EMBO/sd-character-level-ner huggingface dataset:
H. A model delineating the switch role of ciliary Rabl2 in the BBSome-mediated GPCR turnover: (1) GTP hydrolysis induced presumably by a GTPase-activating protein (GAP) dissociates Rabl2 from IFT-B to enable a tight BBSome-IFT-B interaction in the retrograde IFT machinery for concomitant TZ passage; (2) Without the GTP hydrolysis, Rabl2-GTP (or Rabl2Q80L) binds persistently to IFT-B, resulting in shedding of the BBSome and its cargos from the IFT machinery in the TZ passing process and accordingly their ciliary retention.
(B) Immunohistochemistry analysis of RNF114 in mouse ovary shows that RNF114 was mainly expressed in the oocytes (Scale bar = 100um).
Mice housed in germ-free (GF) or specific pathogen free (SPF) conditions received 25 mM ZnSO4 in the drinking water for 1 week and were then challenged i.p. with 35 µg TNF, dissolved in sterile PBS, per 20 g bodyweight. Combined data of 2 experiments.
B,C, Volcano plots representing the genes that conform the Intestinal Stem Cell (ISC) signature (Merlos-Suarez et al., 2011) (B, n = 45 genes, Dataset EV1F), and the EMT signature in cancer cells (Rokavec et al., 2017) (C, n = 171 genes, Dataset EV1G) upon USP42 knockdown in HCT116 cells. Significance was capped at -Log10P = 24.
(B) HEK293T cells transfected with Flag-USP4 and YFP-vector or YFP-p38IP as indicated were lysed and immunoprecipitated with anti-IgG or anti-TAK1 and then immunoblotted with anti-Flag and anti-TAK1.
(B) 3 μg of recombinant proteins were resolved on 4-12% Bis-Tris gradient gel and stained with Instant Blue Coomassie.
Kaplan-Meier analysis for patient OS and PFS based on high vs low expression of CYP46A1 in LGG and GBM. Data were obtained from the CGGA dataset. P-values were obtained from the log-rank test.
A-C. Principal component analysis of transcriptome data from (A) heart, (B) kidney and (C) liver. D-F. Heat map visualization of pathway enrichment analysis (Reactome database). Full pathway analysis is provided in Appendix Table S1. Benjamin-Hochberg FDR-corrected p values are color-labelled as indicated for the three comparisons.
Mean % of 3 and 24 month old mouse CMs staining positive for SA-β-Gal in vivo with representative images above (blue - SA-β-Gal; green - troponin C; red - WGA). Black arrows indicate SA-β-Gal expression in a troponin C expressing CM. Statistical analysis performed using two-tailed t-test; *P<0.05. Data are mean ± SEM from the analysis of >500 CMs per mouse, 4 mice per age group. Scale bar 20µm.
N, Bar plots showing relative proportion of each WT and kit mutant eEC subpopulation in eEC at each time point.
HEK293 cells expressing HA-RAMP4-2 alone or in combination with SPPL2c or SPP were treated with 100 µM (Z-LL)2-ketone (ZLL), 5 µM inhibitor X (InX), 5 µM DAPT or DMSO as control. RAMP4-2 band intensity was quantified from blots of three independent experiments and normalised to cells just over-expressing the substrate.
A, B Lysates from HEK293T cells, transfected with RNAi scrambled or RNAi PRKACA (72 h) and 2R or 66R (24 h), immunoblotted for PKA-Cα and poly-GA (HA-tag) expression. α-Tubulin used as loading control. (B) Quantification of PKA-Cα and poly-GA expression from three biological replicates. Data are mean ± SEM. Two-tailed, unpaired t-test. PKA-Cα: ns siScr 66R vs siScr 2R, ***P = 0.0002 siPRKACA 66R vs siScr 2R, ***P = 0.0003 siPRKACA 66R vs siScr 66R. poly-GA expression: ****P<0.0001 siScr 66R vs siScr 2R, ****P<0.0001 siPRKACA 66R vs siScr 2R, **P = 0.0062 siPRKACA 66R vs siScr 66R . C, D Lysates from HEK293T cells, transfected with RNAi scrambled or RNAi PRKACB (72 h) and 2R or 66R (24 h), immunoblotted PKA-Cβ and poly-GA (HA tag) expression. α-Tubulin used as loading control. (D) Quantification of PKA-Cβ and poly-GA expression from three biological replicates. Data are mean ± SEM. Two-tailed, unpaired t-test. PKA-Cβ: ns siScr 66R vs siScr 2R, **P = 0.0049 siPRKACB 66R vs siScr 2R, **P = 0.0091 siPRKACB 66R vs siScr 66R. poly-GA expression: ****P<0.0001 siScr 66R vs siScr 2R, ****P<0.0001 siPRKACB 66R vs siScr 2R, ***P = 0.0007 siPRKACB 66R vs siScr 66R. E
I. A model delineating the effects of Rabl2 and mutants on the TZ passage of ciliary BBSome and its cargo GPCR: (1) In physiological conditions, the GTP hydrolysis of Rabl2-GTP results in Rabl2-free IFT-B capable of mediating the TZ passage of the BBSome and its cargos together with the retrograde IFT machinery; (2) Rabl2D73GQ80L dissociates from IFT-B to allow similar TZ passage; (3) The BBSome sheds from IFT-B in the presence of Rabl2Q80L or Rabl2-GTP during the passing process and is therefore blocked in the ciliary shaft with its cargos.
(e) Tissue lysates from Atg7+/+-ob/w, Atg7+/−-ob/w, Atg7+/+-ob/ob and Atg7+/−-ob/ob mice were prepared before and 7 min after injection of 5 U kg−1 regular insulin (Ins) into the tail vein, and subjected to immunoblot analysis using antibodies specific for phospho-Akt S473 and total Akt. Numbers below immunoblot bands indicate the fold changes normalized to control bands.
Pleural fluid cell pellets and supernatants from 10 patients (called CRCINA #) with pleural effusion and pleural tumor samples from 17 patients (called TR#) with MPM were subjected to digital droplet polymerase chain reaction (ddPCR) for the detection of mutant (MUT) copies of KRAS codon 12/13 (KRASG12/13) and KRAS codon 61 (KRASQ61), as well as copies of TP53 and TERT. Diagnoses were lung adenocarcinoma (LUAD; n = 4) and MPM (n = 23). The assays were designed for detection of down to 1:20000 copies using EKVX (KRASWTTP53G610T), A549 (KRASG12STP53WT), NCI-H460 (KRASQ61HTP53WT), NCI-H3122 (KRASWTTP53E285V), and NCI-H3255 (KRASWTTP53G560-1A) human LUAD cells as controls. Shown are individual patient (KRAS plot) and individual sample (TP53 plot) allelic frequencies with color code and limits of normal TP53 allelic frequency as vertical dashed lines in the TP53 plot (A) Any number of KRAS-mutant droplets detected in any sample (KRAS plot in A) and any patient that failed to achieve normal TP53 ploidy by any sample (TP53 plot in A) was deemed altered.
a) Scheme of a fate mapping experiment using adult Cx3cr1CreERT2:Rosa26-YFP mice. Tamoxifen (TAM) injection was performed at postnatal day 42 (P42). Mice were evaluated at 2, 12 and 24 weeks post-injections. Administration of TAM leads to excision of a stop sequence flanked by loxP sites (grey triangles) in Cx3cr1 expressing cells in the eye which causes stable YFP expression under the control of the Rosa26 promotor.
(D) PY79 (WT) and ET19 (∆sigX) cells were infected with SPP1 at either high (phages:bacteria 1:1) or low (1:20) MOI, and OD600nm was followed at 2 min intervals. Shown is a representative experiment out of 6 biological repeats, and the average values and SD of 8 technical repeats.
(C) To track ILC210 in vivo, CD45.2+ ILC210 were co-transplanted with islets in diabetic CD45.1+ C57BL/6 mice. Representative FACS analysis showing the proportion of locally transplanted ILC210 (CD45.2+ST2+) in the total CD45+ cell compartment from islet graft at day 5 and 80 post-islet transplantation or at the day when grafts were considered rejected.
Immunoblotting of equal amounts of protein extracts isogenic pairs of parental sensitive and BRAFi-resistant cell lines (E) using antibodies against DDR1, DDR2 or markers of the melanoma cell differentiation AXL, MITF or SOX10. ERK2, loading control.
(G) Venn diagram showing the overlap between MCF7 DVL3 ChIP-seq peaks and FAIRE Seq.
A. Top: Schematic experimental set up of the clonogenic assay. Bottom: Bright-field microscopy images of WT, TP53KO and onco-RNF43/TP53KO human colon organoid lines at day 2 and 14. Scale bars represent 1000 μm.
(D) ATPase activity of WT (green) and E239K mutant (magenta) activated by microtubules. Data are represented as the mean ± SD. The data from at least three independent experiments were analysed. ****, p < 0.0001, two-way ANOVA.
Top: GFP-HDAC5 infected NRVMs were serum-starved for a day, pretreated for two hours with the indicated compounds (BPKDi, 3 µM, IPA-3, 30 µM) alone or in combination, then were stimulated for 4 hours. Representative images. Scale bar is 10 µm. Bottom : Statistical analysis of cellular localization of HDAC5. GFP-HDAC5 localization (nuclear or cytosolic) was assessed in >100 cells of each sample (n=3, technical replicates). *, P<0,05 (one-way ANOVA with Bonferroni post-hoc test, vehicle vs. ET1 or vs. PGE2, P<0.0001; PGE2 vs. PGE2+BPKDi, P=0.0004; PGE2 vs. PGE2+BPKDi, P=0.0114; PGE2 vs. PGE2+BPKDi+IPA-3, P<0.0001). The exact n and P values can be also found in the Source Data excel file for Figure 6
(D) Phosphorylated Syk (P-Syk) and total Syk (T-Syk) levels were determined by western blotting in lysates from wt and Trem2 ko BMDM after 1 h treatment with Aβ alone, together with antibody 2D8 (Aβ-2D8), or an isotype control (Aβ-IC). Actin was used as a loading control.(E) Quantification of P-Syk normalized to T-Syk. (n = 4, +/- SEM; 2 way ANOVA, interaction P=0.0490, genotype P=0.0898, treatment P<0.0001. Bonferroni-corrected pair-wise post hoc tests, ** P =0.0075 vs. wt).
A glioma signature identified by Sandberg et al () was overlapped with gene sets regulated by let‐7 and miR‐125 in Dgcr8Δ/Δ GPCs. Enrichment results are shown as a ratio of % of glioma genes in each group (as labeled on the x‐axis) relative to % of glioma genes in the unchanged gene set.
(A) Imaging of RAD21KD-MCF7 and -SNU16 cells to assess cell morphology. Depletion of RAD21 caused a conversion from an epithelial-like to fibroblast-like morphology.
Quantitative analysis of the effect of Trehalose (100 μM) treatment from 3-5 dpf on liver size as determined by fluorescence microscopy. n>70, ****p<0.0001, two-sided Student's t-test; values represent the mean ± s.e.m
(E) Quantification of mitotic B1dd/B2ko cells following siRNA transfection to deplete Greatwall (siGwl) or ENSA/ARPP19 (siE/A) and/or DIA treatment. Frequencies of mitotic cells with intact (blue) and disassembled (red) Lamin A/C staining are plotted (mean value of three repeats, n>50 per repeat, error bars indicate standard deviation).
(G) Oxygen consumption rate (OCR) in CRISPR-targeted Ramos cells. N = 2 independent infections. P, two-way ANOVA of basal and maximum OCR. (H) OCR in B cells isolated from Sh3gl1-/- and WT littermates. N = 9 mice. P, two-way ANOVA of basal and maximum OCR.
C. HeLa cells were transfected with control (siControl) or Nup358 specific siRNA (siNup358) for 96 h. Western blots indicate the extent of Nup358 depletion and AGO2 immunoprecipitation in siControl and siNup358 samples. Vinculin was used as loading control. Data are presented as mean SD (n = 3), P‐value was calculated using Student's t‐test.
(F) Left panel: Quantification of tumour volume over 52 days in nude male mice xenotransplanted with PC3-docetaxel resistant cells and treated with either MK-1775 (M, black line), MK-1775 and micellar taxane (MT, blue line), micellar taxane and OGX-011 (TO, red line) or MK-1775, micellar taxane and OGX-011 (MTO, green line). The error bars indicate mean ± SEM, n=8. Right panel: Slopes of tumor growth between groups, were compared by ANOVA followed by Dunnett's post hoc analysis..*p<0.05, ***p<0.001 .p=0.0488 (M to TO); p=0.0007 (M to MTO).
D, E) Vessel density assessment by means of fluorescence, statistical significance was analyzed by Anova test (P < 0.05 was considered significant: *=0,0019).
(E and F) iEM analysis of pex19 (E) and pex19 atg1 (F) cells using α-Pex14 antibodies.
E. Muscle fiber size (100 fibers/mouse) was quantified from CHOP −/− (black, n = 6) or CHOP −/−, Beclin-1 +/− mice (white, n = 6) 7 days post sciatic nerve transection. Left panel shows fiber size distribution, middle panel shows cumulative percent of fibers as a function of fiber area, and right panel shows relative fiber cross sectional area (mean +/− SEM). Left, middle panels, p<0.0001 by Mann-Whitney test. Right panel, p<0.001 by Student's t test.
B. 293T cells were transfected with the indicated combinations of DNAs, cultured for 24 hours, and subjected to in vivo ubiquitination assays.
Representative H&E-stained histological sections of ear tissue of tamoxifen-treated mice (Scale bar represents 200 μm). Arrowheads indicate infiltrates of immune cells.
A. Protein sequence alignment of C-terminal regions of UPF3 proteins from different mammalian species (labeled on the left).
(E) The FLIPR Tetra® system was used to determine the effect of LicoB on ATP-induced Ca2+ flux in LPS-primed BMDMs.
B. NLK phosphorylates YAP Ser 128 in vitro. NLK-WT or NLK-KN was transfected into HEK293A cells and immunoprecipitated. An in vitro NLK kinase assay was performed using recombinant GST-YAP as a substrate. Phosphorylation of YAP Ser 128 was determined by immunoblotting with phospho-YAP (S128) antibody.
(C) Type of mutations associated with the indicated functional subclasses (which are indicated following the color codes shown in the inset present in panel B).
N. Percentage of right versus left forepaw use before and 21 days after injection with hSNCA (left hemisphere) and control lentivirus (CTL) or hSNCA and lenti-Ifnb (right hemisphere). Bars are mean + SEM. YYY p<0.001 by ANOVA and **p<0.01 by post hoc Tukey's multiple comparison correction. N=6/hSCNA-CTL and 8/hSCNA-Ifnb.
B. Dsl1pVN•ε-COPVC BiFC foci showed different subcellular distribution depending on the growth status of cells. Cells were cultured in PM+ura medium with or without 2 % glucose at 30 °C for 90 min, and imaged. BiFC signals dispersed under glucose starvation, resulting in an ER exit site-like fluorescence pattern. Scale bar 10 µm.
(f) LC3B puncta and PtdIns(3) P levels were analysed with anti-LC3B and the biotin-2XFYVE domain probe. Representative immunofluorescence images of LC3B and 2XFYVE domain binding are shown (scale bars, 10 μm). (g) Quantification of LC3B puncta from f. Details of quantification are provided in the Methods; Data shown in g-i are mean+s.d. from a minimum of 6 unique fields of view from a representative experiment (see statistical source data in Supplementary Table S1). (h) Total PtdIns(3) P was quantified from the experiment in f. Error bars were calculated as in g. (i) Quantification of PtdIns(3) P that co-localizes with LC3B on amino-acid withdrawal from the experiment described in f.
B. The cells described in (A) were analyzed by RT-qPCR for the indicated target genes (n=4). Error bars indicate the S.E.M. (*p< 0.05, **p < 0.01; paired Student's t-test).
(C) Heatmap showing the altered Hippo related genes in the transcriptome profiles. The parameter of the color key indicated the fold changes converted to log2 of gene fragments per kilobase per million mapped reads (FPKM) values.
(L) A representative western blot of RKO cells following Wnt3a treatment and Atg7 siRNA.
B Ca2+ signals evoked by mixing of sperm with 80 mM KCl and the CatSper inhibitor MDL12330A.
G Electron micrographsin N1E-115 cells treated with siControl or siINPP5Es were cultured in growth medium. Arrowheads indicate autophagosomes. Bar, 1 µm.
Flow cytometry analysis of day 7 cell cultures under retinal differentiation from wildtype, PAX6 KO and PAX6D KO cell lines. Flow cytometry analysis of day 20 cell cultures under retinal differentiation from wildtype, PAX6 KO and PAX6D KO cell lines.
B. Dephosphorylation of T532, T539 and S558 on Apc1 by PP2A-B56. MBP-fused Apc1-loop500 WT or its derivatives (L557A/V560A and E562A) was incubated in anaphase extracts supplemented with non-degradable cyclin B at 23˚C for 1 h, isolated by amylose beads and further incubated in the presence (78 nM) or absence of purified PP2A-B56γ at 23˚C for 20 min. The proteins were recovered by amylose beads, separated by SDS-PAGE and detected by immunoblotting with phospho-specific or MBP antibodies. The signals of a phospho-specific antibody and MBP antibody on the same membrane were detected in the 800- and 700-nm channels, respectively. The two channels were pseudo-coloured (green; pT532, pT539 and pS558, red; MBP) and overlaid in the bottom panel (Overlay). The signal of pS558 was very faint in L557A/V560A mutant probably because these two residue are close to S558, interfering with pS558 antibody recognition.
(A) Scheme of PhotoClick cholesterol methodology to detect C99 interaction with cholesterol.
(H) Similar to (G) except that XO8 GSC transduced with lentiviral shRNAs were treated with MG132. The mean +S.D. values from the three independent experiments are shown after normalization to that of control cells treated with DMSO. For statistical analysis, student t-test (two-sided, one type) was used. * P value: #1, 0.026; #5, 0.0033; #6, 0.0482.
Relative transcript levels of thermogenesis-related genes of iBAT from WT and Parkin-KO mice exposed to acute cold (4ºC, 24h) compared to those maintained at the control temperature (22ºC). (n=8; WT) (n=6; Parkin-KO). Data are presented as means ±s.e.m. *p<0.05, **p<0.01, ***p<0.001, CTL vs. cold; #p<0.05, WT vs. Parkin-KO. ANOVA with Tukey's post hoc test.
Analysis of RV hypertrophy [RV/(LV+S)] for the indicated groups (7 rats in each group). Data information: Values are expressed as mean ± SEM. Statistical test: t-test (*P < 0.05 vs. respective controls or between the indicated groups
(E) RNA electrophoretic mobility shift assay done with 32P-labeled synthetic miR-122 and recombinant HuR proteins. Radiolabelled miR-122 (100 fmol) was incubated with increasing concentration of FL-HuR (5-100nM) or HuRΔIII (100 nM) and gel shifting of miR-122 were marked by arrowhead. Position of the free probes is marked by an arrow. In the right panel, 1pmol of unlabelled TNF-alpha AU-rich element encoding synthetic RNA was used to compete with miR-122 binding of full length HuR. Amount of HuR or HuRΔIII used for gel shift assay were premeasured by densitometric estimation of coomassie stained gel bands from SDS page.
(B) Homozygous BrafAVKA mice show reduced splenic cellularity. n = 7, mean + SEM, t-test, * p < 0.05.
(D) Kaplan-Meier survival graph depicts percentage survival of mock and CHIKV infected irgm1+/+ and irgm1-/- neonates during the course of infection
E. ELISA of IFN-β (upper), IL-6 (lower) levels in the supernatant of (A) and (B), and in HDAC6+/+ and HDAC6-/- BMDMs treated with poly(I:C) (20 µg/ml) or transfected with 5'ppp-dsRNA (1 µg/ml).
Combined median fold-change in RNA (A) levels between NUP58 mutant clones and WT cells (calculated using n=4 RNA-seq and n=3 mass spectrometry datasets). Data were visualized using Cytoscape. White: comparable average expression to WT; red: upregulated relative to WT; blue: downregulated relative to WT. Nodes belonging to the same subcomplex are grouped; edges represent physical interactions
(U and V) ATG-9::GFP puncta in epg-6 (U) and epg-8 (V) mutants colocalize with SQST-1 aggregates. (W and X) In unc-51 (W) and atg-18 (X) mutants, ATG-9::GFP partially colocalizes with SQST-1 aggregates.
H. CSF-arrested extracts were either mock- or RNF4-depleted and recombinant His-RNF4 was supplemented to RNF4-depleted extracts to a final concentration of 7 ng/μL where indicated. Protein samples were immunoblotted with the indicated antibodies.
Bar graph of forepaw digit length in age-matched untreated (blue) vs. losartan-treated C7-hypomorphic mice (red) after 2, 4, and 7 weeks of treatment. The length of digits at the start of the experiment was set to 100%; the quantification procedure is described in detail in the Materials and Methods section. Losartan very potently inhibited the reduction of digit length. Values represent mean ± S.D. Due to the inherent heterogeneity in disease progression, equal variance could not be expected and statistical significance was therefore analyzed by the unpaired t-test with Welch's correction; for 2 weeks, **P = 0.0021, and for 4 and 7 weeks, ***P < 0.001 (n = 14 per group).
SEC-MALLS analysis of Mpc3, colour designation as in (B). The protein fractions across the peak (D, inset) were assessed as in (B).
Mature rRNA analysis on ethidium-stained denaturing agarose gels. The same amounts of total RNA extracted from the indicated flies, and from S2R+ cells depleted or not of Mettl5, were loaded. The 28S/18S ratio was established by densitometry.
(B) Immunofluorescence staining for VIM (green) or E-cadherin (green) and RAD21 (red) in a panel of MCF7 or HCC1143 cells.
(E) Representative images (top) and bar plot quantification (bottom) showing the adhesion of calcein-labeled U937 monocytes to ECs treated with or without TNF-α ± miR-3679-5p. Scale bar represents 250 μm. Graphs are representative of three independent experiments. Data are shown as means ± SD. *P < 0.05 compared to TNF-α (-) mimics (-). † P < 0.05 compared to TNF-α (+) mimics (-). Statistical differences were analyzed by the Tukey-Kramer test.
Fluorescence microscopy recordings showing sfGFPTssM foci in the parental (WT) and TssM mutated strains (TssM Q779C/N780C, TssM ∆777-783). TssM foci containing cells are indicated by arrowheads. Microscopy analyses were performed independently three times, each in technical triplicate, and a representative experiment is shown. Scale bars, 1 µm.
(A) Mitochondrial iron quantified by ICP-MS in quadriceps of C26-tumor bearing mice after iron carboxymaltose supplementation (n=7-8). Data information: For all data, n represents the number of biological replicates. Statistical significance was calculated by unpaired, two-tailed Student's T-test. Data are mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001 compared to control and #p < 0.05, ##p < 0.01, ###p < 0.001 compared to C26 untreated group.
I) Impact of AGR2 blocking antibodies on AGR2-mediated monocytes migration was tested using Boyden chambers as described above. The concentrations of recombinant human AGR2 was of 200 ng/ml and decreasing amounts of antibodies were used from 20 µg to 1 µg. The non-relevant antibody (Isotype) was used at the maximal dose of 20 µg. Data are representative of three independent experiments. ns: non-statistically significant, (*): p=0.0165 (Ab=20μg/ml), 0.0223 (Ab=10μg/ml) and 0.0493 (Ab=5μg/ml), respectively.
(I) oCI inserted into the cochlea (dashed black lines) via a cochleostomy in the basal cochlear turn (black, solid line). The round window niche is highlighted by a dashed white line, the round window by a solid white line. SA: stapedial artery.
(B) Quantification of body weight changes in control (n=9) and cKO (n=10) mice during tumor development.
(C), Cumulative histograms based on fractional anisotropy (FA) values. (D), show the number of tensors relative to FA values. As FA values increased, the structural number of tensors) differences increased between the control and Plcg1f/f;Nes-Cre mice. (n = 4; Shapiro-Wilk and t-test; *p < 0.05). Data are presented as the mean ± s.e.m.
E) Heatmap for H3K27ac ChIP-seq signal in the experimental conditions described in B).
D Quantitative RT‐PCR was performed to assess KLK3 mRNA levels under agonist or antagonist treatments. The data are the mean of triplicates ± SD.
(I) Left: representative confocal images of Stat3-/- and MLS-Stat3 cells subjected to proximity-ligation-assay (PLA) by using anti-Stat3 and anti-ATAD3 antibodies. DAPI serves as a nuclear counterstain. Red dots indicates spacial proximity between Stat3 and the nucleoids marker Atad3. Right: histogram showing quantification of PLA assay performed on Stat3+/+, Stat3-/- and MLS-Stat3 cells. Number of red dots/cell are plotted. Note that double staining in MLS-Stat3 cells results in increased number or red dots compared to Stat3-/- cells Mean and s.e.m. of >15 cells for each sample are shown. Unpaired t-test: ** P<0.01 *** P<0.001. Scale bar, 10µm. See also Appendix Figure S7D.
B, Heatmap showing the expression profiles (ordered by phase) of 482 rhythmic transcripts (JTK-Cycle, p < 0.05, FDR=0.31) C, Phase distribution of circadian transcripts shown in B
D) Q-PCR analysis of Wnt and YAP target gene expression in intestinal crypts isolated at 1 day after 12Gy irradiation. Note the inhibition of Axin2, Sox9, YAP, Ctgf, Cyr61, and TEAD family expression upon treatment with Porcupine inhibitor LGK974. The mild reduction of Sox9 mRNA expression by LGK974 at 1 day after irradiation (1dpi) becomes more pronounced at 3 days after irradiation (3dpi). n = 4 biological replicates per condition, statistical analysis was performed with Student's 2-tailed t-test, error bars = 1 SD, * p<0.05, ** p<0.01, ***p<0.001.