EMBO/sd-character-level-ner huggingface dataset:
E Electrostatic surface potential of the symmetric FAK dimer as seen from the membrane proximal view. Both, the FERM (KAKTLRK) and the kinase (K621, K627) have extensive positive charges on this surface for interaction with negatively charged PI(4,5) P2 lipids. The kinase domains are encircled by a yellow dotted line.
D. Response of HyPer7 probes targeted to indicated compartments to treatment with 25 µM of exogenous H2O2. Indicated cell lines (black, wild type; red, PRDX1/2 DKO) were grown in glucose-containing medium. Solid line represents average, points colored in the lighter version of the respective color are the corresponding ratios measured in individual cells. Data information: Statistical analysis was only performed to compare the PRDX1/2 DKO with the wildtype. As most of the data were not normal distributed, instead of a t-test, a Wilcoxon/Mann-Whitney-U-test was performed and samples were compared in pairs. *, p ≤ 0.05, **, p ≤ 0.01, ***, p ≤ 0.001
(C) Quantification of npc1−/− PC density by lobule in C1.4 at 70 d. Observed and expected densities are shown for npc1−/− PCs in each lobule. No clear rescue of npc1−/− PCs was observed in any lobule (p > 0.05 for all lobules comparing observed versus expected if loss occurs, except II and III, where p-value is between 0.01 and 0.05; p < 0.001 for all lobules comparing observed versus expected if no loss occurs, except lobule X, where p > 0.05).
B Alanine substitution of positively charged residues in the KYKKLR sequence of MOAP-1 abolishes its interaction with p62. Replacement of the positively charged residues in the KYKKLR sequence of MOAP-1 with alanine (referred to as the M3 mutant) disrupts MOAP-1/p62 interaction, whereas alanine substitution in the neighboring region of positively charged KRRR (M1 mutant) and negatively charged EEE (M2 mutant) has no effect. LO2 cells were transfected with plasmid encoding Myc-MOAP-1 or the indicated alanine mutants together with plasmid encoding Flag-p62. The cells were then subjected to co-IP assay with anti-Myc antibody.
B, Western blot analysis for detecting SNCA oligomers. Data are represented as mean ± SEM. n=4; one-way ANOVA. Significantly different at p=2.5E-07*, 1.65E-07**, 0.022#, 0.029##, 0.046+, 0.015++, 0.0136&, 0.0016&& in graph B.
(c) IB3-1 cells were transfected with either HA-tagged human beclin 1 or the empty vector under nutrient starvation. Cells were immunostained with anti-LC-3 (red) and anti-CFTR (green). Yellow indicates co-localization. N, nucleus. Scale bar, 10 μm.
a. Relative mRNA expression levels of PRSS35 in primary fibroblast cultures isolated from WT and PRSS35-/- mice, untreated or after 24 hours stimulation with 10 ng/mL TGF-β1 (n>8 biological replicates per condition) (**** p<0.0001.; Two-way ANOVA with multiple comparisons). Data represent means of three technical replicates ± S.E.M.
(k) NRK cell lines stably expressing LAMP1-Cherry;clathrin-GFP were starved for 8 h and observed by confocal microscopy. The right panels show enlarged regions of interest. Scale bar, 5 μm.
F Purified recombinant GST‐KSHV‐TK and GST‐KSHV‐TK‐KINASE‐DEAD immunoblotted for phosphotyrosine and GST.
(D) Pulse chase reaction on UD and Tg templates performed as shown. Where present, Pol δcat (10 nM) was added directly after addition of the chase.
(E, F) RT-qPCRs to detect histone mRNA levels in the polyA+ (E) or the polyA- fraction (F) in cells treated with Cntl, ALYREF or ARS2 siRNA. The arrowhead and arrows indicate the cleavage site and primer location, respectively. The bars show the relative abundance of polyA+ forms to the actin mRNA (E) and that of polyA- forms relative to the 18S rRNA (F). Data information Error bars represent standard deviations from biological repeats (n=3). Statistical analysis was performed using Student's t-test. *P < 0.05, **P < 0.01, ***P< 0.001.
Schematic of Mitome siRNA imaging screen in OPA1S545R patient fibroblasts. Fibroblasts transfection and imaging as described in A. Supervised ML training performed on OPA1S545R fibroblasts treated with siRNA for OPA1 (hyperfragmented) NT control (normal), and DNM1L (rescued) were applied to single-cell trinary classification of OPA1S545R patient fibroblasts. Passages number P12.
Oct4‐GFP MEFs were introduced with the indicated factors and Oct4‐GFP‐positive colonies were counted on day 16 after virus infection. AP staining of iPSC colonies was shown below.
(T) CD8+ T cell recruitment in a transwell system by macrophages treated with IL10 or MSO/IL10, and glufosinate (10 and 20µM)/IL10 for 24 h versus macrophages treated with LPS/IFNγ; the migration of T cells cultured without macrophages (Mφ-) in presence of CXCL10 was used as positive control (n=4).
(C) HeLa cells transfected with GFP‐PKCδ and infected with Listeria WT for 4 h were analysed by IF using an antibody against NDP52. The arrow indicates an NDP52+ granule.
Confocal single plane images of third instar larval wing discs stained with: (C) anti-Ct (red) and anti-Zfh1 (green), (D) kirre[rp298]-lacZ (anti-β-gal, green) and anti-Zfh1 (red), (E) Ten-a[MI04411]::GFP (green), anti-Ct (red) and anti-Zfh1 (cyan), (F) anti-Nrt (red) and anti-Zfh1 (cyan), (G) Argk[CB3789]::GFP (green), anti-Ct (red) and anti-Zfh1 (cyan), (H) nkd[MI00209]::GFP (green), anti-Ct (red) and anti-Zfh1 (cyan), (I) Ama[NP1297]>GFP (green), anti-Ct (red) and anti-Zfh1 (cyan) and (J) Mef2>CD8-GFP (green), and fluorescent in situ hybridization of Ama-RNA probe (white).
D Immunoprecipitation (IP) assay for Nurr1 and Foxa2 protein binding. The ventral part of midbrains was dissected from 10-week-old mice, lysed, and subjected to IP. Nurr1/Foxa2 protein binding was detected by WB analysis using an anti-Foxa2 antibody in immunoprecipitates generated with anti-Nurr1 antibody (left), as well as by anti-Nurr1 WB assay in immunoprecipitates with anti-Foxa2 antibody (right).
RIGER analysis to identify genes that are preferentially essential in FUS-DDIT3-expressing SCP-1 cells. EV-transduced SCP-1 cells and 20 FUS-DDIT3-negative cancer cell lines screened with the same shRNA library were used as reference set. Genes were ranked according to relative shRNA depletion, and YAP1 was identified as top FUS‑DDIT3‑specific essential gene. NES, normalized enrichment score.
Representative images of phosphorylated histone 3 (pH3) antibody staining in mouse small intestine. Arrows indicate pH3 positive cells (I). Quantification of pH3 positive crypt cells per 100 μm of small intestines (n=4-6 mice per group) (J).
Effect of expression of HA-HuR on Ld infection in mice liver. TNF-α (Values are mean+/- s.e.m. and, n=5) and IL-10 (Values are mean+/- s.e.m. and, n=4) mRNA levels were checked from RNA isolated from liver tissues and 18S rRNA normalized Ct values were plotted (H and I, left panels). Relative fold change was calculated by ΔΔCt method and the values plotted for Ld count, TNF-α and IL-10 mRNA levels (G mean +/- s.e.m., (n=5), H mean +/- s.e.m., (n=6) and I mean +/- s.e.m., (n=4), right panel).
E Analysis of ubiquitin conjugation to endogenous TSC2 in TSC1-KO MEFs transfected (for 48 h) with (+) or without (-) TSC1 WT or K30A and treated with MG132 for 2 h before lysis.
(c) Ser 317/Ser 777 are required for glucose-starvation induced Ulk1 phosphorylation in vivo. HA-Ulk1 and mutants were transfected into HEK293 cells. Cells were starved for glucose for 4 h as indicated. HA-Ulk1 was immunoprecipitated and examined by western blot for mobility.
(B) Definition of transcript classes and putative enhancer RNA (eRNA) annotation. Top: non-coding RNAs are classified into four categories: upstream antisense RNA (uaRNA), convergent RNA (conRNA), antisense RNA (asRNA) and intergenic RNA. asRNAs and bidirectional intergenic RNAs originating from GenoSTAN enhancer state regions (Zacher et al., 2017) are classified as putative eRNAs (green). Bottom: exemplary genome browser view of TT-seq coverage in HCT 116 colorectal cancer cells and transcript annotation at the KLF6 locus (hg38; chr10:3,758,830-3,815,253; Due to the high expression of KLF6 the TT-seq coverage is cut at 200 to allow for better visualization of the surrounding eRNA signal. H3K4me1 ChIP-seq, H3K27ac ChIP-seq and DNase I-seq signal from ENCODE
(j) NRK or stable clathrin-GFP-expressing NRK cell lines were analysed by pre-embedding-immuno-electron microscopy using antibodies against GFP. Scale bar, 100 nm. (k) Quantification of the average number of gold particles per image from control or clathrin-GFP cells. n = 25 images from three independent experiments. The error bars indicate the s.d. Uncropped images of blots are shown in Supplementary Fig. S6.
786-0 cells expressing WT or ED GDH1 were supplemented with or without 500 μM methylated αKG for 36 hours, and then cells were collected to extract total mRNA. WB was performed using the indicated antibodies (E).
G) Proliferation assay of H3122 parental and isogenic drug-resistant cell lines, treated with DMSO, 100nM lorlatinib, 200nM alvocidib or 50nM dinaciclib for 72h (n=4).
A, PTPN3 and PTPN3 (D811A), but not PTPN3 (L232R), enhance Smad2 and Smad3 phosphorylation. HaCaT cells were stimulated with TGF-β (2 ng/mL) for 1 h. Levels of P-Smad2, P-Smad3, Smad2, Smad3, PTPN3 and GAPDH were detected by Western blotting.
(B) MPS1-induced filamentation experiments on the indicated mChRZZSF complexes (4 µM, further diluted to 0.5 µM for imaging) using a confocal spinning disk fluorescence microscope at 561 nm. Scale bar: 5 µm. Two technical replicates were performed.
(B) In B. pseudomallei 3000015237 isolate MX2014, two IS3 family transposable elements that carry two of the T6SS related genes (PAAR and DUF4123) are present upstream to the TA genes. However, in B. pseudomallei Nau24B-3 and vgh16R strains, the IS3 element which flank the TA and T6SS related genes, have been excised and a new ORF encoding hypothetical protein (H.P) has evolved at its place.
a) Rapamycin (Rap) treatment or nutrient deprivation attenuated the expression of the Wnt reporter TopFlash in HEK-293T cells. (n = 3; two asterisks, P 0.01). DMSO, dimethylsulphoxide.
Comparison of single-cell growth rates prior to CIP exposure for "D" cells that die and "S" cells that survive and regrow after CIP washout (E), and lag time of regrowth (F). Cells were cultured in fresh (EXP) or spent (STAT) flow medium. Gray and black lines indicate mean ± SD. Significance by Kruskal-Wallis and Dunn's multiple comparison test (E) and unpaired Mann-Whitney test (F): ns, not significant; ****p < 0.0001; 6 < n < 84. The data shown are from 2 independent experiments. Single-cell fate is independent of the growth rate before exposure to the drug. However, cells cultured in spent medium (STAT) grow at significantly slower rates, survive at higher frequencies, and recover faster after CIP washout compared to cells cultured in fresh medium (EXP).
GFP reconstitution in ATZ-HA transfected CRISPR17 MEF expressing FAM134B-T11 and GFP1-10-LC3. Scale bar: 10 μm. K Same as J by CLEM. ATZ-HA staining in red, LAMP1-positive endolysosomes in cyan. FAM134B:LC-induce GFP reconstitution in green. FAM134B in gold is shown. Scale bar: 1 μm.
(B) Potency of the combination ND-011992 + Q203 against various clinical isolates in an agar plate MIC assay. A dose-range of ND-011992 was tested against the clinical isolates in the presence of Q203. Q203 was used at 100 nM against the strains H37Rv, N1274, N1283, 123-20-0015, 123-20-0091, 123-20-0041, 123-20-0047, and at 20 nM against the stains N0072, N0157, N0145, N0052, and N0136. "S" indicates pan-susceptibility to anti-TB drugs; "MDR": multi-drug resistant; "XDR": extensively drug-resistant.
E-F, phase contrast images of the morphological changes in (E) Du145TXR and (F) MCF-7ADR cells cultured in normal or serum free medium followed by treatment with indicated agents for 12 hours. Scale bars, 10 or 25 μm. The red arrows indicate vacuoles. Data information: Results are representative of three independent experiments.
A. In situ HCR reveals that ccdc108 mRNA is specially detected in ciliated organs in zebrafish. Zebrafish embryos at the long-pec stage (48 hours post fertilization) were fixed and subjected to in situ HCR (purple). Embryos were then incubated with the Ac-tub antibody (green).
G) Ectopic expression of srd-1 in AWB neurons elicited a distinct repulsive behavior toward the sex pheromone in both males and hermaphrodites. Data information: For each transgenic strain, 3 independent lines were examined. We assayed 400 males from each strain in the sex pheromone chemoattraction assay. Two biological replicates were combined into a single value. Significance was determined using one-way ANOVA with Bonferroni correction: ***P<0.001. Means ± SEM (error bars) are shown.
Expression of neuronal nitric oxide synthase (NOS1) mRNA (F Bar graph represent mean±SD Statistics: one-way ANOVA followed by Tukey"s test for Significant differences between groups (p value) are indicated on graphs
A TRAF6 expression in differentiating CD4+ T cells. Naïve CD4+ T cells were obtained from wild type C57BL/6 mice by FACS and activated with anti-CD3/CD28 (1µg, and 2µg/ml) for the indicated times in the presence of distinct Thelper lineage-directing cytokines or under neutral activation conditions (Th0). After total RNA extraction and cDNA conversion, RT-PCR determined of Traf6 mRNA in differentiating Th0, Th1, Th17 and iTregs was determined.
B - C Quantification of spine density, synaptopodin clusters and synaptopodin-positive spines as shown in A (mean ± SEM. Kruskal-Wallis test with Dunn's multiple comparisons post-test. *** p < 0.0001. cald wt n = 34 cells, 2 experiments; cald KO n = 33 cells, 3 experiments; cald KO cald n = 10 cells, 1 experiment; cald KO JPK n = 14 cells, 1 experiment). (B) The total number of synaptopodin clusters is unaffected by the loss of caldendrin. (C) The number of synaptopodin-positive spines is reduced in cald KO compared to the WT neurons. This phenotype could be rescued by over-expression of caldendrin (cald KO + cald), but not by treatment with JPK (cald KO + JPK).
(F) Polysomal abundance of mRNAs (selected based on a nominal p-value < 0.01 cut-off in either the CMB vs. CTRL or CX vs. CTRL as analysed by limma) encoding components of mitochondrial oxidative phosphorylation based on polysome profiling data. Red denotes upregulation, blue denotes downregulation (n=3; genes with an adjusted P value (false discovery rate; FDR) ≤ 0.05 were considered to be significant, and are denoted with a black border).
(K) Diameter of C2C12 myotubes after 48h treatment with Deferoxamine 100µM (DFO), bathophenanthroline disulfonate 100µM (BPS), or apo-transferrin (Apo-Tf). 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.
C The 20‐residue Raver1 491-511 (lane 1) and the Matrin3 346-365 (lane 3) peptide fused to MS2 were transcribed and translated in vitro (Input) and then pulled down with GST‐PTB or with GST‐SXL as a control. Effects of single mutation of the Matrin3 PRI GILPPP to GIAPPP were also tested (lane 4).
(I) TRIP6 expression levels in (H) in control (shEGFP) and TRIP6 (shTRIP6) knockdown cells just prior to stretch were analyzed using RT-qPCR. (Mean ± SD; n=3; *P≤0.05, T-test).
(E) qPCR analysis of the indicated fetal genes in WT and IκBα KO-derived organoids. Data information: 3 technical replicates of a minimum of two organoids per genotype were analyzed Bars represent mean values ± standard error of the mean (s.e.m). p values were derived from an unpaired t-test, two-tailed, ****p-value<0.0001, **p-value<0.005, * p-value<0.05.
(B) Admixture analysis of the indicated HKC strains of Black versus White individuals, on the basis of the SNP genotype dataset with the simplest assumptions of two ancestries (K = 2). On the y-axis admixture proportions are represented as grey and black bars. On the x-axis, individual samples are reported. Dashed lines delimit Black individuals with more than 20% admixture of the other ancestry.
(C) Control of polymerization propensity for the Halo-tagged versions of AAT (lanes 1 and 4) and of ATZ (lanes 2 and 5). Polymers and monomers corresponding to (Miranda et al., 2010; Ronzoni et al., 2021) are seen with anti-Halo (lanes 1-3) or with the polymer-specific 2C1 antibody (lanes 4-6). Synthesis control in SDS-polyacrylamide gel by visualization of tetramethylrhodamine (TMR) ligand-labeled Halo-AATNNN and Halo-ATZNNN (lanes 7-9).
C, Growth curves of tumors, generated by subcutaneous injection of BT308NS, irradiated in the absence (2 Gy × 3 days) or in the presence (combo) of JNJ38877605, which was administered for 15 days as indicated (n = 7/condition). Vehicle: non-irradiated vehicle-treated tumors. *: one-way ANOVA, P=0.0006.
PP2A activity was measured using a protein phosphatase assay kit. PP2A activity assay was performed to evaluate PP2A activity in CIP2A-BP KO, LINC00665 ORF overexpressed (OE) and respective control TNBC cells.
E CMT-93 cell lines stably expressing Smad6 amino acids 400-441 were treated with LPS for the indicated time and expression of IκBα, IKKα, and phospho-IKKα/β was monitored by immunoblotting. As a positive control, CMT-93 cells were pre-treated with TGF-β1 for 2 h. CMT-93 cells stably expressing the empty vector pMSCV-puro were used as a negative control. β-actin was used as a loading control. All data are representative of three independent experiments.
(A) Structural alignment of the yeast Mrp17 (from PDB:5MRC) and its E. coli homolog ribosomal protein S6 (from PDB: 6WD0) viewed from its cytosol-facing side, highlighting regions of structural homology (blue and yellow) and non-homologous C-terminal regions (grey), Tom20-binding domains in Mrp17 are highlighted in green, schematic summaries of such structural alignments for all MRPs and their bacterial homologs are shown in Appendix Fig. S7.
(H) Quantification of the distribution of the progeny (Dx-A555+) of microinjected aRGCs in the VZ, SVZ and intermediate zone/cortical plate (CP+IZ) 48 h after control (Con, white) or gTbr2 (black) microinjection (total number of cells scored: control 37, gTbr2 51, pooled from at least 3 independent experiments). Note that upon gTbr2 microinjection the distribution of cells across the various cortical zones is significantly different (VZ: control 77%, gTbr2 39: SVZ: control 20%, gTbr2 37%; IZ/CP: control 3%, gTbr2 24%, *, P<0.05).(B, F) Controls were set to 100% and the gTbr2 conditions expressed relative to control (B, 48%; F, 50%).(B, D, F) Error bars indicate SD (B, D, F); *, P<0.05; **, P<0.01.
The population size at which Aci2's diauxic shift occurred is linearly correlated to the alanine supply, indicating that Aci2 initially consumes almost entirely alanine. Data Information: Data were collected at 600nm.
(A) Structure of full-length, nucleotide-free, farnesylated hGBP1 (PDB entry 6k1z) and GDP·AlFX-bound LG-domain dimer (PDB entry 2B92). Insert (a) shows the farnesyl moiety and the triple arginine stretch (3R = R584-586). Insert (b) highlights residues required for nucleotide binding and hydrolysis.
F. Caspase-3 activity in Granta-519 cells treated with net-1 mAb antibody or with an unrelated Ig-G1 antibody (Ctl), with or without silencing of DCC via siRNA (siDCC). Results are means+/-std of four independent experiments. $: p=0.05; *: p=0.02; two-sided Mann-Whitney U-test.
A) GSEA plot using BroadC2 database showed that genes differentially expressed in young control compared to young Mfn2KO mice and old control mice are enriched in genes related to hypoxia response.
Immunoblot analysis revealed the reduced IFNγ-inducible PD-L1 expression in VGLL4 knockdown A549 and 16HBE cells
Live cell fluorescence microscopy of Trs85-mNeonGreen and mRFPmars-Ypt1. Localization of Rab1/Ypt1 to punctate structures is indicative of its activation by TRAPPIII. Scale bar is 2 microns. Representative of n=3 independent experiments. (WT = wild-type, EV = empty vector)
A Immunoblot of PPAR-α and Tubulin (control) (top) in WAT from WT and FADD-D mice with relative quantification (bottom). Data are expressed as mean ± SEM from three independent experiments. *P = 0.0035 (Student's t-test).
(E) HEK293 cells were transfected to co-express HA-tagged KDF1 with GST-tagged IKKα or its kinase dead (KD) mutant. IP and WCL were blotted with different antibodies as indicated.
(E) Respiratory exchange ratio (RER) during a graded exercise regimen as described in Materials and Methods. Notably, no significant increase in exhaust speed was observed in 499Tg/PGC-1α mKO mice compared to PGC-1α mKO mice. PGC-1α mKO, n = 5; 499Tg/PGC-1α mKO, n = 8.
B and C. MS2-RIP followed by qRT-PCR analysis of endogenous microRNAs association with LINC00115. 12XMS2 empty vector, LINC00115-12XMS2, or LINC00115-mut- 12XMS2 with Flag-tagged MS2 were co-transfected into 1123 GSCs. Data information data are representative of three independent experiments. Error bars, ± SD. , ***, p < 0.001, by two-tailed t-test.
(E) Smad6 and Pdcd4 (negative control gene) expression levels upon IL-33 full length versus cytokine domain expression compared with HA-empty vector expression in Pam212 cells (n=4 in each group).
C 2D [1H,15N] HSQC spectrum of EDC3104-197 (100 µM EDC3104-197; 20 mM HEPES pH 6.2, 500 mM NaCl, 0.5 mM TCEP; 298 K; 14.1 T). HSQC spectrum shows a single cross peak for each N-HN pair, i.e. one per amino acid (other than prolines). The lack of chemical shift dispersion in the 1H chemical shift dimension is typical for intrinsically disordered protein/region (IDR), as they lack the hydrogen bonding network in secondary structure elements of folded proteins.
α-His Western blot to detect acid trapped partners of LMF1. Samples were TCA precipitated, treated with NEM, and LMF1 was purified via its C-terminal His tag. Samples were resolved by reducing or nonreducing SDS-PAGE. The lanes marked -LMF1 are HEK293∆LMF1 cells included as a negative control.
(B) The response of a mitochondrial matrix-localized roGFP2-Prx1-P233stop probe expressed in wild-type cells to the indicated concentrations of exogenous H2O2. Cells were grown in SGal (-Leu) medium and harvested at early exponential phase. Error bars represent the standard deviation (n = 3 biological replicates, with cells obtained from 3 independent cultures for every strain and probe combinations. For each biological replicate three technical replicates were performed).
(A) Ecto-calreticulin exposure (expressed as MFI) in CT26 cells treated with 800 nM BoxA or 1 μM MTX for 2 and 4 hours. Error bars indicate standard deviation. Data were pooled from two different experiments. Data information: bars and error bars represent mean ± SD; statistics: One-way Anova with Dunnett's post-test, *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001.
D (A) Representative immunoblots and (B) quantitative analysis of AKT (1 μM insulin: P=0.038), (C) AS160 (- insulin: P=0.036, 1 μM insulin: P=0.0038), and (D) AMPK (- insulin: P=0.018) phosphorylation ± 16 hour BAM15 treatment and 15 minute insulin stimulation (N=3 per condition) in C2C12 myotubes.
(F) Number of GFP-LC3 puncta in MR766 and Paraiba infected hNSCs, n =>50 cells. Box plots show the mean and the smallest; largest values in whiskers represent the 10th and 90th percentiles in 50 randomly selected cells per group; and solid horizontal line indicates median. ***p < 0.001 by Student's t test.
(C) Atg16L1Δ/Δ MEFs were transiently transfected with either mock, FLAG-tagged Atg16L1 WT, E226R E230R (ERER), or D237R D239R (DRDR) before analysis by immunoblotting.(D) Statistical analysis of (C) was performed by one-way ANOVA with Tukey's post hoc test. SEM for n = 3. ∗p < 0.05.
D, E ChIP-qPCR analysis indicating that mutations in SDG4 and SEU genes impair H3K4me3 deposition in the WOX5 promoter. ChIP signal was normalized to the WT. Individual values (black dots) are shown. Data information: Chromatin was isolated from 5 mm root tip sections of seedlings at 5 DAG, sonicated, and immunoprecipitated using anti-GFP or anti-H3K4me3 antibodies. The precipitated DNA was used as a template for qPCR analysis. In (D), (E) data represent mean ± SD of three independent replicates. **P < 0.01, *P < 0.05 (Student's t-test).