EMBO/SourceData huggingface dataset:
Figure legend: "Levels of the cellular housekeeping genes GAPDH and 18S rRNA, negative-strand E (negE), and sgE relative to total levels of E RNA were measured in infected cells, clarified supernatants and virus concentrated through a sucrose  cushion by ultracentrifugation. Data points represent four technical replicates from two independent experiments (Cell and Supernatant) or three replicates (Concentrated Virus) and are normalized to the total levels of E for each sample, plotted as mean with error bars plotted as +/- SEM."
NCBI gene IDs:
"18S rRNA: 
negative-strand E: 43740570
sgE: 43740570
GAPDH: 103218453"
Figure legend: "TRF1 immunofluorescence of the lungs. Notice the absence and presence of TRF1 signal in the carcinomas and surrounding healthy tissue of Trf1Δ/Δ mice, respectively."
NCBI gene IDs:
"Trf1: 21749"
Figure legend: "Analysis of Trf1 excision by PCR. Notice the completed excision in carcinomas of Trf1lox/lox lungs."
NCBI gene IDs:
"Trf1: 21749"
Figure legend: "Tumor growth curve of Trf1+/+K-Ras+/G12Vp53+/+ and Trf1Δ/ΔK-Ras+/G12Vp53+/+ measured by computed tomography (CT).Quantification of the number and size of Trf1+/+K-Ras+/G12Vp53+/+ and Trf1Δ/ΔK-Ras+/G12Vp53+/+carcinomas at death point."
NCBI gene IDs:
"K-Ras: 16653
Trf1: 21749
p53: 22059"
Figure legend: "Percentage of tumors that have deleted Trf1 quantified by TRF1 immunofluorescence after mice had been sacrificed. Post-mortem analysis of Trf1 deletion in each tumor revealed that none of the Trf1lox/lox K-Ras+/G12V p53+/+ ones had excised Trf1."
NCBI gene IDs:
"K-Ras: 16653
Trf1: 21749
p53: 22059"
Figure legend: "Tumor growth curve and tumor growth slope of Trf1+/+ K-Ras+/G12V p53−/− and Trf1−/− K-Ras+/G12V p53−/− measured by CT."
NCBI gene IDs:
"K-Ras: 16653
Trf1: 21749
p53: 22059"
Figure legend: "Tumor maximal section of Trf1+/+K-Ras+/G12Vp53−/− and Trf1Δ/ΔK-Ras+/G12Vp53−/−lungs measured by histological analysis before death point by CT."
NCBI gene IDs:
"K-Ras: 16653
Trf1: 21749
p53: 22059"
Figure legend: "Maximum 18F-FDG-glucose uptake by Trf1+/+K-Ras+/G12Vp53−/− and Trf1Δ/ΔK-Ras+/G12Vp53−/−tumors 22 weeks after infection by positron emission tomography (PET).Representative PET-CT image of Trf1+/+K-Ras+/G12Vp53−/− and Trf1Δ/ΔK-Ras+/G12Vp53−/−lungs."
NCBI gene IDs:
"K-Ras: 16653
Trf1: 21749
p53: 22059"
Figure legend: "Survival curve of Trf1+/+ K-Ras+/G12V p53−/− and Trf1−/− K-Ras+/G12V p53−/− mice."
NCBI gene IDs:
"K-Ras: 16653
Trf1: 21749
p53: 22059"
Figure legend: "A-C The latency (A), volume (B), and weight (C) of subcutaneous tumors generated by control and Trf1-downregulated K-RasG12V-transformed lung cells in athymic mice.D Representative images of the subcutaneous tumors."
NCBI gene IDs:
"K-Ras: 16653
Trf1: 21749"
Figure legend: "E Trf1 expression levels measured by qPCR in the injected cell line and in the generated subcutaneous tumors."
NCBI gene IDs:
"Trf1: 21749"
Figure legend: "I Representative images of aberrant giant nuclei and anaphase bridges in the Trf1-downregulated subcutaneous tumors compared to the normal nuclei of control tumors."
NCBI gene IDs:
"Trf1: 21749"
Figure legend: "J TRF1 immunofluorescence shows the downregulation of Trf1 in lung tumors of the mice intravenously injected with control and Trf1-downregulated cells."
NCBI gene IDs:
"Trf1: 21749"
Figure legend: "K Tumor area measured in the lungs of the mice intravenously injected with control and Trf1-downregulated cells.L Representative images of the lungs colonized by control and Trf1-downregulated cells, respectively."
NCBI gene IDs:
"Trf1: 21749"
Figure legend: "P Trf1 expression levels measured by qPCR in the A549 cell line infected either with sh-scrambled or sh-Trf1."
NCBI gene IDs:
"Trf1: 7013"
Figure legend: "Trf1 expression levels in the indicated tissues of wild-type and Trf1lox/lox hUBC-CreERT2 mice subjected to a tamoxifen-containing diet for 7 weeks."
NCBI gene IDs:
"Cre: 
ERT2: 13983///13982
Trf1: 21749
UBC: 7316"
Figure legend: "Representative images of TRF1 immunofluorescence and quantification of the percentage of TRF1-positive cells in skin and intestine sections of wild-type and Trf1lox/lox hUBC-CreERT2 mice subjected to a tamoxifen-containing diet for 7 weeks."
NCBI gene IDs:
"Cre: 
ERT2: 13982///13983
Trf1: 21749
UBC: 7316"
Figure legend: "Survival curve of wild-type and Trf1lox/lox hUBC-CreERT2 mice subjected to a tamoxifen-containing diet for 7 weeks."
NCBI gene IDs:
"Cre: 
ERT2: 13983///13982
Trf1: 21749
UBC: 7316"
Figure legend: "Quantification of the histological alterations observed in tamoxifen-treated Trf1lox/lox hUBC-CreERT2 mice and 4 months after tamoxifen retrieval compared to their wild-type counterparts."
NCBI gene IDs:
"Cre: 
ERT2: 13983///13982
Trf1: 21749
UBC: 7316"
Figure legend: "Quantification of blood cell populations in wild-type and Trf1lox/lox hUBC-CreERT2mice subjected to a tamoxifen-containing diet for 7 weeks and after 3 weeks and 4 months of tamoxifen retrieval."
NCBI gene IDs:
"Cre: 
ERT2: 13983///13982
Trf1: 21749
UBC: 7316"
Figure legend: "Trf1 expression levels in blood, intestine, skin, and bone marrow of Trf1lox/lox hUBC-CreERT2 mice subjected to a tamoxifen-containing diet either for 7 weeks or for 6 months and after 3 weeks tamoxifen retrieval compared to wild-type mice."
NCBI gene IDs:
"Cre: 
ERT2: 13982///13983
Trf1: 21749
UBC: 7316"
Figure legend: "F. IL-1β quantification in THP-1 wild-type cells incubated with SYK inhibitors entospletinib (n = 4 independent experiments) and R406 (n = 2 independent experiments) or in THP-1 SYKKO cells stimulated with SP/N (n = 5 independent experiments)."
NCBI gene IDs:
"SYK: 6850"
Figure legend: "Coq9Q95X mice at 21 postnatal days showing the loss of corporal hair."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "Representative Western blot images of COQ9protein in kidney homogenate from Coq9+/+ (n = 4) and Coq9Q95Xmice (n = 4) at 3 months of age. Antibody sc-271892 was used to map the C-terminal region of the COQ9protein and antibody ab-104189 was used to map the internal sequence of the COQ9protein."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "High-resolution LC-MS/MS proteomic analysis of kidneymitochondria from Coq9+/+ (n = 3) and Coq9Q95Xmice (n = 3) at 3 months of age. None of the six peptides of the COQ9 protein identified in Coq9+/+mice was detected in Coq9Q95Xmice."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "A-F CoQ9 levels in tissue homogenates from brain (A), cerebellum (B), heart (C), kidney (D), extensor (E) and triceps surae (F) of male and female Coq9+/+ and Coq9Q95Xmice at 6 and 12 months of age. Data are expressed as mean ± SD. Statistical analysis was performed on 6-month-old Coq9+/+mice versus 6-month-old Coq9Q95Xmice and 12-month-old Coq9+/+mice versus 12-month-old Coq9Q95Xmice. **P &lt; 0.01; ***P &lt; 0.001. Student's t-test (n = 8 for each group)."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "A-F Residual CoQ9 levels in tissue homogenates from brain (A), cerebellum (B), heart (C), kidney (D), liver (E) and skeletal muscle (F) of Coq9+/+, Coq9Q95X and Coq9R239X mice at 1, 3 and 5 months of age. Data are expressed as mean ± SD. **P &lt; 0.01; ***P &lt; 0.001; Coq9Q95X and Coq9R239Xmice versus Coq9+/+mice. #P &lt; 0.05; ##P &lt; 0.01; ###P &lt; 0.001; Coq9Q95X versus Coq9R239Xmice (one-way ANOVA with a Tukey's post hoc test; n = 8 for each group; numbers above columns indicate P-values of the one-way ANOVA test)."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "A-E mRNA expression levels of Coq9 (A), Coq7 (B), Adck3 (C), Coq5 (D) and Coq6 (E) on cerebrum of Coq9+/+, Coq9Q95X and Coq9Q95X mice at 3 months of age. **P &lt; 0.01; ***P &lt; 0.001; Coq9Q95X and Coq9R239Xmice versus Coq9+/+mice. ###P &lt; 0.001; Coq9Q95X versus Coq9R239Xmice.F-J mRNA expression levels of Coq9 (F), Coq7 (G), Adck3 (H), Coq5 (I) and Coq6 (J) on kidney of Coq9+/+, Coq9Q95X and Coq9Q95Xmice at 3 months of age. ***P &lt; 0.001; Coq9Q95X and Coq9R239Xmice versus Coq9+/+mice. #P &lt; 0.05; ###P &lt; 0.001; Coq9Q95X versus Coq9R239Xmice.K-O mRNA expression levels of Coq9 (K), Coq7 (L), Adck3 (M), Coq5 (N) and Coq6 (O) on triceps surae of Coq9+/+, Coq9Q95X and Coq9Q95Xmice at 3 months of age. *P &lt; 0.05; ***P &lt; 0.001; Coq9Q95X and Coq9R239Xmice versus Coq9+/+mice. #P &lt; 0.05; Coq9Q95X versus Coq9R239Xmice."
NCBI gene IDs:
"Adck3: 67426
Coq5: 52064
Coq6: 217707
Coq7: 12850
Coq9: 67914"
Figure legend: "A-D Representative Western blot and quantitation of Western blot bands of COQ7 (A), ADCK3 (B), COQ5 (C) and COQ6 (D), and VDAC1 as a loading control in the kidneys of 3-month-old mice. *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001; Coq9Q95X and Coq9R239X mice versus Coq9+/+mice. ##P &lt; 0.01; ###P &lt; 0.001; Coq9Q95X versus Coq9R239X mice. One-way ANOVA with a Tukey's post hoc test.E-H Representative Western blot and quantitation of Western blot bands of COQ7 (E), ADCK3 (F), COQ5 (G) and COQ6 (H), and VDAC1 as a loading control in skeletal muscle of 3-month-old mice. **P &lt; 0.01; ***P &lt; 0.001; Coq9Q95X and Coq9R239X mice versus Coq9+/+mice. #P &lt; 0.05; ##P &lt; 0.01; Coq9Q95X versus Coq9R239X mice.Data information: All values are presented as mean ± SD. One-way ANOVA with a Tukey's post hoc test. Numbers above columns indicate P-values of the one-way ANOVA test. Coq9+/+mice n = 4; Coq9Q95X and Coq9R239Xmice n = 5."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "A-C Mitochondrial CoQ9 levels from cerebrum (A), kidney (B) and skeletal muscle (C) of Coq9+/+ and Coq9Q95X males and females. n = 8 for each group."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "D-F CI+CIII activity in cerebrum (D), kidney (E) and skeletal muscle (F) of male and female Coq9+/+ and Coq9Q95X mice. n = 6 for each group.G-I CII+CIII activity in cerebrum (G), kidney (H) and skeletal muscle (I) of male and female Coq9+/+ and Coq9Q95X mice. n = 6 for each group."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "J-L Blue-native gel electrophoresis (BNGE) followed by immunoblotting analysis of mitochondrial supercomplexes from Coq9+/+ (n = 3) and Coq9Q95X mice (n = 4) at 3 months of age."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "A-D Measurement of phosphorylating respiration (represented as State 3o, in the presence of ADP and substrates) in kidney (A) and skeletal muscle (C) from male and female Coq9+/+, Coq9Q95X and Coq9R239X mice at 3 months of age. Representative O2 consumption graphic in kidney (B) and skeletal muscle (D) from female Coq9+/+, Coq9Q95X and Coq9R239X mice.Data information: All values are presented as mean ± SD. (A, C) *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001; Coq9Q95X and Coq9R239Xmice versus Coq9+/+mice. #P &lt; 0.05; Coq9Q95X versus Coq9R239Xmice. One-way ANOVA with a Tukey's post hoc test. Numbers above columns indicate P-values of the one-way ANOVA test (n = 3 for each group)."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "A-H Complex II (SDH) and complex IV (COX) histochemistry of triceps surae showing a decreased stain in 18-month-old Coq9Q95X female mice (D, H) in contrast to normal SDH and COX activity in 6- and 18-month-old Coq9+/+ (A, C, E, G), as well as 6-month-old Coq9Q95X female mice (B, F).I-L Gomori trichrome stain (TGM) of triceps surae showed no differences between 6- and 18-month-old Coq9+/+ and Coq9Q95X female mice.M-P Hematoxylin and eosin (H&amp;amp;amp;E) stains of triceps surae did not reveal any structural abnormality.Data information: Scale bars: 100 μm. n = 3 for each group. Complex IV, cytochrome c oxidase (COX); complex II, succinate dehydrogenase (SDH)."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "A-C Voluntary wheel running test. Distance traveled on the wheel and average speed during the use of the wheel were decreased in female Coq9Q95X mice at 6 months of age (B, C)."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "D Hanging wire test. Coq9Q95X female mice obtained less reaches score in the 'fall and reaches' method."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "E Open-field test. Coq9Q95X mice showed a reduction in the average distance traveled in Coq9Q95X female mice at 6 months of age."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "F Grip test: Muscle strength was not affected in Coq9Q95X mice at 6 months of age."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "A, B KidneyCoQ9 levels in Coq9+/+, Coq9Q95X and Coq9R239Xmice treated with 2,4-diHB (+2,4-diHB) compared with the non-treated littermate (vehicle). Statistical analysis was performed on +2,4-diHBCoq9+/+, Coq9Q95X and Coq9R239Xmice versus vehicle Coq9+/+, Coq9Q95X and Coq9R239Xmice, respectively (n = 3 for each group)."
NCBI gene IDs:
"Coq9: 67914"
Figure legend: "C, D CoQ10 levels in COQ9R244X skinfibroblasts treated with 2,4-diHB (+2,4-diHB, blue bars) compared with the non-treated controls (vehicle, yellow bars). Statistical analysis was performed on +2,4-diHBCOQ9R244X versus vehicle COQ9R244X (n = 4 for each group)."
NCBI gene IDs:
"COQ9: 67914"
Figure legend: "(B) Gal4 DNA-binding domain fusions of MUPs were tested with Gal4 activation domain fusions of ubiquilins (murine) in Y2H."
NCBI gene IDs:
"Gal4: "
Figure legend: "(C) HEK293 cells transfected with indicated MUP-V5, myc-UBQLN1 (human), or empty vector were immunoprecipitated (IP) with anti-myc or anti-UBQLN1 antibodies. Western blot (WB) of IP and lysate were probed as indicated."
NCBI gene IDs:
"UBQLN1: 29979"
Figure legend: "(B) Mtb were incubated with lysate from HEK293 cells transfected with vector control, myc-UBQLN1, GFP, or V5-parkin. WB analysis of the input (I), 5th wash (W5), and elution (E), probed with indicated antibodies. Actin is a loading control for the cell lysate and Ag85b for the bacterial pellet."
NCBI gene IDs:
"parkin: 5071
UBQLN1: 29979"
Figure legend: "(C) Mtb were incubated with lysate from HEK293 cells transfected with myc-UBQLN1-ΔUBA, myc-UBQLN1-ΔUBL, and myc-UBQLN1-UBA. WB containing the input, 5th wash, and elution were incubated with anti-myc antibody. The predicted sizes of myc-UBQLN1-ΔUBL, myc-UBQLN1-ΔUBA, and myc-UBQLN1-UBA are 55 kD, 50 kD, and 6 kD, respectively."
NCBI gene IDs:
"UBQLN1: 29979"
Figure legend: "(D) Mtb were incubated with recombinant GST-UBQLN1, GST-UBQLN1-ΔUBL, or GST-UBQLN1-ΔUBA. WB containing the input and elution was probed with an anti-GST antibody."
NCBI gene IDs:
"UBQLN1: 29979"
Figure legend: "(A) BMDMs were infected with GFP-expressing wt Mtb or ΔesxA for 24h and immunostained with UBQLN1 antibody. IFN-γ was added 1d prior to infection as indicated. (B) Quantification of results from A from 3 independent experiments with at least 100 bacteria analyzed per experiment; ***P&lt; 0.001, Fisher's exact test, comparing the proportion of UBQLN1 positive versus negative Mtb in indicated samples."
NCBI gene IDs:
"esxA: 886209"
Figure legend: "(D) BMDMs were transfected with siRNAs targeting UBQLN1 or a non-targeting control (siCON) and lysates were analyzed by WB using an antibody that recognizes UBQLN1 and UBQLN2. (C-D) Actin served as a loading control."
NCBI gene IDs:
"UBQLN1: 56085"
Figure legend: "(F) BMDMs were transfected with siRNAs targeting UBQLN1 or siCON and infected with live/dead Mtb strain. IFN-γ was added 1d prior to infection if indicated. %Viable bacteria were quantified 24 and 48 hpi. Data are from 2 independent experiments. *P&lt;0.05; ***P&lt;0.001, Fisher's exact test, comparing the proportion of viable and non-viable bacteria in indicated samples."
NCBI gene IDs:
"UBQLN1: 56085"
Figure legend: "(G) BMDMs were treated with the indicated siRNAs three days prior to infection and then activated with IFN-γ one day prior to infection with H37Rv or ΔesxA. CFU were enumerated 4 and 96 hpi. *P&lt; 0.05, unpaired Student's t-test. Data are representative of three independent experiments."
NCBI gene IDs:
"esxA: 886209"
Figure legend: "(H) BMDMs transfected with siRNA targeting UBQLN1 or siCON were infected with wt Mtb (H37Rv) and IFN-γ was measured by ELISA"
NCBI gene IDs:
"UBQLN1: 56085"
Figure legend: "(I) UBQLN1-silenced BMDMs and controls were infected with H37Rv or ΔesxA. (H-I) 24 hpi infected BMDMs were co-cultured with P25TCR-Tg CD4+ T cells, and IFN-γ was measured by ELISA. Data is representative of 3 independent experiments. *P&lt;0.05, **P&lt;0.005, unpaired Student's t-test. (B, F, Γ, H) Results are mean +/- SEM; ns, not significant."
NCBI gene IDs:
"esxA: 886209
UBQLN1: 56085"
Figure legend: "(C) Wt macrophages (Atg16L1flox/flox; Cre-) and autophagy-deficient macrophages (Atg16L1flox/flox Lyz-cre; Cre+) were activated with IFN-γ or not, followed by infection with the live/dead Mtb reporter strain. % viable was quantified after addition of AnTc. **P&lt;0.005, ***P&lt;0.0001, Fisher's exact test (in which the proportions of viable to non-viable Mtb was compared)."
NCBI gene IDs:
"Cre: 
Atg16L1: 77040
Lyz: 17110"
Figure legend: "(D) Atg16L1flox/flox Cre+ and Cre- BMDMs treated with IFN-γ and infected for 24h with GFP-Mtb were immunostained for UBQLN1 and p62. The number of Mtb co-localizating with the cellular markers is shown. (C-D) At least 100 bacteria were analyzed in three independent experiments."
NCBI gene IDs:
"Cre: 
Atg16L1: 77040"
Figure legend: "(A-C) BMDMs transfected with siRNA targeting UBQLN1 or control siRNA. Images show IFN-γ treated macrophages infected with GFP-Mtb (A-B) or DsRed-Mtb (C) for 24h. Cells were immunostained for ubiquitin (Ub) with the FK2 antibody (A) or p62 (B), which are shown in red. (C) GFP-LC3 BMDMs were infected with DsRed-Mtb. LC3 is shown in green, whereas Mtb are red. (A-C) Quantification shows the percentage of Mtb that colocalized with the indicated cellular marker in macrophages that were treated with IFN-γ as indicated. Results are mean +/- SEM from two independent experiments, with at least 100 bacteria analyzed per experiment. ***P&lt;0.001, Fisher's exact test (in which the proportion of Mtb associated with the cellular marker in a given condition was compared to the proportion found in the sample treated with siCON and IFN-γ)."
NCBI gene IDs:
"UBQLN1: 56085"
Figure legend: "(A) WT and Park2-/- BMDMs were pretreated with IFN-γ, infected with GFP-Mtb for 24h, and immunostained with the FK2 antibody. Bacterial colocalization with FK2 immunoreactivity was quantified from 2 independent experiments."
NCBI gene IDs:
"Park2: 50873"
Figure legend: "(B) Park2-/- BMDMs pretreated or not treated with IFN-γ were infected with GFP-Mtb for 24h and immunostained with UBQLN1 specific antibody; Arrows indicate Mtb co-localized with UBQLN1. ns- not significant."
NCBI gene IDs:
"Park2: 50873"
Figure legend: "(C) Park2-/- BMDMs were transfected with siRNA targeting UBQLN1 or control siRNA 3d prior to infection, treated with IFN-γ, and infected with GFP-Mtb for 24h prior to immunostaining for ubiquitin (FK2 antibody). Ubiquitin (FK2+) bacteria were quantified from two independent experiments. (A, C) **P&lt;0.01, Fisher's exact test (comparing the proportion of FK2 positive bacteria in indicated samples). Results are mean +/- SEM. A minimum of 100 Mtb were counted in each experiment."
NCBI gene IDs:
"Park2: 50873
UBQLN1: 56085"
Figure legend: "HeLa and cyclin F Knock-Out (CCNF K/O) cells were treated with Kinase ChemoGenomic Set (KSGS) in 384 well format. After 72 Hours (h) viability was measured using rezasurin. Flowchart representation (left). Robust Z-score difference is plotted for data acquired at 1 μM concentration (right)."
NCBI gene IDs:
"CCNF: 899
cyclin F: 899"
Figure legend: "Differences in viability of HeLa and CCNF K/O cells after treatment with specific Chk1i (LY2603618) at the indicated concentrations plotted on a log10 scale to measure differences in IC50."
NCBI gene IDs:
"CCNF: 899"
Figure legend: "Number of cells was measured in HeLa and CCNF K/O cells left untreated or treated with Chk1i (LY2603618) for 24h, 48h, or 72h as indicated. (n.s. = non-significant)."
NCBI gene IDs:
"CCNF: 899"
Figure legend: "Cell viability measurements using Propidium Iodide staining for HeLa and CCNF K/O cells after treatment with Chk1i (LY2603618)."
NCBI gene IDs:
"CCNF: 899"
Figure legend: "U-2-OS cells were seeded and transfected with non-targeting siRNA siNC (Negative Control) or siCyc F. 24 hours after transfection, cells were treated with UCN-01, or Chk1i (LY2603618) at indicated concentrations for 3 days before viability was measured."
NCBI gene IDs:
"Cyc F: 899"
Figure legend: "Cell viability measurements using Propidium Iodide staining in U-2-OS cells transfected with non-targeting siNC and siCyc F and treated with Chk1i (LY2603618) as indicated."
NCBI gene IDs:
"Cyc F: 899"
Figure legend: "Intensity of γ-H2AX measured as Relative Fluorescence Units (RFU) in early S phase cells treated with Chk1i. Mean intensity of γ-H2AX fluorescence was evaluated from EdU+ cells with 2N DAPI content. Intensity of γ-H2AX measured as Relative Fluorescence Units (RFU) in replicating cells treated with Chk1i. Mean intensity of γ-H2AX fluorescence was evaluated from EdU+. Overall, cell cycle profile of HeLa and CCNF K/O cells after Chk1i treatment. Cells with 2n DAPI staining but EdU- were gated as G1 cells; cells with &gt;2n but &lt;4n DAPI staining but EdU- were gated as EdU- S cells; cells with &gt;2n but &lt;4n DAPI staining but EdU+ were gated as EdU+ S phase; cells with 4n DAPI and pH3 S10 negative staining were gated as G2 phase and cells with 4n DAPI and pH3 S10 positive as M cells. Data from at least 3 independent replicates and plotted as Mean ± SD."
NCBI gene IDs:
"CCNF: 899"
Figure legend: "Representative plots of γ-H2AX vs RPA2 signal of HeLa and CCNF K/O cells after treatment with 1μM Chk1i (LY2603618) at the indicated hours (h). Blue labeled dots represent γ-H2AX positive cells. Relates to materials section for details on representation."
NCBI gene IDs:
"CCNF: 899"
Figure legend: "Representative plots of γ-H2AX intensity vs DAPI signal of CCNF K/O cells transfected with empty GFP and GFP-CCNF untreated (top panels) and after treatment with 1μM Chk1i (LY2603618) for 20h (bottom panels). Normalised γ-H2AX intensity in CCNF K/O cells transfected with either GFP empty vector or GFP-Cyc F and treated with 1μM Chk1i for 20 hours. GFP positive cells were gated. Data from 3 independent experiments were plotted with Mean % ± SD."
NCBI gene IDs:
"GFP: 
CCNF: 899
Cyc F: 899"
Figure legend: "Representative images of neutral and alkaline comet assay from HeLa and CCNF K/O cells treated with Chk1i. Cells were treated with 1μM Chk1i for 24h before being harvested for neutral and alkaline comet assays as indicated. Quantification of comets in alkaline gels. At least 100 cells, across two slides, were analysed in each condition in two biological replicates. Data are shown as medians, with 25/75% percentile range (box) and 10-90% percentile range (whiskers). Fold changes of median values are shown in bold. p-values were calculated using the Mann-Whitney test (two-tailed). Olive tail moment = (Tail.mean - Head.mean)*Tail%DNA/100. Quantification of comets in neutral gels. At least 100 cells, across two slides, were analysed in each condition in two biological replicates. Data are shown as medians, with 25/75% percentile range (box) and 10-90% percentile range (whiskers). Fold changes of median values are shown in bold. p-values were calculated using the Mann-Whitney test (two-tailed). Olive tail moment = (Tail.mean - Head.mean)*Tail%DNA/100."
NCBI gene IDs:
"CCNF: 899"
Figure legend: "Percentage (%) of γ-H2AX positive cells in HeLa and CCNF K/O after transfection of the indicated siRNAs treated with Chk1i for 20 hours. Percent of γ-H2Ax positive cells were plotted as Mean % ± SD. Percentage (%) of hyper-RPA positive cells in HeLa and CCNF K/O after transfection of the indicated siRNAs treated with Chk1i for 20 hours. Percent of hyper RPA positive cells were plotted as Mean % ± SD."
NCBI gene IDs:
"CCNF: 899"
Figure legend: "Relative γ-H2AX intensity in cells transfected with either Empty Vector (EV) or HA-E2F1 treated with Chk1i for 20 hours. γ-H2AX fluorescence in HA positive cells was normalized to the empty vector transfected cells and compared to cells not expressing HA."
NCBI gene IDs:
"E2F1: 
HA: "
Figure legend: "HeLa and CCNF K/O cells transfected with the indicated siRNA and treated with 1μM Chk1i (LY2603618) for 20 hours were harvested and lysed using SDS. Indicated protein were resolved by SDS page and detected by WB. TFIIH served as a loading control."
NCBI gene IDs:
"CCNF: 899"