EMBO/soda-nel huggingface dataset:
Calcium signaling induces a partial EMT (2021)
Figure 2

Figure 2: Ca2+ influx is sufficient to drive a P-EMT phenotype and increased migration and invasion

Representative 20X brightfield and fluorescent images of murine YFP+ tumor cells treated for 72h with vehicle control (DMSO), 2.5μM Ionomycin, or 10ng/ml TGFβ and co-stained for E-cadherin (Red) and DAPI (Blue). Scale bar is 100μm.

Representative flow cytometry analysis of surface ECAD (Left), MFI of surface ECAD (Middle), and percentage of surface ECAD negative cells (Right) in murine PDA cells, after treatment with DMSO, 2.5μM Ionomycin (IONO), and 10ng/ml TGFβ for 72h. Representative of 3 independent murine PDA cell lines run in triplicate. Statistical analysis by ANOVA (****, p<0.0001; non-significant (NS); ±SD).

Top: Relative mRNA expression of Ecad after treatment with 2.5μM ionomycin or 10ng/ml TGFβ for denoted time. Bottom: Western blot analysis of total E-cadherin and Vimentin protein for denoted time. Experiment was run in duplicate with three different murine PDA cell lines. Statistical analysis by ANOVA (***, p<0.001; non-significant (NS); ±SEM).

Normalized MFI of surface E-cadherin in PDA cells treated with DMSO, 2.5μM Ionomycin (IONO), and 10ng/ml TGFβ for 7 days, followed by withdrawal of Ionomycin or TGFβ for 7 days as indicated on the x-axis. Treated cells were analyzed at day 2, 3, and 7. Withdrawn cells were analyzed on days 1, 2, and 7. Experiment was performed in duplicate in two different murine PDA cell lines. Error bars indicate SD.

Quantification of live cellular migration over 4h after treatment with DMSO, 2.5μM Ionomycin (IONO), or 10ng/ml TGFβ for 48hrs. (n=16 cells per condition. Experiment was run in triplicate in two murine PDA different cell lines) (Right). Quantification of transwell migration after treatment with DMSO, 2.5μM Ionomycin (IONO), or 10ng/ml TGFβ for 72h (n= 2 cell lines, 3 replicates per cell line with 3 20X images taken per transwell) (Left). Statistical analysis by ANOVA (*, p<0.05; ****, p<0.0001; non-significant (NS); ±SD).
Calcium signaling induces a partial EMT (2021)
Figure 3

Figure 3: Ionomycin treatment induces mesenchymal gene transcription without repressing epithelial gene transcription

Schematic for RNA sequencing after EMT induction for 48h. Heatmap illustration of EMT related genes in three independent murine PDA cell lines, sequenced in duplicate, treated with DMSO, 2.5μM Ionomycin, or 10ng/ml TGFβ. Scale indicates Z-score.

GSEA of ionomycin versus DMSO (Left) or TGFβ versus DMSO (Right) for EMT signatures. NES, nominal P-value, and FDR are shown. Statistical analysis performed in GSEA.

GSEA of ionomycin versus DMSO (Left) or TGFβ versus DMSO (Right) for calcium signatures. NES, nominal P-value, and FDR are shown. Statistical analysis performed in GSEA.

Leading edge plots showing enrichment of C-EMT gene signatures in TGFβ treated cells (Left) or P-EMT gene signatures in ionomycin (IONO) treated cells (Right), based on GSEA. Enrichment scores (ES), NES, nominal P-value, and FDR are shown. Statistical analysis performed in GSEA.
Calcium signaling induces a partial EMT (2021)
Figure 4

Figure 4: Gαq signaling acts through calmodulin to induce P-EMT

Fura-2 Ca2+ measurements after addition of 5μM CNO (Top) or 10μM ATP (Bottom) in murine PDA cells expressing a Gαq-DREADD. Blue or red line indicates average of n=22 cells. ±SD. Tracings are representative of experiments performed twice in 2 independent cell lines.

Representative 20X brightfield images of Gαq-DREADD-expressing cells 48h after addition of CNO (Left). Scale bar = 100μm. MFI of surface E-cadherin in cells expressing a Gαq-DREADD after treatment with DMSO, 5μM CNO, or 2.5μM ionomycin (Right). Both experiments performed in triplicate in 2 independent cell lines. Statistical analysis by ANOVA (**, p<0.01; ±SD).

MFI of surface E-cadherin in CnB knockout lines after 48h treatment with DMSO, 2.5μM ionomycin, or 10ng/ml TGFβ. Experiment was repeated in two different murine PDA cell lines in triplicate. Statistical analysis by ANOVA (***, p<0.001; ****, p<0.00001; ±SD).

MFI of surface E-cadherin of murine PDA cells pretreated with 20μM W7 for 24h and then DMSO, 2.5μM ionomycin, or 20μM W7 with 2.5μM ionomycin for 24h. Experiment was repeated in two different murine PDA cell lines in triplicate. Statistical analysis by ANOVA (**, p<0.01; ***, p<0.001; non-significant (NS); ±SD).

MFI of surface E-cadherin of shRNA non-targeting (shNT) (Left) or shCAMK2B (Right) after 48h treatment with DMSO, 2.5μM ionomycin, or 10ng/ml TGFβ. Experiment was repeated in two different murine PDA cell lines. Statistical analysis by ANOVA (***, p<0.001; ****, p<0.00001; ±SD).

Expanded View Figure Legends
ATF7IP regulates SETDB1 nuclear localization and increases its ubiquitination (2019)
Figure 1

Figure 1 - ATF7IP represses the SETDB1-regulated exogenous provirus reporter and ERVs in mESCs

A Atf7ip KO cells show increased expression of SETDB1-regulated ERVs and the provirus reporter, MSCV-GFP (EV1B), as evidenced by RT-qPCR analysis. RNA expression was normalized to Hprt expression and is shown relative to the level in WT cells. Data are mean ± SD; n=3, technical replicates.

B Atf7ip KO mESCs (TT#2-12) show decreased H3K9me3 at the LTR of the SETDB1-regulated reporter and the ERVs, as evidenced by Native ChIP followed by qPCR analysis. Gapdh was used as a negative control. Data are mean ± SEM; n=5, independent experiments. *P < 0.05 and **P < 0.01 by paired t-test.

C SETDB1 cellular amount is mostly maintained in Atf7ip KO mESCs. Endogenous SETDB1-ATF7IP interaction is validated by anti-ATF7IP antibody co-IP experiment with anti-ATF7IP antibody.
ATF7IP regulates SETDB1 nuclear localization and increases its ubiquitination (2019)
Figure 2

Figure 2 - ATF7IP controls SETDB1 nuclear localization

A IF analysis shows preferential cytoplasmic localization of SETDB1 in Atf7ip KO mESCs. Representative projected images are shown, and the quantitative analyses are shown in B-D. Scale bar: 10 µm.

B SETDB1 signal in the nucleus that was determined by DAPI staining was calculated. The mean from three independent experiments is shown as a bar-graph with jittered points indicating the average % intensity of each experiment. Over 100 cells were analysed per sample per experiment. ***P < 0.001 by unpaired Student's t-test.

C, D SETDB1 foci in the nucleus that was determined by DAPI staining were calculated. Violin plot for SETDB1's foci numbers from all the cells analysed in three independent experiments is shown in c. The mean from the three independent experiments is shown as a bar with jittered points indicating the average number of each experiment in D. Over 100 cells were analysed per sample per experiment. *P < 0.05 by unpaired Student's t-test.

E, IF analysis shows preferential cytoplasmic localization of SETDB1 in Atf7ip KO mESCs. Representative projected images are shown. Arrows indicate the region used for line-plot analysis. Cells were treated with 10 ng/mL LMB or mock for 5 h before analysis. Scale bar: 10 µm.

F The line-plot analysis for E. Relative intensities of SETDB1 signal were measured by Image J. G The quantitative analysis for E is shown. SETDB1 signal in the nucleus that was determined by DAPI staining was calculated. The mean from three independent experiments is shown as a bar-graph with jittered points indicating the average % intensity of each experiment. Over 100 cells were analysed per sample per experiment. NS: P > 0.05, **P < 0.01 versus "Mock, WT" group by Dunnett's test.
ATF7IP regulates SETDB1 nuclear localization and increases its ubiquitination (2019)
Figure 3

Figure 3 - ATF7IP may have a role in SETDB1 import in HEK293T cells

A ATF7IP KO HEK293T cells shows endogenous SETDB1 cytoplasmic localization phenotype. Endogenous SETDB1 in HEK293T cells shows cytoplasm+nuclear localization profile. Scale bar: 10 µm.

B Over-production of exogenous mouse SETDB1 induces endogenous SETDB1 nuclear localization in both WT and ATF7IP KO HEK293T cells. The representative data of two independent experiments is shown. Scale bar: 10 µm.

C LMB treatment enhances SETDB1 nuclear accumulation in WT HEK293T cells, but no significant impact for ATF7IP KO HEK293T cells. Cells were treated with 10ng/ml of LMB for 5 h and then analysed with immunofluorescent staining. The representative data of three independent experiments is shown. Scale bar: 10 µm.

D SETDB1 signal in the nucleus shown in C was calculated. The mean from three independent experiments is shown as a bar-graph ± SEM; n=3. Over 50 cells were analysed per sample per experiment. **P < 0.01 by Student's t-test (two-sided test).

E 5 h of proteasome inhibitor bortezomib treatment do not have much impact on SETDB1 relative nuclear accumulation in ATF7IP KO HEK293T cells. The representative data of three independent experiments is shown. Scale bar: 10 µm.

F SETDB1 signal in the nucleus shown in E was calculated. The mean from three independent experiments is shown as a bar-graph ± SEM; n=3. Over 50 cells were analysed per sample per experiment. Statistics comparison was only shown between without and with drug treatment in WT and ATF7IP KO cells. *P < 0.05 and **P < 0.01 by Dunnett's method.
ATF7IP regulates SETDB1 nuclear localization and increases its ubiquitination (2019)
Figure 4

Figure 4 - N-terminal region of SETDB1 contributes to its cellular localization

A HEK293T cells were transfected with V5-SETDB1 and either empty or 3xF-ATF7IP expressing vector. Over 50 transfected cells analysed per sample were analyzed. The representative data of two independent experiments is shown. Scale bar: 10 µm.

B HEK293T cells were transfected with V5-SETDB1 d1 mutant and either empty or 3xF-ATF7IP expressing vector. Over 50 transfected cells per sample were analysed. The representative data of two independent experiments was shown. Scale bar: 10 µm. The yellow arrowheads indicate the cells that show nuclear (and cytoplasmic)-localization of introduced exogenous mSETDB1.
ATF7IP regulates SETDB1 nuclear localization and increases its ubiquitination (2019)
Figure 5

Figure 5 - ATF7IP-mediated SETDB1 nuclear localization enhances SETDB1 ubiquitination

A Co-transfection with ATF7IP augments the K885 ubiquitination of SETDB1. HEK293T cells were transfected as in Figure 4A. After the transfection, V5-SETDB1 was immune-purified with anti-V5 antibody and used for WB analysis.

B ATF7IP regulates the ubiquitination of SETDB1 in mESCs. Endogenous SETDB1 was immune-purified from WT or Atf7ip KO mESCs cells and used for WB analysis.

C LMB treatment increased the relative intensity of the upper ubiquitinated upper band of SETDB1 in Atf7ip KO mESCs. Cells were treated with 10 ng/mL LMB or mock for 5 h before analysis.

D HEK293T cells were transfected with either 3xF- or 3xF-NLS-SETDB1. Over 50 transfected cells per sample were analysed. The representative data of two independent experiments is shown. Scale bar: 10 µm.

E Nuclear localization itself promotes the ubiquitination of SETDB1. HEK293T cells were transfected with 3xFLAG- or 3xFLAG-NLS-SETDB1. After FLAG-IP, the purified SETDB1s were analyzed by WB.

F, G IF analysis was performed with Atf7ip KO mESCs stably expressing 3xF- or 3xF-NLS-SETDB1. Representative images are shown in F, and the quantitative analysis is shown in G. Scale bar: 10 µm. Addition of NLS increases nuclear localization of SETDB1 in Atf7ip KO mESCs. The mean from three independent experiments is shown as a bar-graph with jittered points indicating the average % intensity of each experiment. Over 50 cells were analysed per sample per experiment. ***P < 0.001 by unpaired Student's t-test.

H Nuclear localization promotes the ubiquitination of SETDB1 in Atf7ip KO mESCs. Atf7ip KO mESCs expressing 3xF- or 3xF-NLS-SETDB were used for FLAG-IP, and the purified SETDB1s were analyzed by WB.
Quantifying compartment-associated variations of protein abundance in proteomics data (2018)
Figure 3

Figure 3. Remodeling of the mitochondrial and extracellular proteome during C.elegans aging. Analysis of the abundance distribution for (A) cytoplasmic, (B) mitochondrial, and (C) extracellular proteins across 5 age groups in C.elegans (Walther et al, 2015). Each age group was compared against a pool reference sample using SILAC (Ong et al, 2002). Distribution of protein fold changes for the different time points are shown as density plots and as as boxplots (inset); below the boxplots, asterisks mark the time points that show significantly different distribution of fold changes compared to the first time point (Mann-Whitney test p<0.01). Abundance variation of complex members for (D) three mitochondrial complexes (respiratory complex I, mitochondrial ribosome and mitochondrial import/export proteins). For each complex, the abundance variation of each member (colored in grey) over the 5 age groups is reported with the Δ SILAC ratio (difference between the experimental SILAC ratio of a time point and the SILAC ratio at day 1, left) and the CNV value (right). For each age group, the box plot (colored as the corresponding time-point in the panels A-B-C) represents the variance between the abundances of the complex members. Significant changes (Mann-Whitney test p<0.05) are marked with a red star. (E) Variation of the mitochondrial proteome over the lifespan of C.elegans (day 1 and day 22). Respiratory chain complex I and mitochondrial ribosomal proteins are highlighted in green and purple, respectively (selected proteins, with extreme CNV values, are indicated). (F) Variation of the extracellular proteome abundance over the lifespan of C.elegans (day 1 and day 22). Four proteins have been selected (highlighted with a colored circle: purple for NAS-34, green for Y45F10C.4, blue for Vitellogenin-1, black for Y45F10C.2) for their slower or accelerated increase of abundance compared to the rest of extracellular proteins. The variation of the selected proteins (highlighted with the same colors) throughout the worm lifespan is represented in the middle box, with the average of the extracellular proteome colored in yellow. Related to Figure EV5 and Dataset EV6.
A necessary role of DNMT3A in endurance exercise by suppressing ALDH1L1-mediated oxidative stress (2021)
Figure 3

Figure 3. Dnmt3a-KO soleus muscle displays a decreased oxidative capacity with a reduced mitochondrial respiration.

(A-D) Succinate dehydrogenase staining was performed in WT and MCK-KO soleus at sedentary (A, B) and after a bout of low-intensity exercise for 50 min (C, D) (10X, 20X magnifications), and the staining intensity was quantified using ImageJ (n = 6, means ± SEM, * p < 0.05, two-tailed student's t-test).

(E-H) The analogous set of data is shown with WT and MCK-KO GA muscles. (n = 6, means ± SEM, * p < 0.05, two-tailed student's t-test).

(I-L) The analogous set of data is shown with WT and MCK-KO EDL muscles. (n = 6, means ± SEM, two-tailed student's t-test. EDL: Extensor digitorum longus)

(M, N) Mitochondrial respiration was measured in WT and MCK-KO soleus tissue after a bout of low-intensity exercise for 50 min under basal conditions and in response to 4 mM oligomycin (complex V inhibitor), 4 mM FCCP (uncoupler), or 4 mM each of rotenone and antimycin A (complex I inhibitor) (n = 8, means ± SEM, * p < 0.05, two-tailed student's t-test and two-way ANOVA followed by Bonferroni post-hoc testing).

(O, P) Mitochondrial respiration was measured in Dnmt3a knocked down L6 myotubes which were transduced with lentiviral under basal conditions and in response to 4 mM oligomycin (complex V inhibitor), 4 mM FCCP (uncoupler), or 4 mM rotenone and antimycin A (complex I inhibitor) (n = 5, means ± SEM, * p < 0.05, two-tailed student's t-test and two-way ANOVA followed by Bonferroni post-hoc testing).
A necessary role of DNMT3A in endurance exercise by suppressing ALDH1L1-mediated oxidative stress (2021)
Figure 4

Figure 4. Transcriptome analysis identifies Aldh1l1 as a key target gene of DNMT3A in the soleus muscle.

(A, B) (A) RNA-Seq was performed in WT and MCK-KO soleus muscle at rest. The scatter plots show differentially expressed genes in MCK-KO soleus muscle at sedentary (A) and after a bout of low-intensity exercise for 50 min (B) (FDR<0.05, p < 0.05).

(C) Proposed model for ROS regulation during loss of Dnmt3a. Loss of DNMT3A increases ALDH1L1 expression, thus leading to the increase in NADPH levels and increased activity of NADPH oxidase, leading to increased ROS levels. The increased oxidative stress contributes to mitochondrial dysfunction and muscle fatigue.

(D) Q-PCR validation of Aldh1l1 at sedentary and after exercise for 50 min (n = 6, means ± SEM, * p < 0.05, two-tailed student's t-test).

(E, F) ALDH1L1 protein expression and the quantification in WT vs. MCK-KO soleus, GA and EDL muscles at sedentary and normalizing to GAPDH using ImageJ.

(G) The map of CpG-rich promoter regions of Aldh1l1 and MeDIP and ChIP primers (P1-P5) that cover the CpG rich regions. The numbers correspond to the position from the transcriptional start site of Aldh1l1.

(H) MeDIP-qPCR was performed in WT and MCK-KO soleus muscle to assess differential methylation using primer sets from (G) (n = 4, means ± SEM, * p < 0.05, two-tailed student's t-test).

(I) DNMT3A ChIP-PCR was conducted in WT and MCK-KO soleus muscles using primer sets from (G) (n = 3, means ± SEM, * p < 0.05, two-tailed student's t-test).

(J) H3K27ac ChIP-PCR was conducted in WT and MCK-KO soleus muscles using primer sets from (G) (n = 3, means ± SEM, * p < 0.05, two-tailed student's t-test).
A necessary role of DNMT3A in endurance exercise by suppressing ALDH1L1-mediated oxidative stress (2021)
Figure 5

Figure 5. ALDH1L1 contributes to the oxidative stress and mitochondrial defect in loss of Dnmt3a.

(A, B) NADPH levels (A) and NOX (B) level was measured in WT and MCK-KO muscles at rest and after a bout of low-intensity exercise for 50 min (n = 6, means ± SEM, * p < 0.05, two-tailed student's t-test and two-way ANOVA followed by Bonferroni post-hoc testing).

(C-G) L6 myotubes were transduced with lentiviral expression plasmids for Flag-ALDH1L1 and GFP. NADPH levels (C), H2O2 levels (D, E) , Mitochondrial respiration (F, G) were measured from these cells in the presence and absence of NADPH oxidase inhibitor apocynin (n = 3 per group, for (C-E) and n = 5 for (F, G), means ± SEM, * p < 0.05, two-tailed student's t-test and two-way ANOVA followed by Bonferroni post-hoc testing).

(H-K) Single and double knockdowns of Dnmt3a and Aldh1l1 in L6 myotubes were achieved by lentiviral transduction. NADPH levels (H) and NOX activity (I) were measured in single and double knockdowns of Dnmt3a and Aldh1l1 in L6 myotubes. (n = 3, means ± SEM, * p < 0.05, two-tailed student's t-test and two-way ANOVA followed by Bonferroni post-hoc testing). (J, K) H2O2 levels were measured in single and double knockdowns of Dnmt3a and Aldh1l1 in L6 myotubes. (J: n = 3 and K: n = 6 for Control, Aldh1l1 KD, Aldh1l1 KD + Dnmt3a KD, n = 5 for Dnmt3a KD, means ± SEM, * p < 0.05, two-tailed student's t-test and two-way ANOVA followed by Bonferroni post-hoc testing).
A necessary role of DNMT3A in endurance exercise by suppressing ALDH1L1-mediated oxidative stress (2021)
Figure 6

Figure 6. NAC treatment partially rescues reduced oxidative capacity in Dnmt3a KD myotubes and exercise intolerance in MCK-Dnmt3a KO mice.

(A, B) Exercise capacity of MCK-KO and WT mice treated with PBS (vehicle) or NAC (200mg/kg, i.p). (n = 4 WT and n = 6 MCK-KO , mean ±SEM, * p < 0.05, two-tailed student's t-test and two-way ANOVA).

(C-E) (C) Hydrogen peroxide (H2O2) levels (n = 6 for Control groups and Dnmt3a KD with NAC treatment group n = 4 Dnmt3a KD, means ± SEM, * p < 0.05, two-tailed student's t-test and two-way ANOVA followed by Bonferroni post-hoc testing).(D, E) mitochondrial respiration in Dnmt3a knockdown and control L6 myotubes treated with NAC (3mM) or vehicle treatment for 24hrs (n = 5 Control groups n = 3 Dnmt3a KD, n = 4 Dnmt3a KD with NAC treatment groups. means ± SEM, * p < 0.05, two-tailed student's t-test and two-way ANOVA followed by Bonferroni post-hoc testing).
A necessary role of DNMT3A in endurance exercise by suppressing ALDH1L1-mediated oxidative stress (2021)
Figure 7

Figure 7. ALDH1L1 knockdown in vivo partially rescues exercise intolerance in MCK-Dnmt3a KO mice.

(A) Aldh1l1 mRNA expression in various muscles in MCK-KO mice that were transfected with gRNA DNAs against Aldh1l1 or control. (n = 4 for Soleus, n = 3 GA gCont and n = 4 GA gAldh1l1, n = 4 EDL gCont and n = 3 EDL gAldh1l1 , means ± SEM, * p < 0.05, two-tailed student's t-test).

(B, C) ALDH1L1 protein expression and the quantification in MCK-KO muscles that were transfected with gCont vs. gAldh1l1 using ImageJ. (n = 3, means ± SEM, * p < 0.05, two-tailed student's t-test).

(D, E) Exercise capacity of WT and MCK- KO with or without transfection of gCont vs. gAldh1l1 under the low intensity regimen (n = 4 WT + gCont, n = 9 MCK- KO + gCont, and MCK- KO + gAldh1l1, *p<0.05, means ± SEM, two-tailed student's t-test and one-way Anova).

Expanded View Figure Legends
A regulatory region on RIPK2 is required for XIAP binding and NOD signaling activity (2020)
Figure 1

Figure 1. Flag-RIPK2 knock-in mice as a tool to study endogenous NOD signaling mechanisms.

A Tissue distribution of RIPK2 determined by anti-FLAG immunoprecipitation. Organ homogenates from WT (wild-type) and KI (homozygous FLAG-RIPK2) mice were subjected to anti-FLAG immunoprecipitation and immunoblotting.
B Inflammatory signaling in wild-type (WT/WT), RIPK2 CRISPR KO (KO/KO) and FLAG-RIPK2 heterozygous (WT/KI) and homozygous (KI/KI) BMDMs. BMDMs were primed with IFNy, stimulated with MDP for indicated times and analysed by immunoblotting.
C Cytokine production of RIPK2 CRISPR KO (KO), wild-type (WT) and FLAG-RIPK2 heterozygous (WT/KI) and homozygous (KI/KI) BMDMs in response to MDP. BMDMs were left untreated or treated with IFNy or IFNy and MDP over-night and cytokines were measured by ELISA. N = 5-8 mice. Shown is average ± SEM. ns = P > 0.05; ** = P ≤ 0.01; **** = P ≤ 0.0001; two-way ANOVA.
D Serum cytokines in RIPK2 CRISPR KO (KO), wild-type (WT) and FLAG-RIPK2 heterozygous (WT/KI) or homozygous (KI/KI) mice after i.p. MDP administration. Mice were injected i.p. with PBS or MDP, sacrificed after 4h and serum cytokines were measured by ELISA. N = 3-6 mice. Shown is average ± SEM. ns = P > 0.05; ** = P ≤ 0.01; two-way ANOVA.
A regulatory region on RIPK2 is required for XIAP binding and NOD signaling activity (2020)
Figure 2

Figure 2: Identification of RIPK2 PTMs during NOD signaling by mass spectrometry.

A Two step enrichment to isolate ubiquitinated RIPK2 from BMDMs. Protein lysates from FLAG-RIPK2 BMDMs (A) were sequentially subjected to ubiquitin enrichment (UBA, B) and FLAG pulldown (C) prior to protein elution and subsequent mass spectrometry analysis.
B Schematic representation of RIPK2 PTMs detected in MDP-stimulated vs. unstimulated BMDMs. Red: phosphorylation, green: ubiquitination. N = 3 experiments
C DiGly-modifications on RIPK2 in L18-MDP stimulated vs. unstimulated THP-1 cells determined by diGly proteomics. Shown are p-values and log2 differences of modified peptides based on imputed values; t-test. Score: peptide identification score as determined by MaxQuant.
D Sequence conservation of stimulation-dependent modified serine (red) and lysine (green) residues amongst mammals. The degree of conservation is indicated by color saturation.