 1. Error bars indicate ±SD. Statistical analysis was by unpaired, two-tail Student's t test. *p&lt;0.05."
NCBI gene IDs:
"Aβ: 351"
Figure legend: "B: upper panel: pulse and chase experiment to assess clearance of Aβ1-42; lower panel: quantification from three independent experiments. Values of Aβ1-42 signal were normalized to HSP60 signal and the pulse value was arbitrarily chosen as 1. Error bars indicate ±SD. Statistical analysis was by unpaired, two-tail Student's t test. *p&lt;0.05, **p&lt;0.01."
NCBI gene IDs:
"Aβ: 351"
Figure legend: "A: MEFs from Pitrm1+/+, Pitrm1+/-, Mfn1-/-, Mfn2-/-, as well as h-PITRM1 R183Q and h- PITRM1 WT were exposed to Aβ1-40 peptide for 18h. Note that Aβ1-40 signal was still evident in Pitrm1+/- and h-PITRM1 R183Q cells.B: quantification of three independent experiments similar to those shown in panel A. Statistical analysis was by unpaired, two-tail Student's t test. **p&lt;0.01, ***p&lt;0.001."
NCBI gene IDs:
"Aβ: 351
Mfn1: 67414
Mfn2: 170731
PITRM1: 10531
Pitrm1: 69617"
Figure legend: "(C) Fluorescence polarization assays demonstrating that a peptide containing the BH3‐like domain of Beclin‐1 interacts with Bcl‐XL. Recombinant Bcl‐XL ΔTM was incubated with carboxyfluorescein‐labeled Bak BH3 peptide, in the absence or presence of wild‐type (WT) Beclin‐1 BH3 or either of the two mutant peptides described in B."
NCBI gene IDs:
"Bcl‐XL: 598"
Figure legend: "(D) Affinity determination of the interaction between recombinant Bcl‐XLΔTM and fluorescent Beclin‐1 BH3, by fluorescence polarization. A comparison between WT Bcl‐XL(squares) and G138A Bcl‐XL (triangles) is shown (means±s.d., n=3 separate experiments)."
NCBI gene IDs:
"Bcl‐XL: 598"
Figure legend: "(E) Co‐immunoprecipitation of Bcl‐XL and WT or mutant Beclin‐1. HeLa cells were transfected with the indicated constructs, followed by immunoprecipitation of Flag‐tagged Bcl‐XL and immunochemical detection of Beclin‐1."
NCBI gene IDs:
"Beclin‐1: 8678"
Figure legend: "(F) Co‐immunoprecipitation of Beclin‐1 with‐WT and mutant (G138A) Bcl‐XL. Results are representative of at least three experiments yielding similar results."
NCBI gene IDs:
"Bcl‐XL: 598"
Figure legend: "(A) Competition between Beclin‐1 BH3 and ABT737 for Bcl‐XL binding. A fluorescent 25‐mer peptide containing the BH3‐like domain of Beclin‐1 ( Figure 1D) was docked to recombinant Bcl‐XL ΔTM protein in the absence or presence of ABT737. The IC50 of ABT737, as measured in the presence of 15 nM of peptide and 100 nM of Bcl‐XL ΔTM, was 1.7 μM."
NCBI gene IDs:
"Bcl‐XL: 598"
Figure legend: "(A, B) Detection of autophagic vacuoles by LC3‐GFP and their modulation by ABT737 and by Beclin‐1‐specific siRNAs. HeLa cells were transfected with control or Beclin‐1‐specific siRNAs, 24 h later re‐transfected with LC3‐GFP, cultured in complete medium (CM) for 24 h, and finally kept 12 h either in CM or in nutrient‐free (NF) conditions, in the presence or absence of 1 μM ABT737. Representative microphotographs of cells cultured in NF medium are shown in (A) and the percentage (means±s.d., n=3 separate experiments) of LC3‐GFP‐transfected cells bearing LC3‐GFP aggregates in the cytoplasm (LC3‐GFPvac) are quantified in (B). The insert in (B) demonstrates the efficiency of the Beclin‐1‐specific siRNAs, as quantified by immunoblot."
NCBI gene IDs:
"Beclin‐1: 8678"
Figure legend: "(C, D) Detection of cytoplasmicvacuoles using chloromethylfluorescein diacetate (CMFDA). Cells were transfected with control or Beclin‐1‐specific siRNAs, cultured for 48 h in CM, washed, cultured in CM (D) or NF (C, D) for 12 h, stained with CMFDA, and either photographed (C) or subjected to the quantification of the cells that bear at least one discernible cytoplasmicvacuole (arrow head) (means±s.d., n=3 separate experiments)."
NCBI gene IDs:
"Beclin‐1: 8678"
Figure legend: "Quantification of autophagic vacuoles induced by ABT737. HeLa cells transfected with the indicated siRNAs (specific for Emerin or for Beclin‐1 at 0 h) were re‐transfected with LC3‐GFP finally cultured in nutrient‐free (NF) conditions (60-72 h), in the presence or absence 1 μM ABT737 and then subjected to electron microscopy detection of immature (AV1) or mature (AV2) autophagic vacuoles. Representative pictures are shown in (A)."
NCBI gene IDs:
"Beclin‐1: 8678
Emerin: 2010
LC3: 440738///81631///84557"
Figure legend: "(A-D) Modulation of Beclin‐1‐induced autophagy by BH3 mutants and ABT737. Cells were transfected with GFP‐LC3 together with an empty control vector or Beclin‐1 (WT, L116A, F123A) and cultured for 48 h, followed by overnight culture in CM (B) or NF (A, B) in the absence or presence of 1 μM ABT737. Representative microphotographs are shown in (A) and the LC3‐GFP‐positive vacuoles per cell are quantified in (B) (means±s.d.; n=3 separate experiments). Alternatively, cells were not transfected and stained with CMFDA to detect vacuoles, as shown in (C) and (D), yielding similar results as for the LC3‐GFP method."
NCBI gene IDs:
"Beclin‐1: 8678
LC3: 440738///81631///84557"
Figure legend: "(E) BH3‐dependent modulation of Beclin‐1‐induced autophagy by anti‐apoptotic Bcl‐2 proteins. Cells were transfected simultaneously with Beclin‐1 (or control vector) and equivalent amounts of plasmids coding for WT Bcl‐XL, Bcl‐XL G138A, Bcl‐2 or Mcl‐1 (or control vector), as well as GFP‐LC3. The culture in CM or NF in the absence or presence of ABT737 was performed during the last 12 h of the 60 h‐long experiment. The percentage of cells exhibiting the accumulation of LC3‐GFP in vacuoles (LC3‐GFPvac) is quantified as means±s.d. (n=3 separate experiments)."
NCBI gene IDs:
"Bcl‐2: 596
Bcl‐XL: 598
Beclin‐1: 8678
Mcl‐1: 4170"
Figure legend: "(B) Immunoprecipitation of wild‐type and ER‐targeted Bcl‐2 with Beclin‐1. Cells stably transfected with wild type, ER‐ and mitochondrion‐targeted Bcl‐2 were subjected to starvation or treated with ABT737, followed by immunoprecipitation of Bcl‐2 and immunodetection of Beclin‐1."
NCBI gene IDs:
"Bcl‐2: 596"
Figure legend: "(D, E) Impact of Bad depletion on autophagy. Cells were transfected with LC3‐GFP together with siRNAs specific for Bad, siRNAs specific for emerin or the Beclin‐1‐associated PI3 kinase Vps34. Forty‐eight hours later, when the siRNAs had down‐regulated the proteins of interest (D), cells were subjected by nutrient depletion (NF) or addition of rapamycin (E) and the frequency of cells exhibiting LC3‐GFP aggregation as a marker of autophagy was assessed after 18 h (means±s.d., *P0.05, n=3 separate experiments)."
NCBI gene IDs:
"Bad: 572
emerin: 2010
Vps34: 5289"
Figure legend: "(F) Effect of the Bad knock‐out on autophagy. Wild Type (WT) or Bad−/− MEF were transfected with LC3‐GFP and then subjected to nutrient depletion (NF) and/or treatment with ABT737 (18h; means±s.d., n=3). The asterisks denotes a significant (P0.05) effect of Bad deficiency."
NCBI gene IDs:
"Bad: 12015"
Figure legend: "(G) Effect of the Bad knockout on the Beclin‐1/Bcl‐2 interaction. WT or Bad−/− MEF were subjected to the indicated treatments, followed by immunoprecipitation of Bcl‐2 and immunobloting of Beclin‐1."
NCBI gene IDs:
"Bad: 12015"
Figure legend: "(H) Overexpression of Bad triggers autophagy. Cells were transfected with LC3‐GFP alone (Control), together with vector‐only or with a vector encoding Bad, and subjected 48 h later to nutrient depletion (NF). Cells were cultured in the continuous presence or absence of the pan‐caspase inhibitor Z‐VAD‐fmk (50 μM) for 16 h, followed by assessment of autophagy as in (E) (means±s.d., n=3 separate experiments, *P0.01). Immunoblots are representative of at least three independent experiments."
NCBI gene IDs:
"Bad: 12015"
Figure legend: "(A) Representative images of wt and egl‐1 mutant embryos, bearing the plgg−1DsRED"
NCBI gene IDs:
"egl‐1: 179943"
Figure legend: "D Representative confocal  images of HEK293  cells expressing various GFP-fused proteins (green) and supplemented with TopFluor® TMR-PS (red); scale bar = 10 µm. Yellow arrows indicate high intensity PS  fluorescent regions. E %PM  with PS  clusters = area of high intensity fluorescent PS  clusters over total  plasma membrane area from images in panel D. Black bars are control proteins and blue bars are eVP40    proteins. Values are reported as mean ± s.d.; N&gt;18 cells per biological replicate, n=3 for 3 biological replicates; A one-way ANOVA was performed with multiple comparisons compared to the control GFP  %PS  clustering (***p=0.0007, **p=0.004). Data information: PS: phosphatidylserine; PM: plasma membrane."
NCBI gene IDs:
"GFP: 
VP40: 911825"
Figure legend: "D, E PS  concentration in LUVs  enhances the ability of His6-eVP40  to oligomerize on membranes. D Representative western blot of chemical crosslinking performed on His6-WT-eVP40   following incubation with LUVs  of varying PS  content (detected by Mouse α-His  antibody &amp; HRP-Sheep α-Mouse). E Oligomerization  capacity was determined from the western blot  band density ratio of oligomers/(monomer + dimer) from chemical crosslinking experiments. A one-way ANOVA was performed with multiple comparisons compared to the control 0% PS LUVs  control (30% PS  *p= 0.02; 60% PS  *p=0.017). n=3 biological replicates. Values are reported as mean ± s.d.; Data information: LUVs:  large unilamellar vesicles; PS: phosphatidylserine; HRP: horseradish peroxidase."
NCBI gene IDs:
"His: 
VP40: 911825"
Figure legend: "D, E Analysis of PS  clustering in HEK293  cells in response to fendiline  treatment through N&amp;B analysis. D Left panel: Representative images from  time-lapse  (30 frames) imaging of HEK293  expressing GFP-LactC2  and treated with fendiline  for 48 hours; scale bar= 5 µm. Middle panel: Brightness and Intensity plots for each representative image. Right panel: Selection map correlating each pixel in the representative image to an oligomerization  state (b value) (red: monomer-5mer, green: 5mer-10mer, blue: &gt;10mer). E Average % pixels quantification from panel (d)= Percentage of GFP-LactC2  with brightness values corresponding to monomer-5mer (~1.-1.5), 5mer-10mer (~1.5-1.9) and &gt;10mer (&gt;1.9) over the total pixels within each image. Values are reported as mean ± s.d.; N≥9, n=3 biological replicates; A two-way ANOVA was performed with Dunnett's multiple comparisons comparted to the control DMSO  % average pixels (****p&lt;0.0001, **p=0.0043). Data information: GFP-LactC2: phosphatidylserine  sensor; N&amp;B:  Number &amp; Brightness analysis; PS: phosphatidylserine."
NCBI gene IDs:
"GFP: 
LactC2: 281913"
Figure legend: "A-C Effect of fendiline  on eVP40  and mVP40 PM localization  in HEK293  cells after 48 hours of treatment. A Representative confocal  images from live cell imaging  experiments of HEK293  cells expressing EGFP-WT-eVP40 (top panel) and EGFP-WT-mVP40   (bottom panel) after 48 hours of fendiline  treatment. scale bars= 10 µm. Effect of fendiline  on mVP40 (B) and eVP40 (C) PM localization  was quantified by the ratio of EGFP  fluorescence intensity at the PM / total EGFP  fluorescence intensity (and normalized to DMSO  control). N&gt;15 cell per biological replicate, n=3 biological replicates. Values are reported as mean ± s.d. A one-way ANOVA with multiple comparisons was performed compared to the DMSO  control. Data information: PM: plasma membrane"
NCBI gene IDs:
"EGFP: 
VP40: 911825
VP40: 920947"
Figure legend: "D, E Analysis of eVP40 oligomerization  in HEK293  cells in response to 48 hour fendiline  treatment using N&amp;B analysis. D Left panel: Representative images from  time-lapse  (30 frames) of HEK293  expressing EGFP-WT-eVP40 and treated with fendiline  for 48 hours. scale bar = 5 µm. Middle panel: Brightness and Intensity plots for each representative image. Right panel: Selection map correlating each pixel in the representative image to an oligomerization  state (b value) (red: monomer-hexamer, green: hexamer-12mer, blue: 12mer-24mer, pink: &gt;24mer). E Average % pixel quantification from panel (d)= % of GFP-WT-eVP40 with brightness values corresponding to monomer-hexamer (~1.-1.6), hexamer-12mer (~1.6-2.0), 12mer-24mer (2.0-3.2) and &gt;24mer (&gt;3.2) over the total pixels within each image. Values are reported as mean ± s.d.; N≥9 cell per biological replicate, n=3 biological replicates; A two-way ANOVA was performed with Dunnett's multiple comparisons compared to the control DMSO  % average pixels (**p=0.0035). Data information: N&amp;B: Number &amp; Brightness analysis."
NCBI gene IDs:
"EGFP: 
VP40: 911825"
Figure legend: "A-C TEM  analysis of eVLP morphology. A Representative transmission electron micrographs  of eVLPs  purified from HEK293  cells expressing FLAG-eVP40 and eGP following 48 hours of DMSO  (left panel) or 5 µM fendiline  treatment (right panel). B Quantification of eVLP  length (µm) of DMSO-derived eVLPs  (black) and fendiline-derived eVLPs  (blue). N&gt;50 VLPs   per biological replicate, n=3 biological replicates. Values are reported as mean ± s.d. A two-tailed t-test was performed (**p=0.0139). C Quantification of eVLP   diameter (nm) of DMSO-derived eVLPs  (black) and fendiline-derived eVLPs  (blue). N&gt;50 VLPs   per biological replicate, n=3 biological replicates. Values are reported as mean ± s.d. A two-tailed t-test was performed (*p=0.0430). Data information: TEM: transmission electron microscopy; eVLPs: entry-competent VLPs; eGP: Ebola virus glycoprotein"
NCBI gene IDs:
"FLAG: 
glycoprotein: 
GP: 
VP40: 911825"
Figure legend: "(A) Levels of BRCA1 promoter hypermethylation, levels BRCA1 mRNA and the presence of BRCA1 nuclear foci by immunofluorescence are shown T127 and T162 were used as positive controls for hypermethylated BRCA1 promoter. Error bars indicate SEM from independent tumors (n ≥ 2). Dashed line indicates mean of BRCA1 mRNA levels in normal breast. PARPi-response is shown in the summary underneath: white box: PD; black box: PR/CR. Alterations in HRR-related genes in PDX are also indicated."
NCBI gene IDs:
"BRCA1: 672"
Figure legend: "(B) Western blot of PALB2 detected in U2OS cells and PDXs. Three biological replicates of PDX093 are shown; PDX302 is used as PALB2 wild type PDX control."
NCBI gene IDs:
"PALB2: 79728"
Figure legend: "(C) YFP-PALB2 recruitment to laser-induced DSBs is impaired in HeLa cells expressing PALB2 p.M296Nfs (n=4, unpaired t-test at 16min)."
NCBI gene IDs:
"PALB2: 79728"
Figure legend: "Gene-targeting efficiency using Cas9/mClover-LMNA1 homologous recombination assay of (D) siRNA PALB2 cells (n=4, one-way ANOVA) or (E) cells with no PALB2 depletion complemented with wild type and p.M296Nfs siRNA-resistant constructs (n=7, one-way ANOVA). Western blots of PALB2 wild type and PALB2 p.M296Nfs for each condition are shown. Error bars indicate SEM from independent experiments."
NCBI gene IDs:
"mClover: 
LMNA1: 4000
PALB2: 79728
Cas9: 901176"
Figure legend: "(A) Percentage of geminin-positive, RAD51 nuclear foci-containing cells detected by immunofluorescence in FFPE samples from PDX tumors treated with vehicle or PARPi Error bars indicate SEM from independent tumors (n ≥ 2). PARPi-response is shown in the summary underneath: white box: PD; black box: PR/CR. Immunofluorescence staining of RAD51 foci in PARPi- and vehicle-treated PDX tumors is shown. Alterations in HRR-related genes are also summarized: hBRCA1: BRCA1 promoter hypermethylation and lack of BRCA1 expression and BRCA1 nuclear foci formation."
NCBI gene IDs:
"BRCA1: 672"
Figure legend: "(C) Immunofluorescence staining of 53BP1 and BRCA1 nuclear foci [with an antibody towards the N-terminus (B1-NT) or C-terminus (B1-CT) of BRCA1] in three BRCA1-mutant, PARPi-resistant models from PDX cohort-2. The location of the mutation within the gene is indicated. Scale bars: 10µm."
NCBI gene IDs:
"BRCA1: 672"
Figure legend: "(B) Percentage of geminin-positive, RAD51 or γH2AX nuclear foci-containing cells in FFPE tumor samples from patients with HBOC syndrome. The box underneath summarizes the patient's young onset (&lt;35y: &lt;35 years), her family history (FH, purple box for PALB2-related tumors) and the presence of BRCA1 nuclear foci in the analyzed tumor samples."
NCBI gene IDs:
"PALB2: 79728"
Figure legend: "(C) Immunofluorescence staining of γH2AX, BRCA1 and RAD51 foci in three representative FFPE tumors from patients: one RAD51- and BRCA1-positive tumor (Pt03), one RAD51- and BRCA1-negative tumor (Pt11) and one PALB2-related tumor, with BRCA1 but not RAD51 nuclear foci (Pt20.1). Scale bars: 10µm."
NCBI gene IDs:
"BRCA1: 672
PALB2: 79728
RAD51: 5888"
Figure legend: "A Immunoblot analysis with the indicated antibodies of immunoprecipitates (IP) prepared from the SSU fraction of eIF3D-V5/eIF4E-FLAG dKI HEK293T cells (eIF3D/4E dKI) or wild-type (WT) cells with antibodies to the epitope tags. The SSU fraction (input) was also analyzed directly. Cells were fixed with formalin, cell lysates were treated with RNase, and the SSU and RS fractions were separated by sucrose density gradient centrifugation before immunopurification. Molecular sizes are indicated in kilodaltons."
NCBI gene IDs:
"FLAG: 
V5: 
eIF3D: 8664
4E: 1977
eIF4E: 1977"
Figure legend: "B, C Immunoblot analysis with the indicated antibodies of immunoprecipitates prepared as in A from the SSU fraction of eIF4A1-FLAG KI HEK293T cells (eIF4A1 KI) (B) or ASCC3-FLAG KI HEK293T cells (ASCC3 KI) (C)."
NCBI gene IDs:
"FLAG: 
ASCC3: 10973
eIF4A1: 1973"
Figure legend: "Immunoblot analysis with the indicated antibodies of immunoprecipitates prepared as in A from the RS fraction of RPL7A-HA KI HEK293T cells (RPL7A KI) (F)."
NCBI gene IDs:
"HA: 
RPL7A: 6130"
Figure legend: "A RNA-seq results for eIF4A1, eIF4A2, ASCC2, and ASCC3 in HEK293T cells transfected with siRNAs specific for eIF4A1 and eIF4A2 (eIF4A1/A2 dKD #1 or #2) or for ASCC3 (ASCC3 KD #1 or #2) relative to cells transfected with a control siRNA. The dashed line indicates a fold change of 1."
NCBI gene IDs:
"ASCC2: 84164
ASCC3: 10973
eIF4A1: 1973
A2: 1974
eIF4A2: 1974"
Figure legend: "Volcano plots for differential TE (D) The changes in TE and SRO for eIF4A1/A2 dKD #1 and #2 and for ASCC3 KD #1 and #2 HEK293T cells compared with control cells were analyzed with RiboDiff. The gray dashed lines indicate an adjusted P value of 0.05. P values were calculated by chi-square test and adjusted by Benjamini-Hochberg method."
NCBI gene IDs:
"ASCC3: 10973
eIF4A1: 1973
A2: 1974"