EMBO/SourceData huggingface dataset:
Figure legend: "(D) BDR2637 (Pveg-mCherry) (WT, purple) and ET261 (∆yueB, PsigX-sigX-gfp) (cyan) cells were mixed, infected with SPP1 at 5:1 (phages:bacteria) MOI, placed on an agarose pad and followed by time lapse fluorescence microscopy. Shown are overlay images from mCherry (purple), SigX-GFP (cyan), and phase contrast (grey), captured at the indicated time points post infection. Scale bar 1 μm."
NCBI gene IDs:
"gfp: 
mCherry: 
sigX: 938966
veg: 936744
yueB: 936567"
Figure legend: "(B) ET29 (Pveg-mCherry, PIPTG-sigX) (purple) cells were grown in the presence of IPTG and mixed with PY79 (WT) cells. The mixture was infected with SPP1-lysin-yfp 5:1 (phages:bacteria) MOI, placed on an IPTG-containing agarose pad, and followed by time lapse fluorescence microscopy. Shown are overlay images of phase contrast (grey), signal from mCherry labeled cells (purple), and signal from Lysin-SPP1-YFP (cyan), captured at the indicated time points post infection (upper panels). Corresponding signal from Lysin-SPP1-YFP (cyan) is shown separately (lower panels). Arrows highlight the delayed infection of ET29 cells. Scale bar 1 μm."
NCBI gene IDs:
"mCherry: 
yfp: 
YFP: 
sigX: 938966
veg: 936744"
Figure legend: "(E) OF83 (Ppen-lacIΔ11-cfp) (WT) and ET40 (Ppen-lacIΔ11-cfp, PIPTG-sigX) cells, grown in the presence or absence of IPTG, were infected with SPP1-delX110lacO64 at 5:1 (phages:bacteria) MOI. The formation of LacI-CFP foci on phage DNA was monitored 10 min post infection. Non-infected OF83 cells were used for comparison. Shown are overlay images of phase contrast (grey) and signal from LacI-CFP (cyan). Scale bar 1 µm. (F) Quantification of the experiment described in (E). Shown is the percentage of LacI-CFP foci 10 min post infection of OF83 and ET40 cells by SPP1, with average values and SD (n ≥ 850 cells for each population)."
NCBI gene IDs:
"cfp: 
CFP: 
delX: 
pen: 
lacI: 59687637
LacI: 59687637
sigX: 938966"
Figure legend: "(A) ET28 (PIPTG-sigX) and ET42 (∆dltA, PIPTG-sigX) cells, grown in the presence or absence of IPTG, were infected with SPP1 at 1:20 (phages:bacteria) MOI, and OD600nm was followed at 2 min intervals. Shown is a representative experiment out of 6 biological repeats, with the average values and SD of 8 technical repeats."
NCBI gene IDs:
"dltA: 937358
sigX: 938966"
Figure legend: "(D) PY79 (WT) and ET41 (ΔdltA) cells were infected with SPP1 (10-6 PFU/ml), spred over an MB agar plate, and plaque diameter was monitored after 20 hrs of incubation. Shown is plaque diameter distributions for each strain (n ≥ 40)."
NCBI gene IDs:
"dltA: 937358"
Figure legend: "(F) AR16 (PrrnE-gfp) (WT, cyan) and ET411 (Pveg-mCherry, ∆dltA) (∆dltA, purple) cells were mixed, infected with low concentrations (10-8 PFU/ml) of SPP1, placed on an agarose pad, and plaque formation was followed by time lapse confocal microscopy. Shown are overlay images from GFP (cyan) and mCherry (purple) signals of the bacterial lawn captured at the indicated time points (hrs). The plaque is seen as a hole formed on the bacterial lawn. Scale bar 150 µm."
NCBI gene IDs:
"gfp: 
mCherry: 
dltA: 937358
rrnE: 8303206
veg: 936744"
Figure legend: "H1975 cells were treated with 50 μg/ml PM2.5 for 90 days, and the expression levels of TMPRSS2 mRNA were determined by real-time RT‒PCR (A) respectively. (A) p values were determined by one-sample t-test."
NCBI gene IDs:
"TMPRSS2: 7113"
Figure legend: "H1975 cells were infected with sh-TMPRSS2 (sh-TMPRSS2-1 and sh-TMPRSS2-2) or empty vector (Vector). The stable clones of TMPRSS2 knockdown cells were analyzed and their ability to perform anchorage-independent growth in soft agar (C). The data shown in (C) represent the means ± SDs from three independent experiments. (C) p values were determined by one-sample t-test."
NCBI gene IDs:
"TMPRSS2: 50528"
Figure legend: "A-C H1299 cells were transfected with TMPRSS2-HA or the empty vector (Vector). After 48 h, the transfected cells were assayed for the expression of TMPRSS2 (A) and for the induction of IL18 by qRT‒PCR (B) and Western blotting (C). The results shown in (A, C are from one of three similar experiments. β-actin was used as the loading control."
NCBI gene IDs:
"HA: 
IL18: 3606
TMPRSS2: 7113"
Figure legend: "(E) Tadpoles at NF50 were amputated, fixed at the indicated time and then processed for whole mount in situ hybridisation using a probe specific for foxm1. The two last panels show transverse section in the non-regenerating spinal cord (nr) and the regenerate at 3dpa. The red circle highlights the spinal cord and the asterisk the notochord."
NCBI gene IDs:
"foxm1: 100492241"
Figure legend: "(F) Total RNA was isolated from regenerating tails at indicated time points post amputation, reversed transcribed into cDNA and analysed for foxm1 expression by qPCR, using ef1α as a reference gene. The graph represents the mean +/- SD of three independent experiments. One-way ANOVA with Dunnett's multiple comparisons test was used. * p=0.0149"
NCBI gene IDs:
"ef1α: 549446
foxm1: 100492241"
Figure legend: "(A) NF40 tadpoles with the following genotypes foxm1-/- (mut), foxm1+/- (het) and foxm1+/+ (wt) were amputated and left to regenerate for 7 days. The images show representative tails at 3 and 7 dpa. The white arrowheads indicate the amputation site. (B) Quantification of the rate of regeneration. The ratio of the length of the regenerate to the length that has originally be amputated was compared for the whole tail at 3 and 7 dpa. The graph represents the mean+/-SD of 5 independent experiments from 3 different clutches with at least 5 tadpoles in each experiment. "
NCBI gene IDs:
"foxm1: 100492241"
Figure legend: "(A) Endogenous FAM134B forms oligomers. FAM134B knockout (KO) or wild type (WT) 293T cells were treated with 1μM of Thapsigargin (Tg) for different time and the cell lysates were prepared and analyzed by Western-blot."
NCBI gene IDs:
"FAM134B: 54463"
Figure legend: "(E, F) Measurement of the intracellular ER-scission activity. U2OS cells transiently expressing EGFP-FAM134B (WT), EGFP-FAM134B (84-233) or EGFP-FAM134B (Δ84-233) at same levels, lysosomal degradation of EGFP-FAM134B was blocked by Bafilomycin A1 (Baf A1) or DMSO. GFP-positive puncta were quantified for each cell in (F). For Each group, at least 30 cells were counted. Scale bars, 10 μm. ***P&lt;0.001, &quot;ns&quot; means no significance, one-way ANOVA, error bars indicate SEM."
NCBI gene IDs:
"EGFP: 
FAM134B: 54463"
Figure legend: "(G, H) Measurement of the ER-phagy activity. U2OS cells transiently expressing mCherry-EGFP-FAM134B (WT), mCherry-EGFP-FAM134B (84-233) or mCherry-EGFP-FAM134B (Δ84-233) at same levels. ER-phagy is indicated by mCherry-positive but EGFP-negative puncta were quantified for each cell in (H). For mCherry-EGFP-FAM134B (WT), 50 cells were counted (n=50); for mCherry-EGFP-FAM134B (84-233), n=56; for mCherry-EGFP-FAM134B (Δ84-233), n=66. Scale bars, 10 μm. The scale bars in the magnification boxes are 2μm. ***P&lt;0.001, one-way ANOVA, error bars indicate SEM."
NCBI gene IDs:
"EGFP: 
mCherry: 
FAM134B: 54463"
Figure legend: "(I) Lysosomal cleavage of GFP was analyzed by Western blot for the cells co-expressing GFP-SEC61B and FAM134B WT-Flag, FAM134B (84-233)-Flag or FAM134B (Δ84-233)-Flag."
NCBI gene IDs:
"Flag: 
GFP: 
FAM134B: 54463
SEC61B: 10952"
Figure legend: "(B) Comparison of the self-interaction of FAM134B mono-phosphorylation mutants using co-IP."
NCBI gene IDs:
"FAM134B: 54463"
Figure legend: "(C) Comparison of the self-interaction of FAM134 tri-phosphorylation mutants using co-IP."
NCBI gene IDs:
"FAM134: 54463"
Figure legend: "(E) Lysosomal cleavage of GFP was analyzed by Western blot for the cells co-expressing GFP-SEC61B and FAM134B (WT)-Flag, FAM134B (SA)-Flag or FAM134B (SD)-Flag."
NCBI gene IDs:
"Flag: 
GFP: 
FAM134B: 54463
SEC61B: 10952"
Figure legend: "(F, G) Measurement of the intracellular ER-scission activity. FAM134B knockout (KO) U2OS cells was engineered to express EGFP-FAM134B (WT), EGFP-FAM134B (SA) or EGFP-FAM134B (SD) at endogenous levels, lysosomal degradation of EGFP-FAM134B was blocked by Bafilomycin A1 (Baf A1). GFP-positive puncta were quantified for each cell in (G). For control, 25 cells were counted (n=25); For EGFP-FAM134B (WT), n=27; for EGFP-FAM134B (SA), n=29; for EGFP-FAM134B (SD), n=25. Scale bars, 10 μm. ***P&lt;0.001, one-way ANOVA, error bars indicate SEM."
NCBI gene IDs:
"EGFP: 
FAM134B: 54463"
Figure legend: "(H, I) Measurement of the ER-phagy activity. FAM134B knockout (KO) U2OS cells was engineered to express mCherry-EGFP-FAM134B (WT), mCherry-EGFP-FAM134B (S151A) or mCherry-EGFP-FAM134B (S151D) at endogenous levels. Lysosomal mCherry-positive but GFP-negative puncta were quantified for each cell in (I). For mCherry-EGFP-FAM134B (WT), 25 cells were counted (n=25); for mCherry-EGFP-FAM134B (SA), n=23; for mCherry-EGFP-FAM134B (SD), n=21. Scale bars, 10 μm. The scale bars in the magnification boxes are 2 μm. ***P&lt;0.001, one-way ANOVA, error bars indicate SEM."
NCBI gene IDs:
"EGFP: 
mCherry: 
FAM134B: 54463"
Figure legend: "(C) In vitro FAM134B S151 phosphorylation by CAMK2B was detected by Western blot. Recombinant proteins for FAM134BWT and FAM134BS151A were purified from E. coil were incubated with purified CAMK2B by IP in kinase buffer. FAM134B phosphorylation was analyzed by a specific antibody recognizing phos-Serine151 of human FAM134B."
NCBI gene IDs:
"FAM134B: 54463"
Figure legend: "(E) FAM134B S151 phosphorylation in CAMK2B knockdown 293T cells."
NCBI gene IDs:
"CAMK2B: 816"
Figure legend: "(G, H) Measurement of the ER-phagy activity. U2OS cells transiently expressing mCherry-EGFP-FAM134B (WT) were treated with compounds as indicated. Lysosomal mCherry-positive but GFP-negative puncta were quantified for each cell in (H). For vehicle control, 53 cells were counted (n=53), for Ionomycin, n=56; for EB1089, n=54; for KN-93, n=58. Scale bars, 10 μm. The scale bars in the magnification boxes are 2 μm. ***P&lt;0.001, one-way ANOVA, error bars indicate SEM."
NCBI gene IDs:
"EGFP: 
mCherry: 
FAM134B: 54463"
Figure legend: "(I) FAM134B WT or knockout (KO) U2OS cells were treated with CAMK2 activator Ionomycin (Iono), EB1089 or inhibitor KN93 for 24 hours, Western-blot was performed to analyze the proteins as indicated."
NCBI gene IDs:
"FAM134B: 54463"
Figure legend: "(J) CAMK2B WT or knockdown (KD) U2OS cells were treated with 1 μM Thapsigargin (Tg) to induce ER stress for different time as indicated. Cells were collected and analyzed for proteins as indicated by Western blot."
NCBI gene IDs:
"CAMK2B: 816"
Figure legend: "(K) GFP-cleavage assay. CAMK2B WT or knockdown (KD) U2OS cells were co-transfected with FAM134B-Flag and GFP-SEC61B, 24 hours post transfection, cells were treated with drugs as indicated and analyzed for GFP-cleavage by Western blot. Note: the levels of Flag-FAM134B, CAMK2B, GFP-SEC61B and Tubulin were analyzed by Western blot using different membranes."
NCBI gene IDs:
"Flag: 
GFP: 
CAMK2B: 816
FAM134B: 54463
SEC61B: 10952"
Figure legend: "(A) Comparison of the self-interaction of FAM134B WT with mutants as indicated using co-IP. SA-G216R was constructed by simultaneously mutating S149, S151 and S153 to alanine (SA) on the basis of FAM134B-G216R."
NCBI gene IDs:
"FAM134B: 54463"
Figure legend: "(C, D) Measurement of the intracellular ER-scission activity of FAM134B WT, G216R, S151A-G216R and SA-G216R. GFP-tagged FAM134B proteins were expressed in U2OS cells at same levels. The autolyosomal degradation of ER fragments labelled by GFP-FAM134B were blocked by Baf A1 or DMSO. GFP-positive puncta were quantified for each cell in (D). For all of the groups, at least 30 cells were included for quantification; Scale bars, 10 μm. ***P&lt;0.001, one-way ANOVA, error bars indicate SEM."
NCBI gene IDs:
"FAM134B: 54463"
Figure legend: "(E, F) Measurement of the ER-phagy activity of FAM134BG216R. U2OS cells transiently expressing mCherry-EGFP-FAM134B (WT), mCherry-EGFP-FAM134B (G216R), mCherry-EGFP-FAM134B (S151A-G216R) or mCherry-EGFP-FAM134B (SA-G216R) at same levels. Lysosomal mCherry-positive but GFP-negative puncta were quantified for each cell in (F). For WT, 50 cells were counted (n=50); for G216R, n=55; for S151A-G216R, n=51; for SA-G216R, n=52. Scale bars, 10 μm. The scale bars in the magnification boxes are 2 μm. *P&lt;0.05, ***P&lt;0.001, one-way ANOVA, error bars indicate SEM."
NCBI gene IDs:
"EGFP: 
mCherry: 
FAM134B: 54463"
Figure legend: "(A,A') Specific expression of FAM134B mRNA (green) in sensory neurons (red) of P4d vGlut2Cre;R26lsl-tdTommouse. Scale bars, 100μm. The white dotted line indicates the dorsal root ganglia (DRG) where sensory neurons are genetically labeled with Tomato. Insets of (a) and (a') are high magnifications of sensory neurons showing the co-localization of FAM134B mRNA and Tomato. Scale bars, 10 μm."
NCBI gene IDs:
"tdTom: 
Cre: 2777477
R26: 14910
FAM134B: 54463
vGlut2: 140919"
Figure legend: "Cultured sensory neurons from DRGs of E14.5 vGlut2Cre;R26lsl-tdTom embryos were infected with same titers of recombinant lentivirus expressing GFP-FAM134B WT (B), G216R(C), S151A-G216R(D), SA-G216R(E), G216R-ΔLIR (F) respectively. Infected sensory neurons (GFP+/Tom+) are indicated with arrowheads. The nuclei of all cells are shown with DAPI staining. Scale bars, 20 μm."
NCBI gene IDs:
"GFP: 
tdTom: 
Cre: 2777477
R26: 14910
FAM134B: 54463
vGlut2: 140919"
Figure legend: "Cultured sensory neurons from DRGs of E14.5 vGlut2Cre;R26lsl-tdTom embryos were infected with same titers of recombinant lentivirus expressing G216R supplemented with 5μM KN93 (G) Infected sensory neurons (GFP+/Tom+) are indicated with arrowheads. The nuclei of all cells are shown with DAPI staining. Scale bars, 20 μm."
NCBI gene IDs:
"tdTom: 
Cre: 2777477
R26: 14910
vGlut2: 140919"
Figure legend: " E-F Western blot analysis of HSP60 and ATP5a, as mitochondrial marker in the indicated knock out MEF cells (with / without the indicated DRP1 variant) after 48h of IU1 treatment. Bar graphs represent mean ± SEM, n= at least 3. Student's t test; "
NCBI gene IDs:
"DRP1: 74006"
Figure legend: " A-D Wild type MEF (A), Hela (B) and PINK1 KO MEF (C) cells were treated with IU1 (48h, 100 μM) and electron microscope images were evaluated for autophagic vesicle formation. (D) bar graphs represents mean± SEM number of autophagosomes and autolysosome / cell from 3 different set of experiments; at least 40 cells were analysed from each group"
NCBI gene IDs:
"PINK1: 68943"
Figure legend: "Electron microscope images of mitochondria from SH-SY5Y e, as indicated in the figure, with / without USP14 inhibition/knock down. Arrow heads in the IU1 treated groups indicate the mitochondrial rupture point. Bar graphs represent mean (± SEM) of percentage ruptured mitochondria from at least 3 different experiments. For cells, total 150-300 mitochondria for the control group and 150-190 mitochondria from the IU1 treated groups were counted"
NCBI gene IDs:
"USP14: 9097"
Figure legend: "Electron microscope images of mitochondria fro MEF WT, MEF PINK1 K as indicated in the figure, with / without USP14 inhibition/knock down. Arrow heads in the IU1 treated groups indicate the mitochondrial rupture point. Bar graphs represent mean (± SEM) of percentage ruptured mitochondria from at least 3 different experiments. For cells, total 150-300 mitochondria for the control group and 150-190 mitochondria from the IU1 treated groups were counted"
NCBI gene IDs:
"PINK1: 68943
USP14: 59025"
Figure legend: "Electron microscope images of mitochondria fro Hela an e, as indicated in the figure, with / without USP14 inhibition/knock down. Arrow heads in the IU1 treated groups indicate the mitochondrial rupture point. Bar graphs represent mean (± SEM) of percentage ruptured mitochondria from at least 3 different experiments. For cells, total 150-300 mitochondria for the control group and 150-190 mitochondria from the IU1 treated groups were counted"
NCBI gene IDs:
"USP14: 9097"
Figure legend: "Electron microscope images of mitochondria fro Drosophila thoracic muscle, as indicated in the figure, with / without USP14 inhibition/knock down. Arrow heads in the IU1 treated groups indicate the mitochondrial rupture point. Bar graphs represent mean (± SEM) of percentage ruptured mitochondria from at least 3 different experiments For flies, more than 200 mitochondria from each group were counted from 5 different experiments"
NCBI gene IDs:
"USP14: 34387"
Figure legend: " D Dopamine content in the fly heads (15 day old) was measured by HPLC and the individual fold change values are represented in the scatter graph. Graphs represent mean± SEM. N= 14, 11 and 11 fly heads for control, PINK1 and PINK1+USP14 KD fly respectively. ANOVA followed by Newman Keuls test "
NCBI gene IDs:
"PINK1: 31607
USP14: 34387"
Figure legend: " C) Violin plot showing high or low expression levels of MALAT1 in rod photoreceptor clusters. "
NCBI gene IDs:
"MALAT1: 378938"
Figure legend: " D) Distribution of rod photoreceptor populations with high MALAT1 expression (MALAT1-hi) or low MALAT1 expression (MALAT1-lo) in three donor retina samples. "
NCBI gene IDs:
"MALAT1: 378938"
Figure legend: " E) Fluorescent in situ hybridization analysis of human peripheral retina showing heterogeneous levels of MALAT1 expression in the rod photoreceptors located in the outer nuclear layer (ONL). INL: inner nuclear layer; OPL: outer plexiform layer. Scale bar = 20µm. "
NCBI gene IDs:
"MALAT1: 378938"
Figure legend: " D) t-SNE plots showing expression of MALAT1. "
NCBI gene IDs:
"MALAT1: 378938"
Figure legend: " E) Expression pattern of MALAT1 in the rod photoreceptor showing MALAT1-hi (CCA1, CCA10) and MALAT1-lo (CCA0) subpopulations. x-axis depicts normalized transcript levels. "
NCBI gene IDs:
"MALAT1: 378938"
Figure legend: " G) Heatmap of differentially expressed genes between the two MALAT1-hi clusters CCA1 and CCA10. The rows correspond to top 10 genes most selectively upregulated in individual clusters (p&lt; 0.01, Benjamini-Hochberg correction) and the columns show individual cells ordered in CCA1 and CCA10. "
NCBI gene IDs:
"MALAT1: 378938"
Figure legend: " Fluorescent in situ hybridization analysis of the same donor human peripheral retina at different time points post-mortem (7 and 13 hours, Retina 7), showing decreases in MALAT1-hi rod subpopulations in the outer nuclear layer (ONL) at later time point. INL: inner nuclear layer; OPL: outer plexiform layer. Scale bar = 20µm. White arrows indicated MALAT1-hi rod photoreceptors. "
NCBI gene IDs:
"MALAT1: 378938"
Figure legend: " C) Scatter plots showing expression of OPN1LW/OPN1MW or OPN1SW in individual cone photoreceptors for population C10. The colour depicts expression level for OPN1LW/OPN1MW in individual cells. "
NCBI gene IDs:
"OPN1LW: 5956
OPN1MW: 2652
OPN1SW: 611"
Figure legend: "E Example images of TIRFM endpoint colocalization imaging. Top panels show CEN DNA (top-left panel, blue circles) or CDEIIIMUT CEN DNA (top-middle panel, blue circles) visualized in lysates that included Cse4CENP‑A-GFP or CEN DNA in lysates that lacked Scm3HJURP (scm3-AID) (top-right panel, blue circles). Middle panels show Cse4CENP‑A-GFP visualized on CEN DNA (middle-left panel) or CDEIIIMUT CEN DNA (center panel) or on CEN DNA in lysates lacking Scm3HJURP (scm3-AID) (middle-right panel) with colocalization shown in relation to blue DNA circles. Bottom panels show overlay of CEN DNA channel (magenta) with Cse4CENP‑A-GFP (green) on CEN DNA (bottom-left panel) or CDEIIIMUT DNA (bottom-middle panel) or on CEN DNA in lysates lacking Scm3HJURP (scm3-AID) (bottom-right panel). Scale bars 3μm. Graph shows quantification of observed colocalization of Cse4 on CEN DNA and on CDEIIIMUT CEN DNA or on CEN DNA in lysates that lacked Scm3HJURP (47 ± 2.9%, 3.5 ± 3.0% and 0.6 ± 0.4% respectively, avg ± s.d. n=4 experiments, each examining ~1,000 DNA molecules from different extracts)."
NCBI gene IDs:
"HJURP: 851416
Scm3: 851416
scm3: 851416"
Figure legend: "B Immunoblot analysis of whole cell extracts from WT, chl4-K13S and okp1-AID cells using indicated antibodies."
NCBI gene IDs:
"chl4: 851841
okp1: 853090"
Figure legend: "C Example images of TIRFM endpoint colocalization assays. Top panels show visualized Cse4CENP‑A-GFP on CEN DNA in extracts from chl4-K13S (top-left panel) or auxin-treated okp1-AID strains (okp1-AID, top-right panel) with colocalization shown in relation to identified CEN DNA in blue circles. Bottom panels show overlay of CEN DNA channel (magenta) with Cse4CENP‑A-GFP (green), Scale bars 3 μm. D Quantification of Cse4CENP‑A endpoint colocalization with CEN DNA in extracts from WT, chl4-K13S, or okp1-AID genetic backgrounds (19 ± 1.1%, 8 ± 0.7%, 5 ± 0.9%, avg ± s.d. n=4 experiments, each examining ~1,000 DNA molecules from different extracts)."
NCBI gene IDs:
"chl4: 851841
okp1: 853090"
Figure legend: "F Kaplan-Meier analysis of Cse4CENP‑A residence lifetimes on CEN DNA in extracts from WT (blue - median lifetime of 82 s, n=1419 over 3 experiments of ~1000 DNA molecules using different extracts), chl4-K13S (red - median lifetime of 70 s, n=546 over 3 experiments of ~1000 DNA molecules using different extracts) and okp1-AID (purple - median lifetime of 61 s, n=348 over 3 experiments of ~1000 DNA molecules using different extracts) genetic backgrounds. Significant difference (***) between WT extract and chl4-K13S extract residence lifetime plots (two-tailed p-value of 3.4e-5 as determined by log-rank test). No significant difference (n.s.) between chl4-K13S and okp1-AID residence lifetimes in (two-tailed p-value of .40 as determined by log-rank test). 95% confidence intervals indicated (dashed lines), right-censored lifetimes (plus icons) were included and unweighted in survival function estimates."
NCBI gene IDs:
"chl4: 851841
okp1: 853090"
Figure legend: "B. Rev3l+/+ and Rev3l-/- MEFs were pulse-labelled with EdU for 15min, permeabilized, fixed and stained for EdU  incorporation (green). S phase sub-stages from I to IV were evaluated by visual inspection of the cycling population (&gt;300  EdU+ cells, top panel). Scale bar= 5 μm. Dot plots and pie charts show the relative proportion (percentage of total S) of each sub-stage from I to IV (middle and bottom panel, respectively). Each dot represents the mean of two technical replicates."
NCBI gene IDs:
"Rev3l: 19714"
Figure legend: "C. Analysis of the active marks H3K27ac and H3K4me3 and facultative heterochromatin mark H3K27me3 content in early, mid, late and TTR compared to disturbed replicating regions found in Rev3l-/- MEFs. Bar in boxplot represents the median, and red points represents the mean. The limit of the boxes corresponds to the 0.25 to 0.75 quartiles with whiskers extending to the maximum value of 1.5 times the interquartile range. Graphs show data from two biological experiments."
NCBI gene IDs:
"Rev3l: 19714"
Figure legend: "D. Relative mRNA levels of four genes involved in development (Hoxb2, 8, 9 and  WT1) were validated through qRT-PCR from  Rev3l+/+ and Rev3l-/- MEFs  samples. The data were normalized to the amount of GAPDH mRNA. Error bars indicate standard error of the mean for three independent experiments. ***, P&lt;0.001 and **, P&lt;0.005 by Student's t-test. E. Relative mRNA levels of genes involved in imprinting (paternal expressed genes: Dlk1and Slc18a4 and maternal expressed genes: Dcn1 and H19) were validated through qRT-PCR from Rev3l+/+ and Rev3l-/- MEFs samples. The data were normalized to the amount of  GAPDH mRNA. Error bars indicate standard error of the mean for three independent experiments. *** P&lt;0.001 by Student's t-test. "
NCBI gene IDs:
"Slc18a4: 
Dcn1: 102323///100737///76863///233805///114893
Dlk1: 13386
GAPDH: 14433
H19: 14955
Hoxb2: 103889
Rev3l: 19714
WT1: 22431"
Figure legend: "A. Total histones were acid extracted from Rev3l+/+ and Rev3l-/- MEFs. Samples were analyzed by  western-blot  using indicated antibodies specific to histone marks (right panel). An anti-pan H4  or H3 was used as loading control (left panel). Histograms show WT/KO Rev3l  fold change relative to the immunoblot  shown on the top panel (using 1X sample intensity)."
NCBI gene IDs:
"Rev3l: 19714"