EMBO/SourceData huggingface dataset:
Figure legend: "(E) Heat map showing the fold change (log2 basis) in the expression ratio of defense-/stress-related differentially expressed genes in anac032-1 and 35S:ANAC032 compared to WT after spraying with Pst DC3000 (6 hpi) normalised to their respective controls. Blue, downregulated; red, upregulated. Data represent means of three independent experiments, each including the rosettes leaves of at least three plants grown in individual pots. Asterisks indicate significant differences from WT plants (Student's t test, p ≤ 0.05)."
NCBI gene IDs:
"ANAC032: 844081
anac032: 844081"
Figure legend: "(A) MYC2, PDF1.2A and NIMIN1 expression in ANAC032 transgenics compared to WT after spraying with Pst DC3000 (24 hpi) normalised to their respective controls. FCh, fold change. Means ± SD (n = 3; 'n' represents independently performed experiments, each including the rosette leaves of at least three plants grown in individual pots)."
NCBI gene IDs:
"MYC2: 840158
ANAC032: 844081
NIMIN1: 837800
PDF1.2A: 834469"
Figure legend: "(B) EMSA showing binding of ANAC032 to MYC2, PDF1.2A and NIMIN1 promoter regions (in 5´-DY682-labelled double-stranded oligonucleotides) harbouring ANAC032 binding sites. 1, labelled probe only; 2, labelled probe plus GST protein 3, labelled probe plus ANAC032-GST protein; 4, labelled probe, ANAC032-GST protein and 100 x competitor (unlabelled oligonucleotide containing ANAC032 binding site)."
NCBI gene IDs:
"MYC2: 840158
NIMIN1: 837800
PDF1.2A: 834469"
Figure legend: "(C) Confocal microscopy image showing nuclear localization of ANAC032-GFP fusion protein expressed from the ANAC032 promoter in ANAC032prom:ANAC032-GFP/anac032-1 seedlings treated with Pst at 6 hpi. Left, bright field; right, chlorophyll auto-fluorescence (red) and GFP fluorescence (green) under bright field."
NCBI gene IDs:
"ANAC032: 844081
anac032: 844081"
Figure legend: "(D) Expression of MYC2, PDF1.2A, NIMIN1 and ANAC032 in two-week-old ANAC032prom:ANAC032-GFP/anac032-1 seedlings compared to WT at 6 hpi with Pst, normalised to their respective controls. FCh, fold change. Means ± SD (n = 3; 'n' represents independently performed experiments, each including the rosette leaves of at least three plants grown in individual pots). Asterisks indicate a significant difference from WT, normalised to their respective controls (p &lt; 0.05; Student´s t-test)."
NCBI gene IDs:
"MYC2: 840158
ANAC032: 844081
anac032: 844081
NIMIN1: 837800
PDF1.2A: 834469"
Figure legend: "(E) ChIP-qPCR shows enrichment of MYC2, PDF1.2Aand NIMIN1 promoter regions containing ANAC032 binding site compared to a promoter region lacking the ANAC032 binding site (AT5G09810; Neg Cont). Means ± SD (n = 3; 'n' represents independently performed experiments, each including the rosette leaves of at least three plants grown in individual pots). Asterisks indicate a significant difference from negative control (p &lt; 0.01; Student´s t-test)."
NCBI gene IDs:
"AT5G09810: 830841
MYC2: 840158
NIMIN1: 837800
PDF1.2A: 834469"
Figure legend: "Transcript levels of (A) NIMIN1 and (B) PR1 in WT, anac032-1 and 35S:ANAC032 plants after 3 and 6 h of treatment with SA compared to their respective controls."
NCBI gene IDs:
"ANAC032: 844081
anac032: 844081
NIMIN1: 837800
PR1: 815949"
Figure legend: "(C), Expression of PDF1.2A in WT and anac032-1 plants after 3 and 6 h of treatment with SA compared to their respective controls. Transcript levels were measured using qRT-PCR and numbers on the y-axis indicate fold change (FCh; log2 basis). Means are shown ± SD (n = 3; 'n' represents independently performed experiments). Asterisks indicate a significant difference from wild type (p &lt; 0.05; Student's t test)."
NCBI gene IDs:
"anac032: 844081
PDF1.2A: 834469"
Figure legend: "(D) RNAscope in situ hybridization (Dand5, top; Negative probe (dapB); down) and hematoxylin staining of P5 mouse retinas."
NCBI gene IDs:
"dapB: 
Dand5: 23863"
Figure legend: " G Quantification analysis of changes in chromatin openness at Tgfb1 and Notum promoter regions by FAIRE-qPCR among different groups of NSPCs. Data are presented as mean ± SEM of three independent biological replicates, n = 3. Two-tailed unpaired Student's t-test was used to analyze statistical significance; P &lt; 0.05, P &lt; 0.01. "
NCBI gene IDs:
"Notum: 77583
Tgfb1: 21803"
Figure legend: " I, J Quantification analysis of expression changes of Mir-203 (I) and Bmi1 (J) by qRT-PCR among different groups of NSPCs. Data are presented as mean ± SEM of three independent biological replicates, n = 3. Two-tailed unpaired Student's t-test was used to analyze statistical significance; P &lt; 0.05, P &lt; 0.01. "
NCBI gene IDs:
"Bmi1: 12151
Mir-203: 387199"
Figure legend: "(a) Experimental testing of the predicted SR (DU) rescuers of DNMT1 via drug combination experiments in 18 NSCLC cell lines insensitive to Decitabine. The matrix displays drug interactions between Decitabine, a DNMT1 inhibitor, and inhibitors of its predicted rescuer genes (X-axis) across 18 NSCLC cell lines (Y-axis) that are insensitive to Decitabine. Row labels present rescuer genes and their inhibitors. Colors in the matrix show whether the interactions found are significantly synergistic (red), antagonistic (green) or non-significant (in gray). Values in the matrix show average synergism (&lt;1 synergism and &gt;1 antagonism Thirteen predicted DU-SR rescuers (red lines), two predicted DD SR rescuers (green lines) of DNMT1 and one random control (JAK3i) were tested."
NCBI gene IDs:
"DNMT1: 1786
JAK3: 3718"
Figure legend: "The transcriptomic alterations of rescuer genes post PD1/PDL1 blockade in patient tumor biopsies: Their post (vs. pre) treatment expression changes of DU/DD rescuers after anti-PD1 (b) Each panel displays the expression fold change of each predicted rescuer gene (rows) for different tumor samples (columns) and the P-value of over-all paired Wilcoxon test of the expression changes observed in paired samples. Significantly altered up/down-regulated genes are marked by (*). Genes marked in red are those whose CRISPR knockdown enhances melanoma sensitivity to anti-PD1 blockade in mice models."
NCBI gene IDs:
"CRISPR: "
Figure legend: "The transcriptomic alterations of rescuer genes post CTLA4 blockade in patient tumor biopsies: Their post (vs. pre) treatment expression changes of DU/DD rescuers after anti-CTLA4 (c) Each panel displays the expression fold change of each predicted rescuer gene (rows) for different tumor samples (columns) and the P-value of over-all paired Wilcoxon test of the expression changes observed in paired samples. Significantly altered up/down-regulated genes are marked by (*). Genes marked in red are those whose CRISPR knockdown enhances melanoma sensitivity to anti-PD1 blockade in mice models."
NCBI gene IDs:
"CRISPR: "
Figure legend: "The transcriptomic alterations of rescuer genes post PD1/PDL1 and CTLA4 blockade in patient tumor biopsies: Their post (vs. pre) treatment expression changes of DU/DD rescuers after PD1 + CTLA4 combination therapies (d). Each panel displays the expression fold change of each predicted rescuer gene (rows) for different tumor samples (columns) and the P-value of over-all paired Wilcoxon test of the expression changes observed in paired samples. Significantly altered up/down-regulated genes are marked by (*). Genes marked in red are those whose CRISPR knockdown enhances melanoma sensitivity to anti-PD1 blockade in mice models."
NCBI gene IDs:
"CRISPR: "
Figure legend: "I. U2OS cell lines conditionally expressing indicated GFP-FAM111A alleles were fixed at the indicated times after treatment with Doxycycline (DOX) to induce expression of the transgenes and stained with crystal violet."
NCBI gene IDs:
"GFP: 
FAM111A: 63901"
Figure legend: "G. Analysis of FAM111A interactors. U2OS/GFP-FAM111A WT cells were treated or not with DOX for 4 h, subjected to GFP immunoprecipitation (IP) and analyzed by mass spectrometry. Volcano plot shows enrichment of individual proteins (+DOX/-DOX ratio) plotted against the P value. Dashed lines indicate the significance thresholds (FDR&lt;0.05; s0=1)."
NCBI gene IDs:
"GFP: 
FAM111A: 63901"
Figure legend: "H. U2OS or U2OS/∆FAM111A cells were subjected to IP with IgG (control) or RFC1 antibody followed by immunoblotting with indicated antibodies."
NCBI gene IDs:
"FAM111A: 63901"
Figure legend: "B. Immunoblot analysis of U2OS cell lines left untreated or incubated in the presence of DOX to induce expression of the indicated GFP-FAM111A alleles. U2OS/GFP-FAM111A WT (low) cells express the transgene at a lower level than U2OS/GFP-FAM111A WT cells used in Figure 1 and 2 (see Figure EV4A)."
NCBI gene IDs:
"GFP: 
FAM111A: 63901"
Figure legend: "Immunoblot analysis of cell lines treated or not with DOX in the absence or presence of Z-VAD-FMK. J. using U2OS cell lines conditionally expressing ectopic untagged FAM111A alleles."
NCBI gene IDs:
"FAM111A: 63901"
Figure legend: "B. U2OS/GFP-FAM111A WT cells treated or not with DOX were subjected to GFP IP followed by immunoblotting with indicated antibodies. C. As in (B), using U2OS/GFP-FAM111B WT cells."
NCBI gene IDs:
"GFP: 
FAM111A: 63901
FAM111B: 374393"
Figure legend: "J. U2OS/GFP-FAM111B cell lines (Figure 5E) were fixed at the indicated times after DOX treatment and stained with crystal violet."
NCBI gene IDs:
"GFP: 
FAM111B: 374393"
Figure legend: "(A-C) Immunoblots of Gp96 and NMHCIIA levels from whole cell lysates (WCL) and Gp96 IP fractions (IP Gp96) of HeLa cells: (B) left uninfected (U) or infected with wt or Δhly Lm for 1 h. (A, C) Quantifications of NMHCIIA in IP Gp96 are the mean±SEM (n≥3) (a.u. - arbitrary units)."
NCBI gene IDs:
"hly: 987033"
Figure legend: "(F) Confocal microscopy images of HeLa cells infected with wt or Δhly Lm for 6 h immunolabelled for NMHCIIA (green), Gp96 (red) Lm (blue) and stained with DAPI (white). Arrows indicate NMHCIIA-Gp96 cortical bundles at cortical sites close to wt Lm. (D and F) Scale bar - 10 μm. See also Figs EV1 and EV2."
NCBI gene IDs:
"hly: 987033"
Figure legend: "(A) Confocal microscopy images of shCtrl, shGp96 or shNMHCIIA HeLa cells treated with LLO (0.5 nM, 15 min) and immunolabelled for KDEL-proteins (blue), NMHCIIA (green) and Gp96 (red). Insets show compact NMHCIIA bundles in shCtrl cells and dispersed NMHCIIA bundles in shGp96 cells. Scale bar - 10 μm. (B-D) Quantification of the % of cells harbouring NMHCIIA bundles after incubation with (B) LLO (0.5 nM, 15 min), (C) aerolysin (0.2 nM, 40 min) or (D) with wt Lm. Values are the mean ±SEM (n≥3), p-values were calculated using (B-C) one-way-ANOVA with Dunnett post hoc analyses and (D) two-tailed un-paired Student's t-test, *p&lt;0.5, ***p&lt;0.001. For shNMHCIIA, bundles were detected following actin staining (Fig EV3C)."
NCBI gene IDs:
"Gp96: 7184
NMHCIIA: 4627"
Figure legend: "(E-F) Number of (E) blebs per cell or (F) retracting blebs per cell evaluated by time-lapse microscopy analysis of LLO-treated shCtrl or shGp96 cells. shCtrl n=32 cells and shGp96 n=40 cells, p-values were calculated using two-tailed un-paired Student's t-test *p&lt;0.5. (G) Sequential frames of time-lapse microscopy analysis of LLO-treated HeLa cells expressing GFP-NMHCIIA (shCtrl, shGp96 and shCtrl with 25 μM Blebbistatin - shCtrl-BB). LLO was added to culture medium 10 seconds before t0."
NCBI gene IDs:
"Gp96: 7184"
Figure legend: "(H) Immunoblots of Ser19-phosphorylated MRLC (pMRLC), MRLC and actin levels from shCtrl or shGp96 cells left untreated (U) or treated with 0.1 nM LLO for the indicated time points. Quantification of pMRLC levels corresponds to the mean ± SEM (n≥3), p-values were calculated using one-way-ANOVA with Tukey post hoc analyses **p&lt;0.01, ***p&lt;0.001. See also Appendix Fig S2 and Fig EV3."
NCBI gene IDs:
"Gp96: 7184"
Figure legend: "(E-F) Confocal microscopy images of shCtlr, shGp96 or shNMHCIIA HeLa cells stained for actin (red) and DAPI (blue) and immunolabelled for (E) NMHCIIA (green) or (F) focal adhesion kinase (FAK) (green). (A, D-F) Scale bar - 10 μm. Insets show sites with focal adhesion points and arrows indicate stress fibers or distinct focal adhesion points. Quantification of the % of cells with (G) stress fibers or (H) focal adhesion points labelled by FAK."
NCBI gene IDs:
"Gp96: 7184
NMHCIIA: 4627"
Figure legend: "(A) Epifluorescence microscopy images of supernatants from LLO-treated (0.5 nM 15 min) shCtlr, shGp96 or shNMHCIIA HeLa cells collected into poly-lysine-coated cover slips, fixed and stained with FITC-WGA (green) and DAPI (blue). Insets show PM blebs of variable sizes and DAPI staining confirms the absence of cell nuclei. Scale bar - 10 μm. (B) Quantification of released PM blebs (total FITCWGA/field). Values are the means ± SEM (n≥3). ***p&lt;0.001."
NCBI gene IDs:
"Gp96: 7184
NMHCIIA: 4627"
Figure legend: "(C-E) Flow cytometry analysis of the % of PI-positive shCtlr, shGp96 or shNMHCIIA HeLa cells. Cells were treated with (C) 0.5 nM LLO for the indicated times. Levels of PI incorporation by untreated cells were subtracted from all LLO-treated samples. Values are the mean ± SEM (n≥4) and p-values were calculated using one-way-ANOVA with Tukey post hoc analyses *p&lt;0.5, **p&lt;0.01, ***p&lt;0.001."
NCBI gene IDs:
"Gp96: 7184
NMHCIIA: 4627"
Figure legend: "(C-E) Flow cytometry analysis of the % of PI-positive shCtlr, shGp96 or shNMHCIIA HeLa cells. Cells were treated with (D) 1.5 or 3 nM LLO for 15 min; or (E) 0.1 nM LLO for 10 min followed by LLO washed out and recovery for indicated times. Levels of PI incorporation by untreated cells were subtracted from all LLO-treated samples. Values are the mean ± SEM (n≥4) and p-values were calculated using one-way-ANOVA with Tukey post hoc analyses *p&lt;0.5, **p&lt;0.01, ***p&lt;0.001."
NCBI gene IDs:
"Gp96: 7184
NMHCIIA: 4627"
Figure legend: "(C-E) Flow cytometry analysis of the % of PI-positive shCtlr, shGp96 or shNMHCIIA HeLa cells. Cells were treated with (E) 0.1 nM LLO for 10 min followed by LLO washed out and recovery for indicated times. Levels of PI incorporation by untreated cells were subtracted from all LLO-treated samples. Values are the mean ± SEM (n≥4) and p-values were calculated using one-way-ANOVA with Tukey post hoc analyses *p&lt;0.5, **p&lt;0.01, ***p&lt;0.001."
NCBI gene IDs:
"Gp96: 7184
NMHCIIA: 4627"
Figure legend: "(A-B) Epifluorecence microscopy images of HeLa cells (B) infected with GFP-expressing wt Lm for 6 h. Cells were incubated with exofacial-PS probe (Alexa-568 annexin A5) (red) 30 min prior fixation, immunolabelled for NMHCIIA (green) and stained with DAPI (blue). Insets show PM damage marked by exofacial-PS sites. Arrows indicate exofacial-PS associated with intracellular bacteria and in shCtrl cells with NMHCIIA bundles; arrowheads indicate NMHCIIA bundles associated with exofacial-PS sites without detectable bacteria."
NCBI gene IDs:
"NMHCIIA: 4627"
Figure legend: "(D-E) Flow cytometry analysis of the % of PI-positive shCtlr, shGp96 or shNMHCIIA HeLa and RAW264.7 cells, infected with GFP-expressing wt or Δhly Lm for 6 h. The levels of PI incorporation by uninfected cells were subtracted from infected samples. Values are the mean ± SEM (n≥4) and p-values were calculated using one-way-ANOVA with Tukey post hoc analyses *p&lt;0.5, **p&lt;0.01, ***p&lt;0.001. PM permeability was assessed in cells harbouring equivalent numbers of intracellular bacteria (Fig Appendix Fig S3)."
NCBI gene IDs:
"hly: 987033
Gp96: 7184
NMHCIIA: 4627"
Figure legend: "(A) Immunoblots of NMHCIIA and Gp96 levels from whole cell lysates (WCL) and IP fractions (IP Gp96) of extracts of zebrafish larvae 3 dpf uninfected (U) or infected with wt or ∆hly Lm (low dose 200-1500 CFU) for 24h."
NCBI gene IDs:
"hly: 987033"
Figure legend: "(B) Immunoblots of Gp96 and tubulin levels from zebrafish 3 dpf larvae injected with control (Ctrl-mo) or Gp96 morpholino oligonucleotides (Gp96 mo)."
NCBI gene IDs:
"Gp96: 386590"
Figure legend: "(C) Confocal microscopy images of zebrafish larvae (Ctrl mo or Gp96 mo) infected (low dose) in the tail muscle, with the GFP-expressing wt or Δhly Lm for 24 h, immunolabelled for KDEL-proteins (green), and stained with phalloidin (actin, red) and DAPI (white). Images show actin rich structures at the cell cortex (arrows) and ER-KDEL puncta (arrowheads) in larvae infected with wt strain."
NCBI gene IDs:
"hly: 987033
Gp96: 386590"
Figure legend: "(D) CFU counts per zebrafish larvae (Ctrl or Gp96 mo) infected with wt (low dose) or Δhly (high dose &gt; 10,000 CFU) Lm and analysed at 0, 24, 48 hpi. Results are mean ± SEM (n≥3) (horizontal bars) and each circle represents 1 larvae. p-values were calculated using one-way-ANOVA with Tukey post hoc analyses **p&lt;0.01."
NCBI gene IDs:
"hly: 987033
Gp96: 7184"
Figure legend: "(E) Survival curves of zebrafish larvae (Ctrl-mo or Gp96-mo) infected with a wt (low dose) or Δhly (high dose &gt; 10,000 CFU) Lm. Results are the mean ± SEM (n≥3). wt infection of Ctrl and Gp96 mo, n=28 larvae; Δhly infection of Gp96 mo n=13. p-values were calculated using Log Rank test, **p&lt;0.01."
NCBI gene IDs:
"hly: 987033
Gp96: 386590"
Figure legend: "(F) CFU counts per zebrafish larvae infected with a high dose of ∆hly Lm at different times post-infection. Results are mean ± SEM (n≥3) (horizontal bars); each point represents 1 larvae. See also Fig EV5."
NCBI gene IDs:
"hly: 987033"
Figure legend: "A Phenotypes of WT (Col-0), two gso1  mutant alleles (gso1-1, gso1-3) and two independent complementation lines (com-1, com-2). Seedlings  were grown on 1/2 MS for 6 days and then transferred to 1/2 MS medium supplemented with or without 100 mM NaCl  for 10 days. B,C Primary root length and seedling  fresh weight  of seedlings  depicted in (A) were measured at day 10 after transfer. (mean ± SEM, n = 10, P &lt; 0.05, two-way ANOVA)"
NCBI gene IDs:
"gso1: 827760"
Figure legend: "A Co-IP of GSO1  and SOS2  using Arabidopsis protoplasts  transiently expressing Myc-GSO1KD (GSO1  kinase domain) and Flag-SOS2, Flag-HA-SOS3  or Flag-SCaBP8. Protein extracts were immunoprecipitated  with anti-Myc  antibody and immunoblotted  with anti-Myc  antibody or anti-Flag  antibody."
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
SCaBP8: 829437
GSO1: 827760
SOS2: 833502
SOS3: 832494"
Figure legend: "D Phenotypes of WT (Col-0), gso1-3, sos2-2 and gso1-3 sos2-2. Seedlings  were grown on 1/2 MS medium for 6 days and then transferred to 1/2 MS supplemented with or without extra NaCl  for 10 days. E,F  Primary root length and fresh weight  of seedlings  depicted in (D) were measured at day 7 after transfer. (mean ± SEM, n = 10, P &lt; 0.05, two-way ANOVA)"
NCBI gene IDs:
"gso1: 827760
sos2: 833502"
Figure legend: "B Immunoblot  using anti-Myc  antibody and CBB  and autoradiograph  from kinase assays combining Myc-SOS2  with SOS1C300 as substrate. 10-day-old seedlings  stably expressing Pro35S:6Myc-SOS2  in Col-0 or gso1-3 were treated with or without 100 mM NaCl  for 12 h, and Myc-SOS2  protein immunoprecipitated  with anti-C-Myc  antibody-conjugated agarose  from roots  was used in the assays. Signal strength of the phosphorylation  bands has been calculated relative to the left lane."
NCBI gene IDs:
"Myc: 
gso1: 827760
SOS2: 833502"
Figure legend: "A Phenotypes of WT (Col-0), gso1-3, esb1, and casp1 casp3. Seedlings  were grown on 1/2 MS for 6 days and then transferred to 1/2 MS medium with or without 100 mM NaCl  for 10 days. B, C Primary root length and seedling  fresh weight  of seedlings  depicted in (A) were measured at day 10 after transfer. (mean ± SEM, n = 12, two-way ANOVA, P &lt; 0.05)"
NCBI gene IDs:
"casp1: 818183
casp3: 817280
esb1: 817416
gso1: 827760"
Figure legend: "G Phenotypes of WT (Col-0), cif1 cif2, and gso1-3. Seedlings  were grown on 1/2 MS medium for 6 days and then transferred to 1/2 MS medium supplemented with or without 100 mM NaCl  for 10 days."
NCBI gene IDs:
"cif1: 2745542
cif2: 829612
gso1: 827760"
Figure legend: "A-D Protein accumulation (A, C, D) or  gene expression  (B) of SOS2, CIF2, GSO1, and SGN1 displayed as false color fluorescence intensity. Seedlings  from the indicated plant lines were grown on 1/2 MS for 4-5 days and then transferred to 1/2 MS with or without 100 mM NaCl  for 1 day. Scale bars: 200 µm."
NCBI gene IDs:
"CIF2: 829612"
Figure legend: "H-I. Jmjd2a(+/-); Jmjd2a(+/-) (H) or Jmjd2b(+/-); Jmjd2b(+/-) (I) mice were inter-crossed and the number of pups alive at time of weaning reported. P values were calculated using a Chi-square test."
NCBI gene IDs:
"Jmjd2a: 230674
Jmjd2b: 193796"
Figure legend: "C-D. Jmjd2a(+/-); Jmjd2c(+/-) mice were inter-crossed. The number of (C) pups alive at weaning or (D) embryos recovered at E6.5 is presented. P values were calculated using exact binomial test with the most conservative estimate of expected (-/-;-/-) embryos (6.25 %, assuming no linkage between the Jmjd2a and Jmjd2cloci even though they are located on the same chromosome)."
NCBI gene IDs:
"Jmjd2a: 230674
Jmjd2c: 76804"
Figure legend: "A. Examples of ChIP-seq data obtained for Jmjd2a, Jmjd2c (Pedersen et al, 2014), and H3K4me3."
NCBI gene IDs:
"Jmjd2a: 230674
Jmjd2c: 76804"
Figure legend: "B. Heat map showing H3K9me3 ChIP-seq data for Jmjd2a/c bound TSSs (+/- 5kb) sorted according to read number in 2abc #13+OHT."
NCBI gene IDs:
"Jmjd2a: 230674"
Figure legend: "C. ChIP-qPCR validations for selected Jmjd2a/c targets (see Fig 4G). Graphs show mean ± SD for technical triplicates and are representative of results obtained in at least 2 independent experiments."
NCBI gene IDs:
"Jmjd2a: 230674"
Figure legend: "C-D. Density plots showing average ChIP-seq signals for (C) H3K9me3 or (D) H3K36me3 with 95% confidence intervals of the mean indicated in grey. Plots are shown for genes, which are down- or up-regulated according to the microarray analyses (FDR&lt;0.05, absolute fold change log2(|FC|)&gt;0.5) for both 2ac and 2abc KO ESCs (overlaps presented in Appendix Fig S6A), or do not show strong expression changes (log2(|FC|) &lt; 0.2). Genes are further classified as \"Bound\" if containing binding sites for both Jmjd2a and Jmjd2c within +/- 1kb of a TSS."
NCBI gene IDs:
"Jmjd2a: 230674
Jmjd2c: 76804"
Figure legend: "A-C. 2ac clones established after transfection with an empty vector (empty) or plasmids expressing wild type Jmjd2c (2c wt) or a catalytic mutant (2c mut) were exposed to OHT as indicated and subsequently used for (A) WB."
NCBI gene IDs:
"Jmjd2c: 76804"
Figure legend: "A-C. 2ac clones established after transfection with an empty vector (empty) or plasmids expressing wild type Jmjd2c (2c wt) or a catalytic mutant (2c mut) were exposed to OHT as indicated and subsequently used for (B) RT-qPCR analyses"
NCBI gene IDs:
"Jmjd2c: 76804"
Figure legend: "A-C. 2ac clones established after transfection with an empty vector (empty) or plasmids expressing wild type Jmjd2c (2c wt) or a catalytic mutant (2c mut) were exposed to OHT as indicated and subsequently used for (C) serial plating for the generation of growth curves."
NCBI gene IDs:
"Jmjd2c: 76804"
Figure legend: "(D and E) Parent NIH3T3 cells, Atg4B mutant overexpressing NIH3T3 cells stably expressing GFP-tagged LC3, Atg5, WIPI-1, Atg14L1, Atg9L1, or ULK1 were transfected with Effectene-coated latex beads for 3 h and subjected to immunocytochemistry for galectin3. The percentages of Atg-positive per galectin3-positive beads were enumerated. At least 30 beads were counted (n = 3). The values are the mean ± SD."
NCBI gene IDs:
"Atg4B: 66615"
Figure legend: "(E) wild-type MEFs, and Atg5-KO MEFs stably expressing GFP-tagged LC3, Atg5, WIPI-1, Atg14L1, Atg9L1, or ULK1 were transfected with Effectene-coated latex beads for 3 h and subjected to immunocytochemistry for galectin3. The percentages of Atg-positive per galectin3-positive beads were enumerated. At least 30 beads were counted (n = 3). The values are the mean ± SD."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "(C) Purified recombinant GST or GST-Ub-immobilized glutathione Sepharose beads were incubated with lysates from HEK293T cells transiently expressing FLAG-tagged Atg16L1 constructs for 1 h at 25°C with gentle agitation. The beads were washed three times with ice-cold PBS and the bound complexes were eluted with 50 mM reduced glutathione and then subjected to Western blotting for FLAG."
NCBI gene IDs:
"Atg16L1: 55054"