EMBO/SourceData huggingface dataset:
Figure legend: "A, CRISPR-modified cells (Brightfield, left) that express GFP-nesprin-2 (middle) and mCh-LAC (right) show nesprin (orange arrow) but not lamin accumulation at the front of the nucleus as it is deformed through a narrow constriction. B, Quantification of intensity of GFP-nesprin-2 and mCh-LAC, normalized to the intensity at the sides. Error bars correspond to the standard deviation. Constriction: n=19 cells over 5 biological replicates, 15 µm: n= 27 over 6 biological replicates. A Wilcoxon signed-rank test is used to compare matched samples, stars (*P &lt; 0.05, **P &lt; 0.01) denote comparisons to the measurement at the side, and pounds (#P &lt; 0.05, ##P &lt; 0.01) denote a comparison to the \"before\" time point."
NCBI gene IDs:
"CRISPR: "
Figure legend: "Assessment of receptor channel activity using MK-801 inhibition kinetics. Representative current traces from oocytes expressing either wild-type (WT) or GluN1-E698C/GluN2B-L795C mutant receptors in response to 10 nM MK-801 during agonist application. Responses were scaled to the current amplitude obtained before MK-801 application. Inset, mono-exponential fits of MK-801 wash-in and wash-out. Note the strikingly faster kinetics in mutant receptors, both at the onset and offset of MK-801"
NCBI gene IDs:
"GluN1: 24408
GluN2B: 14812"
Figure legend: "Zinc, ifenprodil and pH dose-response curves of wild-type (WT) GluN1/GluN2B receptors and mutant GluN1-E698C/GluN2B-L795C receptors. For comparison, zinc and ifenprodil dose-response curves of GluN1/GluN2B receptors lacking the whole GluN2B NTD (GluN1 WT/GluN2B-delNTD) are also shown (dashed lines; data from Rachline et al, 2005)"
NCBI gene IDs:
"GluN1: 24408
GluN2B: 14812"
Figure legend: "Spermine (200 µM, pH 6.3) potentiation of WT GluN1/GluN2B and mutant GluN1-E698C/GluN-L795C receptors. Spermine (200 µM, pH 6.5) sensitivity is also shown for WT GluN1/GluN2B receptors and receptors lacking either the GluN1 (GluN1-delNTD/GluN2B WT) or GluN2B (GluN1 WT/GluN2B-delNTD) NTD (data from Mony et al, 2011)"
NCBI gene IDs:
"GluN1: 24408
GluN2B: 14812"
Figure legend: "Glutamate and glycine dose-response curves of WT GluN1/GluN2B receptors and mutant GluN1-E698C/GluN2B-L795C receptors"
NCBI gene IDs:
"GluN1: 24408
GluN2B: 14812"
Figure legend: "Representative recordings of patches containing one single wild-type (WT) or GluN1-E698C/GluN2B-L795C receptor. The bottom trace is an expanded view. C, closed channel; O, open channel"
NCBI gene IDs:
"GluN1: 24408
GluN2B: 14812"
Figure legend: "Single channel properties (equilibrium channel open probability, mean open time, mean closed time) of the WT and super-active GluN1-E698C/GluN2B-L795C receptors"
NCBI gene IDs:
"GluN1: 24408
GluN2B: 14812"
Figure legend: "Closed (left) and open (right) time histograms for WT (upper panels) or super-active GluN1-E698C/GluN2B-L795C (lower panels) receptors. Closed time histograms were best fit with 5 exponentials, whereas open time histograms were best fit with 2 exponentials (see Online Methods and Appendix Fig S8). Smooth lines are associated exponential fits"
NCBI gene IDs:
"GluN1: 24408
GluN2B: 14812"
Figure legend: "(B) 48h post-transfection of HeLa-CIITA  cells with siRNAs targeting NDP52, T6BP, OPTN, and p62, AR  expression was analyzed using  Western Blot. Tubulin  was used as control. The results are representative of at least 3 independent experiments and correspond to AR  expression levels of the experiment in Figure 1B, left panel."
NCBI gene IDs:
"NDP52: 10241
CIITA: 4261
OPTN: 10133
p62: 8878
T6BP: 8887"
Figure legend: "(C) Monitoring of Gag-specific T cell  activation. HeLa-CIITA cells were treated as indicated above and transfected with a plasmid encoding Gag-LC3. Left panel, a representative experiment is shown (+/- SD of three technical replicates). Right panel, three biological replicates are combined and presented as mean percentage (+/- SD). The y-axis represents the relative percentage of IFNγ  spots reported to the secretion of IFNγ  by the CD4+ T cell clones incubated with the siCTRL-treated HeLa-CIITA  and set to 100%. The mean  T cell activation levels of the three experiments using siCTRL or siT6BP were (100, 195, 119) and (35, 53, 38) IFNγ+ spots, respectively. 5000 T cell clones were seeded per well in technical triplicates. Data information: For all ELISPOT  experiments, the background secretions of IFNγ  by CD4+ T cells  co-cultured with mock-treated HeLa-CIITA  cells were used as negative controls and subtracted. CTRL: control. Wilcoxon's test; the symbols correspond to ** p&lt;0.01 and # p&gt;0.05 comparing each experimental conditions solely with its internal control (siCTRL)."
NCBI gene IDs:
"CIITA: 4261
Gag: 155030
LC3: 64862///362245
T6BP: 8887"
Figure legend: "(D) Left panel, as in Figure 1B right panel, but using DNA encoding Gag-LC3, Gag-LC3G120A, or Gag. With Gag-LC3, Gag-LC3  G120A or Gag  antigens, the mean  T cell  activation levels using siCTRL or siT6BP were (199, 435, 384), (91, 141, 119) and (343, 415, 385) or (98, 273, 171), (27, 50, 19) and (97, 148, 131) IFNγ+ spots, respectively. 5000 T cell  clones were seeded per well in technical triplicates. Three biological replicates are combined and presented as mean percentage (+/- SD). Right panel, influence of T6BP  silencing on peptide presentation by Hela-CIITA  cells. The cognate peptide was added exogenously (gag2, 0,1µg/mL) on siRNA-treated cells (2h, 37°C), washed and  T cell  activation monitored using IFNγ-ELISPOT. The mean T cell activation levels using siCTRL or siT6BP were (100, 45, 42) and (71, 45, 33) IFNγ+ spots, respectively. 1000 T cell  clones were seeded per well in technical triplicates. Three biological replicates are combined and presented as mean percentage (+/- SD). Data information: For all ELISPOT  experiments, the background secretions of IFNγ  by CD4+ T cells co-cultured with mock-treated HeLa-CIITA  cells were used as negative controls and subtracted. CTRL: control. Wilcoxon's test; the symbols"
NCBI gene IDs:
"CIITA: 4261
Gag: 155030
LC3: 64862///362245
T6BP: 8887"
Figure legend: "(E) As in (D) but using cDNA encoding HCMV pp65  antigen (left panel) or pp65  peptide (0,5µg/mL; right panel) and a pp65-specific CD4+ T cell  line. Results of three independent experiments are represented. The mean T cell  activation levels using siCTRL or siT6BP  and pp65  DNA were (66, 106, 99) and (39, 50, 33) IFNγ+ spots, respectively. For the peptide: siCTRL or siT6BP: (185, 317, 415) and (163, 292, 381) IFNγ+ spots, respectively. 1000 or 2000  T cell  clones were seeded per well in technical triplicates. Data information: For all ELISPOT  experiments, the background secretions of IFNγ   by CD4+ T cells  co-cultured with mock-treated HeLa-CIITA  cells were used as negative controls and subtracted. CTRL: control. Wilcoxon's test; the symbols correspond to ** p&lt;0.01 and # p&gt;0.05 comparing each experimental conditions solely with its internal control (siCTRL)."
NCBI gene IDs:
"CIITA: 4261
T6BP: 8887
pp65: 3077579"
Figure legend: "(D) T6BP  silencing affects the formation of stable MHC-peptide complexes. HeLa-CIITA  cells were transfected as above and pulse-labeled with 35S-Met/Cys  for 30 min, washed and chased for 4h at 37°C. MHC-II  molecules were then immunoprecipitated  using TÜ36  antibody and analyzed on SDS-PAGE  after incubation of the immunoprecipitated protein complexes with SDS at 95°C (B: boiled) or room temperature  (NB: non-boiled) to visualize α, β and Ii chains and SDS  resistant αβ dimers, respectively. The bands corresponding to α, β and Ii chains are indicated. The arrow indicates the SDS-resistant stable HLA αβ heterodimers. This gel is representative of two independent experiments."
NCBI gene IDs:
"CIITA: 4261
T6BP: 8887"
Figure legend: "(A) MHC-II  and T6BP expressions  were assessed using confocal microscopy. HeLa-CIITA  cells were transfected with control and T6BP-silencing siRNAs. 48h post-treatment, MHC-II  and T6BP  were detected using L243 and anti-T6BP  antibodies, respectively, and revealed with species specific secondary antibodies. Nuclei  were stained  using DAPI. (B) Quantitative analysis using in-house ImageJ script displaying distance of each MHC-II+ vesicles  to the nucleus  and number of vesicles  per cell. At least 20,000 vesicles  from 160 cells corresponding to five biological replicates were analyzed. Right panel, quantification in the siCTRL cells of the colocalization  between MHC-II+ and T6BP+ dots using Pearson's coefficient where the dotted lines (at 0.5) indicate the limit under which no significant  co-localization is measured (number of cells = 54). Data information: In graphs representing the number of vesicles  per cells, each dot displayed corresponds to a single cell. Within the violin plots, continuous and dotted lines correspond to medians and quartiles, respectively. Scale bars: 2μm. CTRL: control. Mann-Whitney's test; * p&lt;0.05; ** p&lt;0.002; *** p&lt;0.0003; **** p&lt;0.0001; # p&gt;0.05."
NCBI gene IDs:
"CIITA: 4261
T6BP: 8887"
Figure legend: "(A) CD74  expression was assessed using Western Blot. HeLa-CIITA  cells were transfected with siCTRL and siT6BP. 48h post treatment, the Iip33 CD74  isoform, a degradation product (Iip16), T6BP  and actin  were detected using indicated antibodies. Left panel, a representative Western Blot experiment is shown. Right panel, expressions levels five biological replicates were quantified using ImageJ and are presented as mean of ratios (+/-SD) of CD74  to actin  used as control housekeeping gene expression."
NCBI gene IDs:
"CIITA: 4261
T6BP: 8887"
Figure legend: "(D) CD74  expression is partially recovered by blocking lysosomal  acidification. As in (A), following siRNA transfection of Hela-CIITA  cells, CD74  expression was assessed. The last 16h prior to harvesting, cells were treated with chloroquine  (CQ) or epoxomicin  (Epo). Left panel a representative experiment is shown, membranes were blotted  using anti-T6BP, -CD74  and -actin  antibodies. The different degradation fragments of CD74  are indicated (Iip33, Iip22 and Iip16). Right panel, expression levels of Iip33 (top) and Iip16 (bottom) were quantified in three biological replicates using ImageJ and are presented as mean of ratios of each fragment to actin  (+/-SD). Data information: (D) One-way Anova statistical test combined with Bonferronis multiple comparison test was applied. Dotted lines indicate statistically significant differences between conditions."
NCBI gene IDs:
"CIITA: 4261"
Figure legend: "(E Analysis of CD74 proteolysis. HeLa-CIITA  cells were transfected with siCTRL and siT6BP. 48h post treatment, cells were pulsed for 30 min with 35S-Met/Cys, washed and chased for 1, 2 and 4h. HLA-DR/CD74  complexes were first immunoprecipitated  using Tü36 antibody (E) Samples were boiled and analyzed using  SDS-PAGE. The bands corresponding to CD74  isoforms (Iip41 and Iip33) and the cleavage products (Iip16) are indicated. (E right panel) Iip16 expression was quantified using ImageJ and presented as a percentage of Iip16 normalized to the highest quantity of Iip16 detected after 1h of chase in the control condition. Results are representative of two biological replicates. Ii: invariant chain (CD74); CTRL: control."
NCBI gene IDs:
"CIITA: 4261
T6BP: 8887"
Figure legend: "F). Analysis of CD74 proteolysis. HeLa-CIITA  cells were transfected with siCTRL and siT6BP. 48h post treatment, cells were pulsed for 30 min with 35S-Met/Cys, washed and chased for 1, 2 and 4h.  HLA-DR/CD74  complexes were immunoprecipitated  using VICY1 antibody (F). Samples were boiled and analyzed using SDS-PAGE. The bands corresponding to CD74  isoforms Iip33) Results are representative of two biological replicates. Ii: invariant chain (CD74); CTRL: control."
NCBI gene IDs:
"CIITA: 4261
T6BP: 8887"
Figure legend: "(A-B) CANX co-immunoprecipitates with T6BP  in model and professional APCs. Endogenous T6BP  was immunoprecipitated  from HeLa-CIITA, B (DG-75) and dendritic-like (KG-1, DC) cells. The input, the flow through (FT) and the immunoprecipitation  (IP) fractions were analyzed by Western blot using the indicated antibodies. Bottom panels, control IPs  using the beads without antibody (IP  CTRL) are presented for each IP. (B) As in (A) but using anti-CANX  Ab for the IP. For A and B, one representative experiment out of three biological replicates is shown."
NCBI gene IDs:
"CIITA: 4261"
Figure legend: "(C) CANX interacts  with T6BP  using proximity ligation assay (PLA). 48h post-transfection with the indicated siRNAs, HeLa-CIITA  cells were fixed, stained  with anti-T6BP  and anti-CANX  antibodies and proximity revealed using PLA  (Duolink). Nuclei  were stained  using DAPI. Top panel, two representative fields are shown. Bottom panel, quantitative analysis using ImageJ displaying the number of PLA  per cell. The continuous line indicates the mean (+/-SEM). PLA  were quantified in at least 130 cells corresponding to three biological replicates. Scale bars: 10μm. CTRL: control; Mann-Whitney's test; ***: p&lt;0.0003."
NCBI gene IDs:
"CIITA: 4261"
Figure legend: "(D) Calnexin interacts  with T6BP  through its cytosolic  tail. HeLa-CIITA  cells were transfected with a plasmid encoding the GST-tagged transmembrane  (TM) and cytosolic  (CytoTail) domains of CANX  (GST-TM-CytoTail-CANX) or the vector not encoding TM-CytoTail-CANX  as control and immunoprecipitated with anti-GST  antibodies. The input, FT, the wash and the IP  fractions were analyzed by Western blot  and revealed using the indicated antibodies. One representative experiment out of three biological replicates is shown."
NCBI gene IDs:
"GST: 
CANX: 821
CIITA: 4261"
Figure legend: "(E) Silencing of T6BP  does not influence CANX  expression levels while silencing of CANX  reduces the level of CD74  expression. HeLa-CIITA  cells transfected with the indicated siRNAs and samples analyzed, 48h post transfection, by Western blot  with the indicated antibodies. These western blot  results are representative of at least three biological replicates."
NCBI gene IDs:
"CANX: 821
CIITA: 4261
T6BP: 8887"
Figure legend: "B. Overall survival of 107 patients without alterations versus 37 patients with ROCK1 and/or ROCK2 gene amplification, significantly increased mRNA or truncation mutation from TCGA research network. Survival p value determined by Log-Rank test."
NCBI gene IDs:
"ROCK1: 6093
ROCK2: 9475"
Figure legend: "C, D. Log2 median-centered ROCK1 or ROCK2 RNA expression in normal (n=39) vs PDAC (n=39), normal (n=5) vs pancreatic adenocarcinoma (PAC) (n=12), or normal (n=6) vs pancreatic carcinoma (PC) (n=11) samples from indicated studies. Exact p values determined by Mann-Whitney test."
NCBI gene IDs:
"ROCK1: 6093
ROCK2: 9475"
Figure legend: "E. ROCK1 and ROCK2 mRNA expression in human PDAC (n=146) from the TCGA research network. Significance (p value) of slope deviation from 0 determined by Deming regression."
NCBI gene IDs:
"ROCK1: 6093
ROCK2: 9475"
Figure legend: "H. Survival analysis of Pdx1-Cre; LSL-KRasG12D/+; LSL-Trp53R172H/+; LSL-ROCK2:ER (RKPC) mice without (n=21) or with conditional ROCK activation with tamoxifen citrate (n=19). Survival p value determined by Log-Rank test."
NCBI gene IDs:
"ER: 13983///13982
KRas: 16653
Pdx1: 18609
ROCK2: 19878
Trp53: 22059"
Figure legend: "B. Schematic representation of ROCK domains (RBD, Rho binding domain; PH, pleckstrin homology domain; CR, cysteine-rich). Conditionally-activated human ROCK1, human ROCK2 and GFP control fusion proteins (EGFP, enhanced green fluorescent protein; hbER, estrogen receptor hormone binding domain) were expressed in KPflC mouse PDAC cells and blotted with anti-GFP antibody."
NCBI gene IDs:
"ER: 2100///2099
ROCK1: 6093
ROCK2: 9475"
Figure legend: "C. KPflC cells expressing GFP:ER, ROCK1:ER or ROCK2:ER fusion proteins were treated for 24 h with EtOH vehicle or 1 µM 4HT in the presence or absence of 1 µM or 10 µM H1152. Immunoblotting shows endogenous ROCK1 and ROCK2, ER-fusions, and phosphorylation of MLC2 (T18S19). Total MLC (MRCL3/MRLC2/MYL9) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were blotted as loading controls."
NCBI gene IDs:
"ER: 13983///13982
ER: 2100///2099
ROCK1: 6093
ROCK2: 9475"
Figure legend: "E. Cell proliferation determined by Ki67 immunofluorescence. Scale bar: 20 µm.F. Quantification of cell number at the collagen matrix surface per 0.046 mm2 field. Means ± SEM (n=30), one-way ANOVA with multiplicity adjusted exact p value by post hoc Dunnett's multiple comparison test.G. Ki67 positive cell percentages at the surface and within the collagen matrix. Means ± SEM (n=30; n=12 for GFP:ER/Matrix), one-way ANOVA with multiplicity adjusted exact p value by post hoc Dunnett's multiple comparison test."
NCBI gene IDs:
"ER: 2100///2099"
Figure legend: "A. Volcano plots of RNA sequencing data of genes that pass a threshold false discovery rate (FDR) &lt; 5%, with log10 fold-change (FC) in expression in 4HT treated ROCK1:ER expressing cells relative to GFP:ER expressing cells (left) or 4HT treated ROCK2:ER expressing cells relative to GFP:ER expressing cells (right) versus log10 adjusted p value (n=3). ROCK1:ER+4HT vs GFP:ER+4HT; 3828 genes. ROCK2:ER+4HT vs GFP:ER+4HT; 4481 genes."
NCBI gene IDs:
"ER: 2100///2099
ROCK1: 6093
ROCK2: 9475"
Figure legend: "E. Mmp10 mRNA levels relative to Gapdh determined by qPCR following treatment with EtOH vehicle (-) or 1 µM 4HT for 24 h (left). Means ± SEM (n=4), p value by unpaired t test. Mmp10 mRNA levels relative to Gapdh determined by qPCR following treatment with EtOH vehicle (-), 1 µM 4HT or 4HT + 1 µM H1152 ROCK inhibitor for 24 h (right). Means ± SEM (n=3), one-way ANOVA with multiplicity adjusted exact p value by post hoc Tukey multiple comparison test.F. Mmp13 mRNA levels relative to Gapdh determined by qPCR following treatment with EtOH vehicle (-) or 1 µM 4HT for 24 h (left). Means ± SEM (n=4), p value by unpaired t test. Mmp13 mRNA levels relative to Gapdh determined by qPCR following treatment with EtOH vehicle (-), 1 µM 4HT or 4HT + 1 µM H1152 ROCK inhibitor for 24 h (right). Means ± SEM (n=3), one-way ANOVA with multiplicity adjusted exact p value by post hoc Tukey multiple comparison test."
NCBI gene IDs:
"Gapdh: 
Mmp10: 17384
Mmp13: 17386"
Figure legend: "A. Confocal microscope images of ROCK1:ER-expressing cells co-stained for F-actin, MMP10 (left) or MMP13 (right) and DAPI following treatment with vehicle or 1 µM 4HT for 24 h. Multiple z-planes were used to generate x-z and y-z images. Scale bar = 5 µm."
NCBI gene IDs:
"ER: 2100///2099
ROCK1: 6093"
Figure legend: "C. Representative stained gel of ultracentrifuge-enriched microvesicle protein from GFP:ER or ROCK1:ER-expressing cell-conditioned media following treatment with vehicle (-) or 1 µM 4HT for 24 h (top). Absolute arbitrary unit values for total microvesicle protein levels in stained gels (bottom). Means ± SEM (n=4), p value by ratio paired t-test."
NCBI gene IDs:
"ER: 2100///2099
ROCK1: 6093"
Figure legend: "D. Transmission electron microscopy of ultracentrifuge-enriched microvesicles (top center), and immunogold labeling of MMP10 in ROCK1:ER 4HT-treated microvesicles, indicated by red arrows (top right)."
NCBI gene IDs:
"ER: 2100///2099
ROCK1: 6093"
Figure legend: "D. Cell proliferation determined by Ki67 immunofluorescence. Scale bar: 20 µm.E. Ki67 positive cell percentages at the collagen matrix surface. Means ± SEM (n=20; n=19 for GFP:ER/vehicle, n=18 for GFP/GM6001), one-way ANOVA with multiplicity adjusted exact p value by post hoc Tukey multiple comparison test.F. Ki67 positive cell percentages in collagen matrix. Means ± SEM (n=20; n=8 for GFP:ER/ vehicle, n=10 for GFP:ER/GM6001, n=17 for ROCK1:ER/GM6001, n=15 for ROCK2:ER/GM6001), one-way ANOVA with multiplicity adjusted exact p value by post hoc Tukey multiple comparison test."
NCBI gene IDs:
"ER: 2100///2099
ROCK1: 6093
ROCK2: 9475"
Figure legend: "A. Survival analysis of Pdx1-Cre; LSL-KRasG12D/+; LSL-Trp53R172H/+; (KPC) mice without (n=13) or with Fasudil treatment (n=13). Survival p-value determined by Gehan-Breslow-Wilcoxon test."
NCBI gene IDs:
"Cre: 
KRas: 16653
Pdx1: 18609
Trp53: 22059"
Figure legend: "p53 has been show to response with a series of undamped pulse to ionizing irradiation leading to cell cycle arrest while intrinsic DNA damage during cell cycle does not induce regular pulsatile p53 and subsequent gene expression programs. Schematic representations of p53 dynamics in both cellular conditions are shown."
NCBI gene IDs:
"p53: 7157"
Figure legend: "Induction of selected p53 target genes after DNA damage induction in A549 wild-type and p53 knockdown cells. RNA levels were measured by qRT-PCR before and 3h after treatment with 10 Gy R. Fold changes relative to basal levels are shown for each cell line."
NCBI gene IDs:
"p53: 7157"
Figure legend: "Amount of p53 bound to indicated target gene promoters before (basal, grey) and 3 h (red), 6 h (blue) and 9 h (orange) after DNA damage (10 Gy IR) as measured by ChIP. The amount of bound p53 was calculated as percentage of input and normalized to the time-point of the first p53 peak at 3 h. Individual data points (mean values of triplicate quantification in qRT-PCR measurements) from 3-4 biological repeats are shown as dots, mean values are displayed as black horizontal lines. Dashed lines serve as guide to the eyes. We could not detect p53 binding above IgG controls at the published p53 response element in the PPM1D promoter (indicated by n.d.)"
NCBI gene IDs:
"PPM1D: 8493"
Figure legend: "We quantified promoter activity of BAX (B, sustained archetype) and PPM1D (C, pulsatile archetype) before (basal, grey) and 3 h (red), 6 h (blue) and 9 h (orange) after irradiation with 10 Gy IR and inhibition of the second p53 pulse by Chk2 inhibition. Left panel: The percentage of cells with active TSS, subdivided into populations with strong (&gt; 75% of TSS, solid colors) and weak (&lt;75% of TSS, shaded colors) activity, is shown as stacked bar graphs, the mean fraction of active promoters is indicated above each bar. Right panel: Distributions of calculated transcription rates at active TSS are presented for each time point as probability density estimates (PDF, see Data Visualization section). The fraction of active promoters was reduced at 6 h and 9 h after irradiation; the transcription rate was not notably affected."
NCBI gene IDs:
"BAX: 581
PPM1D: 8493"
Figure legend: "We quantified promoter activity of MDM2 (E, transient archetype) and CDKN1A (F, transient archetype) before (basal, grey) and 3 h (red), 6 h (blue) and 9 h (orange) after irradiation with 10 Gy IR and sequential Nutlin-3 treatment. Left panel: The percentage of cells with active TSS, subdivided into populations with strong (&gt; 75% of TSS, solid colors) and weak (&lt;75% of TSS, shaded colors) activity, is shown as stacked bar graphs, the mean fraction of active promoters is indicated above each bar. Right panel: Distributions of calculated transcription rates at active TSS are presented for each time point as probability density estimates (PDF, see Data Visualization section). The relative fraction of active promoters strongly increased, changing transient to sustained archetypes. The transcription rate increased as well both compared to basal levels and to previous experiments with pulsatile p53 dynamics (inset, fold change relative to IR alone for each time point)."
NCBI gene IDs:
"CDKN1A: 1026
MDM2: 4193"
Figure legend: "The p53-K370 methylase Smyd2 was down-regulated in a clonal stable A549 cell line expressing a corresponding shRNA. Transcript levels were measured in wild type and knockdown cells by qRT-PCR. Mean levels and standard deviation from technical triplicates are indicated."
NCBI gene IDs:
"Smyd2: 56950"