EMBO/SourceData huggingface dataset:
Figure legend: "(B) Brain or lung viral RNA contents, determined by conventional E-specific or sub-genomic Esg-specific qRT-PCR  at 3 dpi. Two mice out of the 5 sham-vaccinated mice  did not have detectable viral RNA  in the lungs  despite high  viral RNA content in the brain  and  hACE2  mRNA expression levels comparable to that of the other mice in the same group. Data information: Statistical significance was evaluated by Mann-Whitney test (*= p &lt; 0.05, **= p &lt; 0.01, ****= p &lt; 0.0001)."
NCBI gene IDs:
"hACE2: 59272
Esg: 43740570"
Figure legend: "(E) Wild type or  µMT KO mice (n = 5-9/group) were injected by LV::S or sham following the time line shown in (A), then pretreated with Ad5::hACE2 4 days before challenge with the ancestral SARS-CoV-2 strain. Lung viral RNA contents were determined at 3 dpi. Data information: Statistical significance was evaluated by Mann-Whitney test (*= p &lt; 0.05, **= p &lt; 0.01, ****= p &lt; 0.0001)."
NCBI gene IDs:
"hACE2: 59272"
Figure legend: "survival curves (G) of Cre+ or TKO mice injected subcutaneously with B16F10 OVA cells (n = 7 per genotype). Survival time was defined as the time required for a tumor to reach a volume of 500 mm3."
NCBI gene IDs:
"Cre: 2777477"
Figure legend: "(J) Representative plots (left panels) and quantification (right panels) of IFNγ- and TNFα-producing CD8 TILs of B16F10 OVA tumors from Cre+ (n = 10) and TKO (n = 12) animals at day 14."
NCBI gene IDs:
"Cre: 2777477"
Figure legend: "(F) Oxygen consumption rate of Cre+ (n = 8 mice) or TKO (n = 7 mice) CD8 T cells activated ex vivo as in B after mitochondrial stress test analysis. Two representative WT and TKO animals are shown (left panel); the corresponding quantification for basal and maximum respiration is shown (right panels). Values are normalized to basal Cre+ measurements. T cells were isolated as in A."
NCBI gene IDs:
"Cre: 2777477"
Figure legend: "(C) qPCR of Cpeb4 mRNA in CD8 T cells resting or activated ex vivo with CD3/CD28/IL-2 at the indicated time-points; Tbp is used as endogenous control (n = 5 mice). CD8 T cells were isolated from the spleen and lymph nodes from WT mice."
NCBI gene IDs:
"Cpeb4: 67579
Tbp: 21374"
Figure legend: "(D) qPCR analysis of Atf4, Ddit3, Xbp1s and Hspa5 mRNA levels in Cpeb4+/+ (n = 5) and Cpeb4-/- (n = 6) CD8 cells activated as in a; Tbp is used as endogenous control (n = 5)."
NCBI gene IDs:
"Atf4: 11911
Cpeb4: 67579
Ddit3: 13198
Hspa5: 14828
Tbp: 21374
Xbp1s: 22433"
Figure legend: "(F) Ddti3 mRNA levels in CD8 T cells from B16F10 tumors and spleen of WT (n=8) and TKO (n=10) mice. The data are shown as ratio between tumors and spleen."
NCBI gene IDs:
"Ddti3: 13198"
Figure legend: "(G) Flow cytometry analysis of apoptotic AnnexinV+ Cre+ (n = 4) or TKO (n = 6) CD8 cells activated as in A."
NCBI gene IDs:
"Cre: 2777477"
Figure legend: "(A) Western blot of CPEB4 in input and immunoprecipitated fractions using anti-CPEB4 antibody of Cpeb4+/+ and Cpeb4-/- CD8 T cells activated ex vivo with CD3/CD28/IL-2 for 48 h; β-actin is used as control (n = 3)."
NCBI gene IDs:
"Cpeb4: 67579"
Figure legend: "(D) RIP-seq data from several 3′ UTRs depicting normalized RIP-seq coverage for inputs (light grey and blue) and IP (dark grey and blue) from Cpeb4+/+ and Cpeb4-/- CD8 T cells. Image obtained using the integrated genome viewer (IGV)."
NCBI gene IDs:
"Cpeb4: 67579"
Figure legend: "(E) Western blot (left panel) and quantification (right panel) of DDIT4 protein levels in Cre+ and TKO CD8 T cells activated as in A; β-actin is used as loading control (n = 7). (F) Western blot (left panel) and quantification (right panel) of HERPUD2 protein levels in Cre+ and TKO CD8 T cells activated as in A; β-actin is used as loading control (n = 8)."
NCBI gene IDs:
"Cre: 2777477"
Figure legend: "(G) Basal oxygen consumption rate (left panel) and maximal oxygen consumption rate (right panel) after mitochondrial stress test analysis. Cre+ and TKO CD8 T cells were activated as in A, but were treated with either Tauroursodeoxycholic Acid (TUDCA, T) 250 μM or vehicle for the last 24 h. Values are normalized to basal Cre+ measurements. n = 7 for all conditions in basal respiration; n = 6 for all conditions in maximal respiration."
NCBI gene IDs:
"Cre: 2777477"
Figure legend: "(I) Quantification of IFNγ+ CD8 cells activated and treated as in G (n = 9 for Cre+ and n = 12 for TKO in both conditions). *P = 0.0168, ** P = 0.0014 for Cre+ vs. TKO, P = 0.0029 for Cre+ vs. Cre+ TUDCA, **** P &lt;0.0001."
NCBI gene IDs:
"Cre: 2777477"
Figure legend: "A RNA-seq. of freshly isolated, proliferating and differentiating satellite cells reveals an increased expression of linc-MYH in proliferating and differentiating MuSCs, but no expression is found in in freshly isolated MuSCs."
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "Expression of linc-MYH is confined to skeletal muscle in mouse (B) tissues."
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "Expression of linc-MYH is confined to skeletal muscle in human (C) tissues."
NCBI gene IDs:
"linc-MYH: "
Figure legend: "D Expression of linc-MYH is not detected in limb buds at E10.5 (n = 3), E13.5 (n = 3) and E15.5 (n = 3). Expression of linc-MYH in hindlimb muscle of E18.5, newborn and 7 day old animals (n = 3/3/3). Expression of linc-MYH in m. soleus (soleus), m. tibialis anterior (TA) and and m. extensor digitorum longus (EDL) muscle at 3 weeks (n = 3) and 8 weeks of age (n = 5). Biological replicates were used for all PCR experiments, data are mean ± S.E.M."
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "E Murine linc-Myh is localized in nuclear extracts of C2C12 cells. Xist (nuclear) and Gapdh (mainly cytoplasmic) were used as controls (n = 2 nuclear / 3 cytoplasmic biological replicates.) Data are mean ± S.E.M."
NCBI gene IDs:
"Gapdh: 
Xist: 
linc-Myh: 74184"
Figure legend: "F-H RNA-FISH identifies linc-Myh in nuclei (DAPI, blue) of C2C12 myoblasts. (G) Adipor (cytoplasmic) and (H) Xist (nuclear) were used as controls."
NCBI gene IDs:
"Adipor: 
Xist: 
linc-Myh: 74184"
Figure legend: "(J) Heat map of proteins pulled down in the same experiments as in I, demonstrating that INO80 chromatin remodeler complex exclusively interacts with linc-MYH. Blue color indicates pull-down of the respective protein, white color indicates that the protein was not detected in the respective sample."
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "Body weight (A) of male linc-MYH KO and ctrl mice at 10 weeks (n = 24 KO/17 WT; Student's t test, two-tailed, **p &lt; 0.01)"
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "tibia length (B) of male linc-MYH KO and ctrl mice of 10 weeks (n = 9 KO/13 WT; Student's t test, two-tailed, not significant). Data are mean ± S.E.M."
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "C, D Weight of m. tibialis anterior (TA) and m. digitorum longus (EDL) of male linc-MYH KO and ctrl mice at 10 weeks (n = 9 KO/10 WT for TA, n = 10 KO/11 WT for EDL; Student's t test, two-tailed, **p &lt; 0.01, ***p&lt;0.001). Data are mean ± S.E.M."
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "Size distribution of fibers in cross sections of TA (E, F) and EDL (G, H) muscle in male linc-MYH KO (blue) and ctrl (grey) animals at 10 weeks. A significant increase of fiber size was observed for TA and EDL muscles of linc-MYH KO mice (n = 5 KO/4 WT for TA, n = 3 KO/3 WT for EDL muscle, two-way ANOVA with Fisher's multiple comparisons; *p &lt; 0.05, **p &lt; 0.01; &gt; 250 fibers per animal were counted). Data are mean ± S.E.M."
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "Size distribution of fibers in cross sections of TA and EDL muscle in male linc-MYH KO (blue) and ctrl (grey) animals at 10 weeks. A significant increase of fiber size was observed for TA and EDL muscles of linc-MYH KO mice (n = 5 KO/4 WT for TA, n = 3 KO/3 WT for EDL muscle, two-way ANOVA with Fisher's multiple comparisons; *p &lt; 0.05, **p &lt; 0.01; &gt; 250 fibers per animal were counted). Data are mean ± S.E.M."
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "L-O Number of myonuclei / fiber and of Pax7pos (red) MuSCs (red arrows) on myofibers isolated from flexor digitorum brevis muscle. Nuclei were stained using DAPI (blue). Scale bar in L indicates 50 µm for L and M. (N) The number of myonuclei / isolated fiber is increased in linc-MYH KO compared to WT myofibers (n = 4 KO/4 WT, &gt; 26 fibers/animal; Mann-Whitney test two-tailed, * p &lt; 0.05). (O) Number of MuSCs on isolated fibers from linc-MYH KO and WT mice (n = 4 KO/4 WT animals, Mann-Whitney test two-tailed; ****p &lt; 0.0001). Data are mean ± S.E.M."
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "P-S Number of Pax7 (red) positive MuSCs in cross sections of tibialis anterior muscle (P-R); the relative amount of quiescent MuSCs identified by double staining (yellow arrows) for Pax7 and CalcR (green) does not significantly differ between WT and linc-MYH KO animals (S). Nuclei were stained with DAPI (blue). Scale bar in P indicates 25 µm for P and Q. (n = 3 KO/3 WT animals, Mann-Whitney test one-tailed; *p = 0.05, ns: not significant). All data are mean ± S.E.M."
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "T The number of MuSC-related events in FACS experiments is significantly increased in linc-MYH-KO animals (n = 7 KO/7 WT, Student's t test, two-tailed, *p = 0.0126). Data are mean ± S.E.M."
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "U-V Structure of MuSCs and the heterochromatin content of MuSC nuclei is not changed in linc-MYH KO (V) compared to WT mice (U)."
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "RNA in situ hybridization proximity ligation assay (rISH-PLA) detects the close proximity of a specific RNA with proteins in situ modified from Roussis et al.. (B-C) rISH-PLA confirms the proximity of linc-MYH to endogenous INO80-V5 in the nucleus of proliferating WT MuSCs (B). The specific signal is lost in linc-MYH deficient MuSCs (C). (n = 3 WT/3 KO biological replicates; Mann-Whitney test, *p = 0.05). Data are mean ± S.E.M."
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "E-I Representative images of TA muscle sections of 10 weeks old mice stained for PAX7 (green) and EdU incorporation (red). MuSCs without (green arrows) and with EdU-labeling (red arrows) are indicated. (E, F) Deletion of linc-MYH results in increased numbers of muscle stem cells and pronounced increase of the ratio of EdU-positive MuSCs. (G-I) The increase in both the number of MuSCs and EdU positive MuSCs in linc-MYH mutant muscle is abolished by constitutive (G: Pax7-Crepos / INO80-/-, Ino80 KO; H: linc-MYH-/- / Pax7-Crepos / INO80-/-, dKO) and induced (I: linc-MYH-/- / Pax7-CreERT2pos / INO80-/-, dKO CreERT) deletion of INO80 in Pax7 expressing cells."
NCBI gene IDs:
"linc-MYH: 74184
Cre: 2777477
ERT: 2099
ERT2: 2099
INO80: 68142
Ino80: 68142
Pax7: 18509"
Figure legend: "Statistical evaluation of the number of muscle stem cells observed in TA muscles (J). ; (n = 5 WT/5 linc-MYH KO/4 Ino80 KO/5 dKO/3 CreERT dKO animals in J/K, n = 6 WT/6 linc-MYH KO/5 Ino80 KO/6 dKO/3 CreERT dKO animals in L **p &lt; 0.01, ****p &lt;0.0001, > 31 MSCs /animal in K; ANOVA test with multiple comparisons against WT. Sidak-Holm correction was used. Data are mean ± S.E.M.)."
NCBI gene IDs:
"linc-MYH: 74184
Cre: 2777477
ERT: 2099
Ino80: 68142"
Figure legend: "Statistical evaluation of the ratio of EdU-incorporating MuSCs relative to all Pax7-positive MuSCs (K). ; (n = 5 WT/5 linc-MYH KO/4 Ino80 KO/5 dKO/3 CreERT dKO animals in J/K, n = 6 WT/6 linc-MYH KO/5 Ino80 KO/6 dKO/3 CreERT dKO animals in L **p &lt; 0.01, ****p &lt;0.0001, &gt; 31 MSCs /animal in K; ANOVA test with multiple comparisons against WT. Sidak-Holm correction was used. Data are mean ± S.E.M.)."
NCBI gene IDs:
"linc-MYH: 74184
Cre: 2777477
ERT: 2099
Ino80: 68142"
Figure legend: "Statistical evaluation of the number of myonuclei in myofibers of TA muscles from different genotypes (L) (n = 5 WT/5 linc-MYH KO/4 Ino80 KO/5 dKO/3 CreERT dKO animals in J/K, n = 6 WT/6 linc-MYH KO/5 Ino80 KO/6 dKO/3 CreERT dKO animals in L **p &lt; 0.01, ****p &lt;0.0001, &gt; 31 MSCs /animal in K; ANOVA test with multiple comparisons against WT. Sidak-Holm correction was used. Data are mean ± S.E.M.)."
NCBI gene IDs:
"linc-MYH: 74184
Cre: 2777477
ERT: 2099
Ino80: 68142"
Figure legend: "A-D Isolated linc-MYH KO MuSCs reach confluence much faster than WT MuSCs indicating higher proliferation rates. Deletion of INO80 eliminates the difference between Pax7-Crepos / INO80-/- (Ino80 KO) and linc-MYH-/- / linc-MYH-/-/ Pax7-Crepos / INO80-/- (dKO). Images are representative images for cultures after 13 days in culture."
NCBI gene IDs:
"linc-MYH: 74184
Cre: 2777477
INO80: 68142
Ino80: 68142
Pax7: 18509"
Figure legend: "E Differences in proliferation rates are abolished by additional deletion of INO80 in MuSCs. Cell confluence was monitored by a live cell imaging analysis system for 13 days (n = 7 WT / 6 linc-MYH KO / 3 Ino80 KO / 3 dKO independent preparations of MuSCs)."
NCBI gene IDs:
"linc-MYH: 74184
INO80: 68142
Ino80: 68142"
Figure legend: "F Statistical analysis of cell confluence after 13 days of muscle stem cell proliferation (n = 7 WT / 6 linc-MYH KO / 3 Ino80 KO / 3 dKO independent preparations of MuSCs, Student's t test, two-tailed; *p &lt; 0.05, ns = not significant). Data are mean ± S.E.M."
NCBI gene IDs:
"linc-MYH: 74184
Ino80: 68142"
Figure legend: "G-I Gene set enrichment analysis (GSEA, broadinstitute.org) of microarray data from proliferating MuSCs. Comparison of linc-MYH-/- vs. WT proliferating MuSC transcriptomes shows enrichment of genes related to cell proliferation (G), enrichment of genes containing cis regulatory elements for YY1 (H) and p53 (I). Enrichments are highly significant using the most conservative familywise-error rate method (FWER). Enrichments were lost in linc-MYH-/- MuSCs after additional deletion of INO80 (dKOs) compared to Pax7-Crepos / INO80-/- MuSCs."
NCBI gene IDs:
"linc-MYH: 74184
Cre: 2777477
INO80: 68142
Pax7: 18509"
Figure legend: "Heat maps of the 10 most upregulated genes of the respective gene sets depicted in G-I in linc-MYH-/- vs. WT MuSCs and in linc-MYH-/-/ Pax7-Crepos / INO80-/- dKO vs. Pax7-Crepos / INO80-/- MuSCs. Expression of up-regulated genes in linc-MYH-/- was normalized after additional deletion of INO80 (dKOs), indicating that effects of linc-MYH completely depend on INO80 (WT n = 4, linc-MYH-/- n = 4, Pax7-Crepos / INO80-/- n = 4, Pax7-Cre dKO n = 3 animals used for independent isolations of MuSCs)."
NCBI gene IDs:
"linc-MYH: 74184
Cre: 2777477
INO80: 68142
Pax7: 18509"
Figure legend: "A-D γ-H2AX staining of proliferating MuSCs from WT (A), linc-MYH deficient (B), Pax7-Crepos / INO80 KO (C), and linc-MYH/INO80 dKO (D) mice. Deletion of INO80 results in increased γ-H2AX signals while deletion of linc-MYH has no effects (asterisk: low γ-H2AX signals, arrow: γ-H2AX-foci detected in nuclei, arrowhead: pan-nuclear γ-H2AX signal."
NCBI gene IDs:
"linc-MYH: 74184
Cre: 2777477
INO80: 68142
Pax7: 18509"
Figure legend: "H-I Gene set enrichment analysis of microarray data obtained for proliferating MuSCs shows enrichment of genes related to activity of ATR in response to replication stress recovery (H) and enrichment of genes involved in chromosome maintenance (I) in WT compared to Pax7-Crepos INO80-/- MuSCs. Enrichment of these or similar gene sets was not observed when comparing WT to linc-MYH-/- MuSCs."
NCBI gene IDs:
"linc-MYH: 74184
Cre: 2777477
INO80: 68142
Pax7: 18509"
Figure legend: "A, B Co-Immunoprecipitation of INO80 complex subunits from TA muscles of WT and linc-MYH KO mice followed by Western Blot analysis. (B) Statistical analysis of Co-IP/Western Blot data. The amount of RUVBL1 and RUVBL2 in the INO80 complex is not changed after deletion of linc-MYH, while the amounts of YY1, WDR5 and TFPT pulled down by INO80 increase (n = 3 WT / 3 linc-MYH KO animals; one-way ANOVA, multiple comparisons by Fishers LSD test, *p&lt;0.05). Data are mean ± S.E.M."
NCBI gene IDs:
"linc-MYH: 74184"
Figure legend: "(A) Coimmunoprecipitation of SMO-HA and Myc-Smaug proteins. Extracts of Cl8 cells expressing combinations of SMOWT-HA or SMOPKA-SD-HA with Myc-SmaugWT in the absence or presence of HH were immunoprecipitated (IP) with anti-HA. The input (lower panel) and the IP complexes (upper panel) were analyzed by western blot with anti-Myc (αMyc) or anti-HA (αHA) antibodies. Here and in the other figures, the names of the proteins detected are indicated on the left and the molecular weights on the right, in kDa; the samples loaded for the input and the supernatants are equivalent to a tenth of the volume loaded for the IPs. * corresponds to higher molecular weight forms of SMO of unknown origin. Here and in panel F, the black arrow indicates unphosphorylated SMOWT-HA and the bracket indicates the phosphorylated forms of SMOWT-HA or SMOPKA-SD."
NCBI gene IDs:
"Myc: 
Smaug: 39034
SMO: 33196"
Figure legend: "(D, E) Mapping of the Smaug interaction domain in SMO. Extracts from Cl8 cells transfected with Myc-SmaugWT and various regions of SMO fused to either HA (D) or to GFP (E) were immunoprecipitated with αMyc (D) or αGFP (E) and analyzed by western blotting with αMyc (lower panel in D and upper panel in E), αHA (D, upper panel) or αGFP (E, lower panel). In: Input; Sup: supernatant. See also Fig EV1D-F."
NCBI gene IDs:
"GFP: 
Myc: 
Smaug: 39034
SMO: 33196"
Figure legend: "(F) Hyperphosphorylated forms of SMO do not interact with Smaug. Left panel: Extracts of Cl8 cells expressing SMOWT-HA with or without Myc-SmaugWT, in the absence or presence of HH were IP with an αMyc antibody before analysis by western blot with αHA (upper panel) or αMyc antibodies (lower panel). Right panel: Cl8 cells expressing SNAP-SMOWT with Myc-SmaugWT in the presence of HH were extracellularly labelled with a membrane-nonpermeable fluorescent SNAP substrate before cell lysis and immunoprecipitation (IP) with anti-Myc. Labelled SNAP-SMO was directly visualized after electrophoresis. Note its presence in the IP fraction with a relative enrichment of the less phosphorylated forms compared to the hyperphosphorylated forms. See also Fig EV1G-J."
NCBI gene IDs:
"Myc: 
SNAP: 
Smaug: 39034
SMO: 33196"
Figure legend: "(G) SMO and Smaug colocalize. Representative fluorescent images of Cl8 cells expressing GFP-SmaugWT alone (1-2) or together with SMOWT-mCherry (3-3'' and 4-4'') either without (1, 3-3&quot;) or with HH (2, 4-4&quot;). The merge images in 3&quot; and 4&quot; show GFP-SmaugWT in green and SMOWT-mCh in red. The same results were seen with different fluorescent tags as well (Fig EV2B). The lack of effect of HH on GFP-SmaugWT in absence of SMOWT-mCh is likely due to limiting amounts of endogeneous SMO. A least 20 cells were assayed for each condition. In absence of HH, all co-transfected cells exhibited greater than 90% colabelled SMOWT-mCherry. Scale bar (shown in G1, identical for all panels):10μm. See also Fig EV2."
NCBI gene IDs:
"GFP: 
mCherry: 
Smaug: 39034
SMO: 33196"
Figure legend: "(B, C) Smaug downregulates reporter expression. Mean values of the relative levels of SNAP-GUS reporter (SNAP-GUS/GFP-SNAP ratio, in arbitrary units) in extracts of transfected Cl8 cells in the absence (black) or presence of λN-SNAP-Smaug (red), λN-SNAP (pale grey) or SNAP-Smaug (dark grey). See Fig EV3A for the representative gel and Fig EV3B which shows that λN-SNAP-Smaug has no effect on a SNAP-GUS construct that lacks the 5BoxB. N=3 (biological replicates). See also Fig EV3A-C. Here and in D-F: SNAP-GUS/GFP-SNAP ratios were set to 1 in cells expressing λN‐SNAP-Smaug. The error bars correspond to the standard deviation of the mean (SD). Statistical analysis was done by a Kruskal-Wallis test by ranks followed by a Dunn test and p values are: black bracket &lt;0.05, red bracket &lt;0.01, green bracket &lt;0.0001. Here and in D-E: 15 ng of pAct.λN-SNAP-smaug plasmid were used per transfection."
NCBI gene IDs:
"5BoxB: 
Act: 
SNAP: 
smaug: 39034"
Figure legend: ", E) HH/SMO reduces Smaug levels and its overall negative effect on reporter expression. Mean values of the relative levels of reporter expression (determined as above) (D) or of λN-SNAP-Smaug (ratio λN-SNAP-Smaug/GFP-SNAP) (E) in the absence of SMO constructs (red) or in the presence of SMOWT-HA (green), SMOPKA-SD-HA (blue) or SMO∆958-HA (yellow), without HH (plain boxes) or in presence of HH (striped boxes). N=6 (independent biological replicates), except for \"no SMO, no HH\" and \"SMOWT with HH\" conditions where n=10 (independent biological replicates). A representative gel is shown in Fig EV3D. Note that SMOWT-HA or HH alone had reproducible weak effects that were observed in two independent biological triplicates but were not statistically significant. See also Fig EV3E-F."
NCBI gene IDs:
"SMO: 33196"
Figure legend: "(F) HH/SMO reduces Smaug's intrinsic repressive ability. A similar experiment was conducted with different amounts of λN-SNAP-smaug expressing plasmid (ranging from 0 to 50 ng) as indicated). The mean values of the relative levels of reporter (y-axis) are plotted against the relative levels of λN-SNAP-Smaug (x-axis). SNAP-GUS/GFP-SNAP ratios were set to 1 in cells expressing λN‐SNAP-Smaug in absence of SMOPKA-SD/HH. The colored area represent the extent of the values observed for the relative amounts of reporter expression obtained with (blue) and without (red) SMOPKA-SD/HH, respectively. N=3 (biological triplicates). See Fig EV3H and also a representative gel in Fig EV3G."
NCBI gene IDs:
"SNAP: 
λN: 2703540
smaug: 39034
Smaug: 39034"
Figure legend: "(A) HH/SMO promotes slow-migrating forms of Smaug. Western blot analysis of Cl8 cells that transiently express HA-SmaugWT alone, or together with either SMOWT-GFP or SMOPKA-SD-GFP, in the presence or in absence of HH. GMAP serves as a loading control. Here and in the other panels, the antibodies used are indicated on the left. Here and in (B,C), the black arrows indicate the unphosphorylated form of HA-SmaugWT and the brackets indicate the slower migrating phosphorylated forms of HA-SmaugWT. NT: not transfected. See a phosphatase assay in Fig EV4A."
NCBI gene IDs:
"GFP: 
Smaug: 39034
SMO: 33196"
Figure legend: "(B) Smaug phosphorylation requires its interaction with SMO. Western blot analysis of Cl8 cells expressing HA-SmaugWT, in presence of HH, in combination with SMO∆958-GFP, SMOPKA-SD-GFP or SMOPKA-SD, ∆978-GFP, as indicated."
NCBI gene IDs:
"GFP: 
Smaug: 39034
SMO: 33196"
Figure legend: "(C) FU controls Smaug phosphorylation. Extracts of Cl8 cells expressing SNAP-Smaug with SMOPKA-SD FU-SD-GFP (with HH) in combination with GFP-FUWT, GAP-GFP-FUWT, Myc-FUEE or GAP-null-FUDANA (as indicated) were labeled for the SNAP tag before electrophoresis. After quantification of the gels, the percentage (%) of phosphorylated Smaug (% of phosphorylated forms of SNAP-Smaug total amounts of SNAP-Smaug) was estimated. In C to E, the mean values and (SD) for independent biological triplicates (N=3) are shown in the graph at the bottom, and the statistical analysis was done by one tailed bivariate Wilcoxon rank test. See also fig EV4C, D."
NCBI gene IDs:
"GFP: 
Myc: 
SNAP: 
FU: 32855
GAP: 2596
Smaug: 39034
SMO: 33196"
Figure legend: "(D) Phosphorylation of Smaug by activated FU requires the co-expression of SMO. Mean values of the percentage of phosphorylated Smaug in extracts of Cl8 cells that express λN-SNAP-Smaug with GAP-GFP-FUWT and SMOWT alone or together (as indicated) N=3 (billogical triplicates). Note that the effect of GAP-GFP-FUWT and SMOWT together is lower than the one observed with GAP-GFP-FUWT and SMOPKA-SD FU-SD-GFP together (in panel C). This could have multiple nonexclusive causes, including the fact that SMOWT is present at much lower levels than SMOPKA-SD FU-SD [38] and/or the involvement of another kinase. See also Fig EV4B. Note that Smaug does not coIP FU unless SMO is present see Appendix Figure S2."
NCBI gene IDs:
"GFP: 
SNAP: 
FU: 32855
GAP: 2596
λN: 2703540
Smaug: 39034
SMO: 33196"