EMBO/SourceData huggingface dataset:
Figure legend: "p16-3MR  mice were treated with vehicle (PBS, 7 consecutive days), doxorubicin (5 mg/kg, 3 consecutive days) or abemaciclib (50 mg/kg, 7 consecutive days). n=6 mice/group. RNA isolated from  kidneys and mRNA encoding p16 quantified by qRT-PCR (C). SA-β-gal activities in vehicle-, doxorubicin- or  abemaciclib-treated mouse kidney sections at 15 dpt quantified (E). Data information: Data are means ±SD. One-way ANOVA *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, N.S.=not significant."
NCBI gene IDs:
"p16: 12578"
Figure legend: "(G) RNA was isolated from abemaciclib ±  pifithrin-α  treated  kidneys  and mRNA encoding p16  and p21 genes was quantified by qRT-PCR and normalized on tubulin (n=5 mice/group). Data information: Data are means ±SD. Two-way ANOVA *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, N.S.=not significant."
NCBI gene IDs:
"p16: 12578
p21: 67676
tubulin: 22142"
Figure legend: "(B) BJ cells transduced with a NF-κB reporter were treated with vehicle, doxorubicin, paclitaxel (50 nM for 24 hours),  palbociclib  (1 μM for 8 times 24 hours) or abemaciclib and luciferase activity measured 8 dpt.  TNFα treatment was used as positive control (n=3 independent experiments). Data information: Data are means ±SD. One-way ANOVA *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, N.S.= Not significant."
NCBI gene IDs:
"NF-κB: 4791///4790"
Figure legend: "p16-3MR mice were treated with vehicle (PBS, 7 consecutive days), doxorubicin (5 mg/kg, 3 consecutive days) or  abemaciclib (50 mg/kg, 7 consecutive days). RNA isolated from kidneys and mRNA encoding indicated NF-κB  associated genes (J) quantified by qRT-PCR. n=6 mice/group. Data information: Data are means ±SD. Two-way ANOVA *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, N.S.= Not significant."
NCBI gene IDs:
"p16: 12578"
Figure legend: "p16-3MR  mice were treated with vehicle (PBS, 7 consecutive days), doxorubicin (5 mg/kg, 3 consecutive days) or abemaciclib (50 mg/kg, 7 consecutive days). From a subset of the mice, RFP+ cells were sorted from the  renal cortex using  FACS and mRNA encoding indicated NF-κB associated pro-inflammatory genes quantified by qRT-PCR. The values of fold change over vehicle were plotted in the heatmap. n=4 mice/group (K)."
NCBI gene IDs:
"p16: 12578"
Figure legend: "(B)  Human BJ fibroblasts,  hTERT-RPE1 epithelial cells  and lung mesenchymal stem cells were treated with vehicle (DMSO for 8 times 24 hours) or doxorubicin (250 nM for 24 hours) or paclitaxel (50 nM for 24 hours) or palbociclib (1 μM for 8 times 24 hours) or abemaciclib  (1 μM for 8 times 24 hours). At 8 dpt, RNA was isolated and mRNA for the indicated  p53-associated SASP genes quantified by qRT-PCR relative to  tubulin (n=3 independent experiments). Data information: Data are means ±SD. Two-way ANOVA *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001."
NCBI gene IDs:
"p53: 7157
tubulin: 7846"
Figure legend: "(D and E) RNA was isolated from vehicle, abemaciclib (1 μM) (D) or palbociclib (1 μM) (E) treated scramble/shp53 BJ cells and quantified by qRT-PCR for  IGFBP3 or LIF genes (n=3 independent experiments). Data information: Data are means ±SD. Two-way ANOVA *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001."
NCBI gene IDs:
"IGFBP3: 3486
LIF: 3976
p53: 7157"
Figure legend: "(F) RNA isolated from  kidneys treated with  doxorubicin or abemaciclib and mRNA encoding indicated  p53-associated SASP genes quantified by qRT-PCR (n=6 mice/group). (G) RNA was isolated from kidneys of  p16-3MR mice treated with abemaciclib (50 mg/kg, 7 consecutive days) ± pifithrin-α (2 mg/kg, 7 consecutive days), and mRNA encoding  p53 associated SASP genes was quantified by qRT-PCR and normalized on  tubulin (n=5  mice/group). ( Data information: Data are means ±SD. Two-way ANOVA *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001."
NCBI gene IDs:
"p16: 12578
p53: 22059
tubulin: 22142"
Figure legend: "(I) RNA was isolated from vehicle or nutlin-3a (1 μM for 8 times 24 hours) treated BJ  cells at 8 dpt and quantified by qRT-PCR for p53 target cell cycle genes, SASP genes (n=3 independent experiments). Data information: Data are means ±SD. Two-way ANOVA *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001."
NCBI gene IDs:
"p53: 7157"
Figure legend: "(J)  Mouse dermal fibroblasts  (MDF) or MDF-p53-/- fibroblasts were transfected with empty vector (EV) or p53-overexpressing vector (p53OE), then the cells were treated with vehicle (water) or doxorubicin (250 nM for 24 hours) and qRT-PCR  was performed for Igfbp3  and Lif  genes (n=3 independent experiments). Data information: Data are means ±SD. Two-way ANOVA *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001. EV, empty vector"
NCBI gene IDs:
"Igfbp3: 16009
Lif: 16878
p53: 22059"
Figure legend: "(H and I) 2*105 cells of vehicle-treated (water for 8 times 24 hours) mouse dermal fibroblasts  (MDF) were injected into the  left flank  of the p16-3MR  mice. Doxorubicin-induced (250 nM for 24 hours) (H) or abemaciclib-induced (4 μM for 8 times 24 hours) (I) MDFs were injected into the  right  flank  of the same animal. 7 dpt, the above-mentioned mice  were injected with coelenterazine and bioluminescence from the p16-3MR  mouse was visualized/quantified by the IVIS spectrum in vivo imaging system and quantified. Lower panel, scheme of experimental design (n=4 mice/group). Data information: Data are means ±SD. Paired student t-test *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, N.S.=not significant."
NCBI gene IDs:
"p16: 12578"
Figure legend: "A ATX gene expression from publicly available datasets in NASH patients (n=9) compared to healthy controls (n=7) (*P &lt; 0.05); cirrhosis patients (n=40) compared to healthy controls (n=19) (***P &lt; 0.001). Bars represent the mean ± SEM, statistical analysis was performed by two-tailed student's t-test. *P &lt; 0.05, ***P &lt; 0.001 denotes significance versus respective healthy controls."
NCBI gene IDs:
"ATX: 5168"
Figure legend: "B Relative ATX gene expression in the MCD-diet-fed (n=9) compared to control mice  (n=9) (***P &lt; 0.001); CCl4  (n=8) compared to control mice  (n=5) (*P &lt; 0.05). Bars represent the mean ± SEM, statistical analysis was performed by two-tailed student's t-test. *P &lt; 0.05, ***P &lt; 0.001 denotes significance versus respective healthy controls."
NCBI gene IDs:
"ATX: 18606"
Figure legend: "C Relative gene expression (normalized with GAPDH) for CCL2   and iNOS  in control (M0) and LPS- and IFNγ-induced M1 RAW 264.7 macrophages  treated with medium alone, PF8380  (1μM) or Cpd17  (1μM). Bars represent the mean + SEM, n=4. Statistical analysis was performed by one-way analysis of variance (ANOVA) with Bonferroni post-hoc test. ####P &lt; 0.0001 denotes significance versus M0 (non-stimulated macrophages) and *P &lt; 0.05, **P &lt; 0.01 denotes significance versus vehicle (LPS- and IFNγ-induced  M1 macrophages); ns=non-significant."
NCBI gene IDs:
"CCL2: 20296
GAPDH: 14433
iNOS: 106736473"
Figure legend: "D Relative gene expression (normalized with 18s RNA) for CCL2  and iNOS  in control (M0) and LPS-induced PMA-differentiated human THP1 macrophages  treated with medium alone, PF8380  (1μM) or Cpd17  (1μM). Bars represent the mean + SEM, n=4. Statistical analysis was performed by one-way analysis of variance (ANOVA) with Bonferroni post-hoc test. ##P &lt; 0.01, ###P &lt; 0.001 denotes significance versus M0 (non-stimulated macrophages) and **P &lt; 0.01, ***P &lt; 0.001 denotes significance versus vehicle (LPS- and IFNγ-induced M1 macrophages); ns=non-significant."
NCBI gene IDs:
"18s RNA: 
CCL2: 6347
iNOS: 111365141"
Figure legend: "B Relative Collagen I, α-SMA and PDGFβR gene expression (normalized with GAPDH) in control and TGFβ-activated LX2  cells with or without PF8380  (1μM) or Cpd17  (1μM). Bars represent the mean + SEM, n=3. Statistical analysis was performed by two-tailed student's t-test. #P &lt; 0.05, ###P &lt; 0.001 denotes significance versus control (non-TGFβ  cells) and **P &lt; 0.01 denotes significance versus vehicle (TGFβ-activated cells); ns=non-significant."
NCBI gene IDs:
"α-SMA: 59
Collagen I: 1277///1278
GAPDH: 2597
PDGFβR: 5159"
Figure legend: "(A) Tamoxifen schedule: pulse of the pregnant dam at E9.5, harvest at E10.5. Representative fluorescent immune-staining of E10.5 Sox7iECKO mutants and sibling control embryos. The endothelium is delineated by endomucin (EMCN) (blue) and endothelial cells by ETS-related gene (ERG) (red), SOX7 positive cells are shown in white. (Top right graph) The percentage of SOX7 positive endothelial cells in different vascular beds, quantified from 10 sequential transverse sections in 2 control and 3 Sox7iECKO mutants. (Bottom right panel) Graph indicating the levels of Sox7 transcript in sibling controls and Sox7iECKO mutants. Mean ± SEM; scored sibling control, n=9; Sox7iECKO mutants, n=7; Mann-Whitney U-test. P&lt;0.0005 (***)."
NCBI gene IDs:
"Sox7: 20680"
Figure legend: "(C) Brightfield images and whole-mount immunostaining of Sox7iECKO mutant and sibling control skin at E13.5, after Cre induction at E9.5 and E10.5. Dermal lymphatic structures are marked by Neuropilin 2 (NRP2) (membranous white), lymphatic endothelial cells by Prospero-related homeobox 1 (PROX1) (red), and blood vessels by EMCN (green). Dash line represents the midline of the embryo. Scored sibling controls, n=7; Sox7iECKO mutants, n=7"
NCBI gene IDs:
"Cre: 2777477
Sox7: 20680"
Figure legend: "(D-H) Quantification of (D) Distance of the lymphatic vessel front from the midline (μm) (E) lymphatic branch points/area (F) lymphatic vessel width (μm) (G) PROX1+ nuclei/area and (H) PROX1+ nuclei/lymphatic vessels across the whole skin. Total area = 4200 x 1500 μm on both sides of the midline, in sibling controls (n=3) and Sox7iECKO mutants (n=5-6). (F,H) Average of width and PROX1+ nuclei was obtained from 7 random representative leading lymphatic vessels, of fixed length at 200 μm, from both sides of the midline in each skin. (I,J) Quantification of (I) PROX1+ nuclei in each LEC cluster with each colour dot representing a different embryo and (J) disconnected lymphatic endothelial cell (LEC) clusters (&lt;100 μm) and vessel branches (&gt;100μm)/area. Total area quantified = 4200 x 2200 μm on both side of midline in sibling controls (n=3) and Sox7iECKO mutants (n=5). PROX1+ nuclei were quantified from n=29 and n=122 LEC clusters, respectively."
NCBI gene IDs:
"Sox7: 20680"
Figure legend: "(C) Arterial endothelial cells express Vegfc transcripts. Transverse section of a E10.5 wild-type embryo stained by single molecule FISH (smFISH) for Gapdh (green) and Vegfc (magenta) and immuno-stained for PECAM (white). The first panel shows a merged version of the pseudo colour signals for the 3 markers. Inset 1 shows the expression of Vegfc in endothelial cell of the dorsal aorta (black and white, pink arrows). Inset 2 shows the high expression levels of mesenchymal Vegfc expressed in the dorso-lateral aspects of the cardinal vein."
NCBI gene IDs:
"Gapdh: 14433
Vegfc: 22341"
Figure legend: "(E-F) qPCR on human arterial endothelial cells (HUAECs) transfected with SiSOX7 or SiCTRL for (E) 30 h and (F) 17 h. (G) qPCR on human venous endothelial cells (HUVECS) transfected with SiSOX7 or SiCTRL for 17 h. D"
NCBI gene IDs:
"SOX7: 83595"
Figure legend: "(A-D) SOX7 transcriptionally activates Notch effector, HEY1, to repress Vegfc. (A) qPCR on FAC-sorted PECAM+CD45-endothelial cells of Sox7iECKO mutants and sibling controls at E14.5 after Cre induction with tamoxifen at E11.5 and E12.5. Expression is normalised to the endothelial marker Pecam and Cdh5. Scored sibling controls, n=9; Sox7iECKO mutants, n=8. (B-C) qPCR on (B) human arterial endothelial cells (HUAECs) and (C) human venous endothelial cells (HUVECs) transfected with SiSOX7 or SiCTRL for 17 h. In addition to HEY1, DLL4 levels were also downregulated in the human cell line experiments. Expression is relative to HPRT and GAPDH. Data from one siRNA experiment performed in triplicates. (D) HEY1 represses human VEGFC promoter activity. HeLa cells were co-transfected with human or mouse VEGFC-luc and either EV (empty vector) or HEY1 expression constructs as indicated. VEGFC luciferase activity was measured and normalised to Renillla luciferase activity, which was then made relative to the promoter-less vector, pGL3-basic, which was set to 1. Biological replicates, n=3 independent repeats of the same experiment. Mean ± SEM; t-test. P&lt;0.05 (*); P&lt;0.005 (**); P&lt;0.0005 (***)."
NCBI gene IDs:
"HEY1: 
luc: 
Cdh5: 12562
Cre: 2777477
DLL4: 54567
GAPDH: 2597
HEY1: 15213
HEY1: 23462
HPRT: 3251
Pecam: 18613
SOX7: 20680
Sox7: 20680
SOX7: 83595
Vegfc: 22341
VEGFC: 7424
VEGFC: 22341"
Figure legend: "SOX7 physically interacts with transcription repressor, HEY1. (G) Co-immnuno-precipitation analysis of SOX7 and HEY1. HEK293 cells were transfected with indicated plasmids and harvested 24 h after transfection, immunoprecipitated by anti-GFP or Ig control before immunoblot analysis to determine the presence of bait/prey (top) and the input (bottom). N=2."
NCBI gene IDs:
"HEY1: 23462
SOX7: 83595"
Figure legend: "(A) SOX7 represses human VEGFC promoter activity. HeLa cells were co-transfected with human or mouse VEGFC-luc, EV (empty vector), or SOX7 expression constructs as indicated. VEGFC luciferase activity was measured and normalised to Renillla luciferase activity, which was then made relative to the promoter-less vector, pGL3-basic, which was set to 1. Biological replicates, n=3. Mean ± SEM; t-test. P&lt;0.05 (*)."
NCBI gene IDs:
"luc: 
SOX7: 
SOX7: 83595
VEGFC: 7424
VEGFC: 22341"
Figure legend: "(G) Quantitation of Vegfc transcript using single molecule FISH in vivo. (colored panel) Representative low magnification images of the trunk transverse sections of E10.5 sibling controls and Sox7iECKO mutants showing the similar relative position of the DA and the CV across genotypes. Sections were stained by single molecule FISH (smFISH) for Gapdh (green) and Vegfc (magenta) and immuno-stained for PECAM (white). Individual molecules of Vegfc transcript (pink arrows) are detectable within the cytoplasm of PECAM positive cells of the dorsal aorta (Middle panel). (Left graph) Quantitation of Vegfc transcript level in the PECAM positive endothelial cells of the dorsal aorta, in sibling controls and Sox7iECKO mutants at E10.5. The mean grey scale intensity of the Vegfc probes in control was 5845. ­­­­­­­­­The mean grey scale intensity of the Vegfc probes in Sox7iECKO was 8956. Mean probe intensity was significantly higher in Sox7iECKO compared to the control (P&lt;2e-16). (Right graph) No differences were observed for the average probe area, meaning that distribution of the probes across the dorsal aorta remained unchanged between control and Sox7iECKO. Scored sibling controls, n=5; Sox7iECKO mutants, n=7. Mean ± SEM; t-test. P&lt;0.0005 (***), Graph: box, interquartile range, central band, median, whiskers, indicate maximum and minimum. Scale bars; low magnification 150 μm, high magnification, 30 μm"
NCBI gene IDs:
"Gapdh: 14433
Sox7: 20680
Vegfc: 22341"
Figure legend: "(A) At 2 days post Cre induction, E11.5 Sox7iECKO mutants showed ectopic expression of PROX1+ (red) in medial ventral regions of the cardinal veins (CVs), close to dorsal aorta (DA) (yellow arrowheads)."
NCBI gene IDs:
"Cre: 2777477"
Figure legend: "(D) Whole-mount immunostaining of control and Sox7iECKO embryonic skin at E12.5 after Cre induction at E9.5, E10.5. Dermal lymphatic structures are stained with NRP2 (membranous white), lymphatic endothelial cells, PROX1 (red), and blood vessels, both EMCN (green) and SOX7 (white nuclei). Arrowheads indicate EMCNlow/-PROX1+NRP2+/low individual LECs on blood vessels (type I), and arrow shows EMCN+PROX1+ NRP2low/- LEC within the vessel wall (type II). (E) Graph shows the total events of PROX1+ single LECs or LEC clusters cells associated with EMCN+ blood vessel plexus within each embryo. PROX1+ cells were quantified from n=4 controls and n=5 Sox7iECKO mutants."
NCBI gene IDs:
"Cre: 2777477
Sox7: 20680"
Figure legend: "(a-c) HeLa cells transfected with ARL8B or KIF2 siRNA, or with ARL8B overexpression construct (non-targeting siRNA and empty pcDNA vector used as transfection controls), were either left untreated, serum/amino-acid starved for 5 h, or starved and then recovered in amino-acid- and FBS-containing medium for 30 min. Cells were immunostained using LAMP1 antibody (a) and the percentage of cells with predominantly peripheral localization of LAMP1-positive vesicles was quantified (b) or subjected to immunoblotting (c) using antibodies as shown. Quantification of phospho-S6K levels relative to the total S6K is shown in (c). Values are means ± s.e.m. of three independent experiments carried out in triplicate. All comparisons are with the control within each treatment condition, *P0.05, **P0.01, ***P0.005 Student's t-test; n.s. not significant. Uncropped images of blots are shown in Supplementary Fig. S7."
NCBI gene IDs:
"ARL8B: 55207
KIF2: 11004///84643///3796"
Figure legend: "(e) Changes in lysosomal localization have no effect on pHi. ARL8B and KIF2 were overexpressed or knocked down in HeLa cells followed by pHi measurement."
NCBI gene IDs:
"ARL8B: 55207
KIF2: 11004///84643///3796"
Figure legend: "(c) ARL8B knockdown increases autophagosomal synthesis. siRNA-transfected HeLa cells were incubated for 48 h, then left untreated or incubated with bafilomycin A1. LC3-II levels versus actin were quantified (bottom graphs). Asterisk: nonspecific band."
NCBI gene IDs:
"ARL8B: 55207"
Figure legend: "(d) ARL8B overexpression inhibits autophagosome synthesis and degradation. HeLa cells overexpressing ARL8B or empty vector were analysed as in (c)."
NCBI gene IDs:
"ARL8B: 55207"
Figure legend: "(e) HeLa cells were co-transfected with either ARL8B overexpression construct or siRNA (non-targeting siRNA and empty peGFP vector were transfection controls) together with mCherry-LC3 for 48 h. After fixation, cells were stained for endogenous LAMP1 and DNA (DAPI). Representative maximum-intensity projections of serial confocal optical sections are shown. Co-localization panels show overlapping mCherry-LC3 and LAMP1 signals. (f-h) Quantification of autophagosome-lysosome fusion in HeLa cells. Percentages of autolysosomes (positive for both mCherry-LC3 and LAMP1) to autophagosomes (positive for mCherry-LC3 and negative for LAMP1) were quantified. In (h), we analysed cells treated for 2 h with nocodazole before fixation, which dispersed the perinuclear lysosomal cluster (see Fig. 2a). (i) Autophagosomal and autolysosomal numbers in tfLC3-expressing cells after ARL8B overexpression and knockdown (Supplementary Fig. S5o shows representative cells.). In (f-i) we analysed 20 cells per group in three independent experiments. Values are means ± s.e.m of three independent experiments carried out in triplicate. *P0.05, **P0.01, ***P0.005 Student's t-test; other comparisons not significant (n.s.). Uncropped images of blots are shown in Supplementary Fig. S7."
NCBI gene IDs:
"ARL8B: 55207"
Figure legend: "A. Steady state protein levels in wild-type (WT) and Tim50-depleted mitochondria visualized by Western blotting and immunodetection with indicated antisera."
NCBI gene IDs:
"Tim50: 856042"
Figure legend: "B. Jac1488 was imported into wild-type (WT) and Tim50-depleted mitochondria for indicated times and samples were treated with Proteinase K. p, precursor"
NCBI gene IDs:
"Tim50: 856042"
Figure legend: "C. Quantification of Jac1488 import into wild-type (WT) and Tim50-depleted mitochondria. The amount of imported protease-protected protein in WT mitochondria at 15 min was set to 100%; error bars indicate SEM (n=3)."
NCBI gene IDs:
"Tim50: 856042"
Figure legend: "D. [35S]Jac1 was imported into wild-type (WT) and Tim50-depleted mitochondria for indicated times and samples were treated with Proteinase K. p, precursor; m, mature."
NCBI gene IDs:
"Tim50: 856042"
Figure legend: "E. Quantification of [35S]Jac1 import into wild-type (WT) and Tim50-depleted mitochondria. The amount of imported protease-protected protein in WT mitochondria at 15 min was set to 100%; error bars indicate SEM (n=3)."
NCBI gene IDs:
"Tim50: 856042"
Figure legend: "F. Steady state protein levels in wild-type (WT) and tim44-804 mitochondria visualized by Western blotting and immunodetection with indicated antisera."
NCBI gene IDs:
"tim44: 854790"
Figure legend: "G. pAmJac1680 was imported into wild-type (WT) and Tim50-depleted mitochondria for indicated times and samples treated with proteinase K. Samples were analyzed in 96-well format and by SDS-PAGE. The amount of imported protease-protected protein in WT mitochondria at 15 min was set to 100%; error bars indicate SEM (n=5 for 96-well plate analysis, n=4 for SDS-PAGE)."
NCBI gene IDs:
"Tim50: 856042"
Figure legend: "G. Atp5488 (left panel) or [35S]Atp5 (right panel) were imported into wild-type and atp21∆ mitochondria for indicated times and in the presence or absence of a membrane potential (∆ψ). After proteinase K treatment, samples were solubilized in digitonin buffer and separated by BN-PAGE. Aliquots of the samples was analyzed by SDS-PAGE (lower panels). Subsequently proteins were visualized by fluorescence scanning or digital autoradiography. Complex V dimer, (CVD) and monomer (CVM). Prec., purified precursor ; p, precursor; m, mature protein."
NCBI gene IDs:
"atp21: 851922"
Figure legend: "A) Ten-fold serial dilutions from overnight cultures of wild-type and cdc14-1 cells dropped and grown on solid rich media or media containing MMS at 25, 28, 30 or 33ºC. Note that cdc14-1 cells exhibit growth sensitivity to MMS at 28ºC and 30ºC compared to wild-type cells."
NCBI gene IDs:
"cdc14: 850585"
Figure legend: "B) Ten-fold serial dilution from mid-log phase cultures of wild-type and cdc14-1 cells grown on solid rich media or media containing mock DMSO (as non-treated control), 4NQO, HU, phleomycin and benomyl at 30ºC. Note that cdc14-1 cells present a market sensitivity to all DNA damaged agents tested."
NCBI gene IDs:
"cdc14: 850585"
Figure legend: "C) Left panel: Schematic representation showing relevant genomic structure of the strain used to assess intra-chromosomal repair. The location of a MAT specific probe and the restriction endonuclease cleavage sites used for Southern blot analysis to detect repair product formation are indicated. Arrow depicts the localization of the double-strand break. Right panel: Physical analysis of intra-chromosomal repair in wild-type and cdc14-1 cultures at the semipermisive temperature. After DSB formation by the expression of the HO, glucose was added to repress it, thus allowing repair with HM donor sequences. Genomic DNA was digested with StyI, separated on agarose gel and blotted. Blots were hybridized with a probe corresponding to the MATa-distal sequence. A second probe for the actin gene was used to control the amount of genomic DNA loaded at each time-point. Immunoblot analysis of Rad53 during mating type switching experiments is shown. Coomassie blue staining is depicted as loading control. Graphs show quantification of gene conversion (GC) leading to the re-establishment of MATa or switching to MAT and DSB formation. The data was normalized with the actin loading control. Graphs show the mean ± S.D. from three independent experiments. Replicates were averaged and statistical significance of differences assessed by a 2-tailed unpaired Student t test."
NCBI gene IDs:
"MATa: 
actin: 
MAT: 
cdc14: 850585"