EMBO/SourceData huggingface dataset:
Figure legend: "C-H Geometric mean of BFP (C, E) and GFP fluorescence (D, F, H) of cells grown at 37°C (non-stress, NS) or incubated for 1 h at 43°C with a recovery period of 3 h at 37°C (heat shocked, HS) in the GFPhigh (C, D), GFPlow (E, F), and GFPlow-BFPhigh (H) gates. (G) Geometric mean of BFP fluorescence weighted by the relative number of cells in the GFPlow-BFPhigh gate (fluorescence * fraction forward scatter singlets). Note that the GFPlow gate also comprises the GFPlow-BFPhigh gate. Hsf1-202SSS, Hsf1-I202S,L203S,V205S; Hsf1-209SSS, Hsf1-I209S,L211S,L213S; Hsf1-427SSSS, Hsf1-M427S,L429S,L432S,L436S; Hsf1-465SSS, Hsf1-L465S,V466S,Y468S; Hsf1-473SSSS, Hsf1-L473S,F474S,L475S,L476S"
NCBI gene IDs:
"Hsf1: 3297"
Figure legend: "A Schematics of the used system. HeLa cells were stably transfected with mTag-BFP expressed under the control of the HSPA6 promoter and subsequently transiently transfected with plasmids that expressed HSF1wt or mutant variants in an artificial operon with hrGFP, which is translated from an IRES element. Exemplary flow cytometry data plotting BFP fluorescence versus GFP fluorescence, indicating the gates used for analysis. Numbers indicate the fraction (%) of cells (forward scatter singlets) in each gate. Color indicates the cell density from dark blue (low) to red (high). NS, cells grown at 37°C; HS, cells heat shocked at 43°C for 1 h with a recovery period of 3 h at 37°C."
NCBI gene IDs:
"BFP: 
GFP: 
mTag: 
HSF1: 3297
HSPA6: 3310"
Figure legend: "C-H Geometric mean of BFP (C, E) and GFP fluorescence (D, F, H) in the GFPhigh (C, D), GFPlow (E, F), and GFPlow-BFPhigh43 (H) gates. Of note, the number of data points show the number of experiments in which a significant number of cells was found in this gate and missing bars indicate that cells did not fall within this gate in more than two out of four experiments. (G) Geometric mean of BFP fluorescence weighted by the relative number of cells in the GFPlow-BFPhigh43 gate (fluorescence * fraction forward scatter singlets). Note that the GFPlow gate also comprises the GFPlow-BFPhigh37 and that the GFPlow-BFPhigh37 gate also comprises the GFPlow-BFPhigh43 gate. Hsf1-202SSS, Hsf1-I202S,L203S,V205S; Hsf1-209SSS, Hsf1-I209S,L211S,L213S; Hsf1-427SSSS, Hsf1-M427S,L429S,L432S,L436S; Hsf1-465SSS, Hsf1-L465S,V466S,Y468S; Hsf1-473SSSS, Hsf1-L473S,F474S,L475S,L476S"
NCBI gene IDs:
"Hsf1: 3297"
Figure legend: "Figure 4. Decrease of nucleoid number without mtDNA depletion in HeLa cells overexpressing the CHCHD10S59L and CHCHD10P34S alleles. A. Transfections were performed with empty vector (EV) or vectors encoding wild-type CHCHD10-FLAG (WT), CHCHD10-FLAG (S59L) or CHCHD10-FLAG (P34S) mutants. Mitochondria were stained with Mitotracker. Cells overexpressing wild-type and mutant CHCHD10 were labeled with FLAG antibodies. Nucleoids were visualized with an antiserum against DNA. Image analysis was performed by confocal microscopy. Scale bar: 10 µm."
NCBI gene IDs:
"CHCHD10: 400916"
Figure legend: "Figure 7. CHCHD10 mutant fibroblasts are less sensitive to apoptotic cell death compared to control fibroblasts. A. Control (C1, C2) and patient (P1, P2) fibroblasts were treated with 1 μM of staurosporine (STS) for 16 h. Cell death was determined by flow cytometry using Annexin V/DAPI staining. Three independent experiments were performed per condition with two points analyzed per experiment. Differences between the control and patient fibroblasts were analyzed by Student's t-test (two-sided): significant (*: p=0.0116) or extremely significant (***: p=0.0001)."
NCBI gene IDs:
"CHCHD10: 400916"
Figure legend: "Figure 8. Overexpression of the CHCHD10 mutant alleles in HeLa cells leads to inhibition of apoptotic cell death. Transfections were performed with empty vector (EV) or vectors encoding either wild-type CHCHD10-FLAG (WT) or mutant CHCHD10-FLAG (P34S and S59L). A. Western blot on HeLa cells extracts using antibodies against FLAG or Hsp90."
NCBI gene IDs:
"CHCHD10: 400916"
Figure legend: "B-D. HeLa cells transiently expressing the WT or mutated forms of CHCHD10-FLAG (P34S or S59L) were treated with 1 μM Actinomycine D (ActD) for 4, 6 or 8 h with measurement of Annexin V/DAPI staining (B), DEVD-ase activity (C) from three independent experiments. Differences between the mutated and non mutated alleles were analyzed by Student's t-test (two-sided): significant (*:0.05&gt;p&gt;0.01) or very significant (**:0.01&gt;p&gt;0.001). P34S versus WT: **: p=0.0055 (4h), *: p=0.0103 (8h). S59L versus WT: *: p=0.0304 (4h), *: p=0.0129 (8h)."
NCBI gene IDs:
"CHCHD10: 400916"
Figure legend: " H) Epifluorescence microscopy images of the prApe1-GFP/Atg19-mCherry/ypt7Δ, prApe1-GFP/Atg19Δ/ypt7Δ S. cerevisiae cells that were used to analyze the fluorescence intensity of all prApe1-GFP spots. BF represents bright-field images. "
NCBI gene IDs:
"ypt7: 855012"
Figure legend: " I) Bar plot showing the ratio between the GFP intensity of prApe1 spots in prApe1-GFP/Atg19-mCherry/ypt7Δ versus prApe1-GFP/Atg19Δ/ypt7Δ S. cerevisiae cells. The intensity of Ape1-GFP was normalized over the average fluorescence intensity of Nuf2-GFP measured in kinetochores as performed in [36]. Data information: a total of 54 prApe1-GFP spots and 80 Nuf2-GFP spots were analyzed in prApe1-GFP/Atg19Δ/ypt7Δ cells, whereas 52 prApe1-GFP spots and 98 Nuf2-GFP spots were analyzed in prApe1-GFP/Atg19-mCherry/ypt7Δ control cells. Error bars indicate standard error of the mean (SEM). *P = 0.03 (Z test). "
NCBI gene IDs:
"Atg19: 854072
ypt7: 855012"
Figure legend: " Figure 4: Quantification of the Ape1, Ams1, Atg19 protein abundances in living cells. (A) Epifluorescence microscopy images of the prApe1-GFP/Atg19-mCherry/ypt7Δ, Ams1-GFP/Atg19-mCherry/ypt7Δ, Atg19-GFP/Ape1-mCherry/ypt7Δ S. cerevisiae cells that were used to quantify the fluorescence intensity of GFP spots. Only co-localizing GFP and RFP spots were considered. BF represents bright-field images. (B) Bar plot showing the number of molecules of prApe1, Ams1 and Atg19 found in Cvt vesicles in living cells. Data information: data are representative of two independent experiments in which a total of 217 prApe1-GFP, 181 Ams1-GFP and 233 Atg19-GFP spots were analyzed. Error bars indicate standard deviation (SD). ***P &lt; 0.001; *P = 0.0176 (Z test). "
NCBI gene IDs:
"Ams1: 852721
Ape1: 853758
Atg19: 854072
ypt7: 855012"
Figure legend: " (A) Fluorescence microscopy image of a resin section of prApe1-GFP/Atg19-mCherry/ypt7Δ cells, merge of green (prApe1-GFP) and red (Atg19-mcherry) channels. Tetraspeck beads are detected in the blue channel. (B) Electron tomography slice of the boxed area in (A). The outer and inner dashed green circles of 160 and 60 nm radius represent estimated 50% and 90% localization accuracy, respectively. Insets show close-up views of a double (top) and single (bottom) membrane. Corresponding tomogram Movie EV2. (C) Plot of the x and y dimensions of the Cvt vesicles obtained from localization correlation. The average dimensions give rise to spheroids with an average ellipticity of 11 % (shown in dark grey). Both prApe1-GFP and prApe1-GFP/Atg19-mCherry datasets were included. The cases representing autophagosomes were excluded. "
NCBI gene IDs:
"ypt7: 855012"
Figure legend: "(e) The heatmap shows the expression of genes most strongly associated with SSTR2 expression within the pericytes (left color bar indicates significant correlation or anti-correlation)."
NCBI gene IDs:
"SSTR2: 6752"
Figure legend: "(i) The bar graph shows the genes most strongly correlated with SSTR2 belonging to the GO category &quot;transcription regulators&quot;. The dotted line marks a correlation coefficient of zero."
NCBI gene IDs:
"SSTR2: 6752"
Figure legend: "(c) Relative expression level of CRTAC1 across human organs."
NCBI gene IDs:
"CRTAC1: 55118"
Figure legend: "(d) The box plots illustrate differences in mRNA detection for CRTAC1 in alveolar epithelial cells from fibrosis patients compared to control samples across the three indicated patient cohorts (Chicago cohort: ILD n = 9, controls n = 8; Nashville cohort: ILD n = 20, controls n = 10; Munich cohort: ILD n = 3, controls n = 11)."
NCBI gene IDs:
"CRTAC1: 55118"
Figure legend: "(e) Relative gene expression levels of CRTAC1 in GSE47460. Dots represent average expression in the tissue of individual patients. The line represents the mean, error bars show SD. CRTAC1 is significantly downregulated in ILD but not COPD patients"
NCBI gene IDs:
"CRTAC1: 55118"
Figure legend: "(f) For each single cell cohort, the gene-gene correlations with CRTAC1 within the SFTPC+ AT-2 cells were calculated. The indicated genes were selected based on their common direction of correlation across cohorts."
NCBI gene IDs:
"CRTAC1: 55118"
Figure legend: "(h) The bar graph shows the gene categories most strongly correlated with CRTAC1 belonging to the GO category of &quot;transcription regulators&quot;. The dotted line marks a correlation coefficient of zero."
NCBI gene IDs:
"CRTAC1: 55118"
Figure legend: "Figure 1. Identification of non-canonical p53 binding sites in human subtelomeres. (A and B) ChIP-seq tracks for p53 in camptothecin (CPT) treated or untreated HCT116 cells were aligned with RNAPII, CTCF, RAD21, and SMC1 for human chromosome18q (A) or 13q (B) subtelomeres. Position relative to the centromeric end of the terminal TTAGGG repeat tract are indicated in bp at the top. Subtelomeric DNA paralogy segment tracks, internal telomere-like sequence tracks (red CCCTAA), and annotated RefSeq gene tracks are indicated above the ChIP-seq tracks. (C) Alignment of human subtelomeric elements containing non-canonical p53 recognition sequences. The position of the RepeatMasker-defined LTR10c element is shown; also note the (TG)n microsatellite repeat adjacent to the p53 binding site. (D) Schematic organization of non-canonical p53 binding sites found in human subtelomeres."
NCBI gene IDs:
"RNAPII: 
CTCF: 10664
RAD21: 5885
SMC1: 8243
p53: 7157"
Figure legend: "Stress-induced p53 binding at human subtelomeres. (A) Western blot of HCT116 p53-/- and p53+/+ cells treated with DMSO (D) or 50 µM etoposide (E) for 24 hrs. Cell lysates were assayed for total p53, phospho-Ser15 p53 (p-p53), γH2AX, or GAPDH."
NCBI gene IDs:
"p53: 7157"
Figure legend: "(B) ChIP-qPCR was assayed in HCT116 p53-/- or p53 +/+ cells treated with DMSO or etoposide as in panel A, and assayed by ChIP with antibodies to p53 (Ab6) or control IgG, followed by qPCR for p53 binding site in subtelomere 18q (top panel) or 13q (lower panel)."
NCBI gene IDs:
"p53: 7157"
Figure legend: "(C) HCT116 p53-/- and p53+/+ cells were cultured in DMEM with 10% FBS or Hank's buffered saline solution (HBSS) lacking FBS and then assayed by ChIP with either IgG control (grey) or two different p53-specific antibodies Ab6 (red) or FL(black). ChIP was assayed by qPCR with primers proximal to p53 binding sites at 18q, 13q, or p21 promoter."
NCBI gene IDs:
"p53: 7157"
Figure legend: ". (D) Doxycyclin (Dox)-inducible p53 H1299 cells were treated without (-) or with (+) Dox in media containing 10% serum or in serum free HBSS, and then subject to ChIP assay with control IgG or p53-specific Ab6 antibody. ChIP DNA was assayed by qPCR using primers specific for p53 binding site at p21 (top panel), p53-negative control IGX1A (middle panel), or p21 positive control (lower panel). Error bars represent SD, and * indicates p value &lt; .05. p-values were determined by Student t-test."
NCBI gene IDs:
"IGX1A: 
p53: 7157"
Figure legend: ". Transcriptional activity of subtelomeric p53-response elements. (A) Luciferase test constructs containing either empty test vector (top), p53-response elements from 18q subtelomere (middle) or MDM2 promoter (lower) were assayed in HCT p53-/- cells transfected with two independent preparations of empty vector or p53 WT expression vector."
NCBI gene IDs:
"MDM2: 4193
p53: 7157"
Figure legend: "(B) RT-qPCR measure of p21 (top panel) or PARD6G (lower panel) in HCT116 p53-/- or p53+/+ cells after treatment with DMSO or 50 µM etoposide."
NCBI gene IDs:
"p21: 1026
PARD6G: 84552
p53: 7157"
Figure legend: "(D) RT-qPCR analysis of TERRA transcripts from 18q using two independent primer sets pr1 (top panel) or pr2 (lower panel) from HCT116 p53+/+ cells cultured with serum (grey bars) or in HBSS lacking serum (black bars). Error bars represent SD and * indicates p value &lt;.05 using student t-test comparing treated and untreated samples."
NCBI gene IDs:
"p53: 7157"
Figure legend: ". p53-dependent cell viability and telomere protection in response to DNA damage. (A) Western blot of total p53, γH2AX, and GAPDH in HCT116 p53-/- or p53+/+ cells treated with 1 µM or 50 µM etoposide for 24 hrs."
NCBI gene IDs:
"p53: 7157"
Figure legend: "s. (B) Cell cycle analysis of HCT116 p53-/- or p53+/+ cells untreated or treated with 50 µM etoposide for 24 hrs. Cell cycle was determined by FACS analysis of propidium iodide stained cells."
NCBI gene IDs:
"p53: 7157"
Figure legend: "(C) Cell clonal survival assay for HCT116 p53-/- or p53+/+ cells treated with DMSO or 1, 1.5 or 2 µM etoposide for 24 hr prior to replating."
NCBI gene IDs:
"p53: 7157"
Figure legend: "E) TIF assay for HCT116 p53+/+ or p53-/- cells treated with 1 µM etoposide for 3 hrs. Telomere DNA FISH with TelC probe (red), γH2AX (green), Dapi (blue)."
NCBI gene IDs:
"p53: 7157"
Figure legend: "(F) Quantification of TIF assay for % cells with &gt; 4 TIFs per cell for p53+/+ (black) or p53-/- (red) cell."
NCBI gene IDs:
"p53: 7157"
Figure legend: "G) Telomere length assay showing p53-/- or p53+/+ cells treated with either DMS0, 1 or 50 µM etoposide. Ethidium bromide (EtBr) stained agarose gels (left panel), Southern blot hybridized with Tel C probe (middle panel) or with α Satellite DNA promote (right panel). Quantification of telomereDNA signal relative to invariant bands in α Sat. Error bars represent SD and * indicates p values &lt;.05 determined by student t-test (TLA), or chi-square (TIF assay)."
NCBI gene IDs:
"p53: 7157"
Figure legend: "(H) Two-dimensional agarose gel analysis of telomeric DNA from HCT p53+/+ or or p53-/- treated with 50 µM etoposide for 24 hrs. Ethidium gel (top) and Southern blot probed with TelG probe (lower panel). Single stranded telomere DNA (red arrow) and recombination/ replication-associated structures (blue arrow) are indicated."
NCBI gene IDs:
"p53: 7157"
Figure legend: "Figure 5. p53-dependent histone modification changes in response to DNA damage stress. HCT116p53-/- (left panels) or p53 +/+ (right panels) were treated with DMSO (black) or 50 µM etoposide (red) for 24 hrs and assayed by ChIP-qPCR at various locations relative to the TTAGGG repeats across the chromosome18qsubtelomere (panel A) or 13qsubtelomere (panel B) or for control regions (p21 promoter, GKN1/2, PARKIN) as indicated below. ChIP-qPCR for p53, H3K9Ac, H3K27Ac, γH2AX, or IgG control were quantified as % input. Error bars indicates SD and * indicates p value&lt;.05 using student t-test comparing ChIP values in p53+/+ relative to p53-/- cells for specific primer pairs."
NCBI gene IDs:
"p53: 7157"
Figure legend: "(C) Dot blot analysis of telomere repeat or Alu repeat DNA from p53+/+ or p53-/- HCT116 cells treated with DMSO or etoposide (ETP) (as described in panel A), that were subject to ChIP with antibodies to IgG, p53, γH2AX, TRF2, or TRF1. Quantitation of three independent ChIP-assays for TRF1 and TRF2 is shown in the panel to the right. ("
NCBI gene IDs:
"p53: 7157"
Figure legend: "(A) HCT116 p53+/+ or p53-/- cells treated with 50 µM etoposide were assayed by Western blot with antibodies for p53, γH2AX, H3K9Ac, panH3, and GAPDH at times 0, 8, 16, or 24 hr post-treatment."
NCBI gene IDs:
"p53: 7157"
Figure legend: "C-D) RT-qPCR analysis for cells treated as shown in panel A. (C) RT-PCR for the p21 (top), or PARD6G mRNA (lower). (D) RT-PCR for primer pairs spanning subtelomere18q as indicated below. Lower panel shows the No-RT control for 18qsubtelomere primers. RT-qPCR was quantified as relative to Actin with error bars indicating SD and * indicating p value &lt;.05 using student t-test comparing etoposide (24 hr) relative to untreated for specific primer pairs."
NCBI gene IDs:
"Actin: 
p21: 1026
PARD6G: 84552"
Figure legend: "(B) Western blot analysis of CRISPR deleted cell lines 18q WT and 18q Δp53 treated with DMSO (D) or 50 µM etoposide (E) for 24 hr. Blots were probed with pan-p53, phospho-p53, γH2AX, or GAPDH (as loading control)"
NCBI gene IDs:
"p53: 7157"
Figure legend: "(C-E) RT-qPCR for p21 (C), PARDG6 (D), or 18q subtelomeric RNA (E) in 18q WT or18q Δp53 treated with DMSO (black) or 50 μM etoposide (red) for 24 hr. (F) ChIP-qPCR assay for γH2AX at 18q subtelomere in 18q WT or 18q Δp53 treated as in panels B-E."
NCBI gene IDs:
"p21: 1026
PARDG6: 84552
p53: 7157"
Figure legend: "B NPCs differentiated into neurons by overexpressing Ngn2 (one representative experiment is shown). Two weeks after the infection differentiated NPC were positive for neuronal markers βIII-tubulin (Tuj1), Map2, NeuN and humannuclei (hNu) and synaptic markers, the voltage-gated Na+ channels (PanNav) and the vesicular glutamate transporter 1 (VGlut1)."
NCBI gene IDs:
"Ngn2: 63973"
Figure legend: "B Representative images of ultrastructural analysis of fixed neurons examined with electron microscope. PANK2 panel represents PKAN neuronal cells overexpressing PANK2 protein. Scale bar 500nm. Mitochondrial size was measured at level of the larger diameter along the perpendicular axis for all the mitochondria in &gt;30 field (200 mitochondria in total) for each sample (one-way ANOVA)."
NCBI gene IDs:
"PANK2: 80025"
Figure legend: "A Representative images of neurons stained with the neuron specific anti-NCAM antibody, ROS sensible fluorescent probe DCF, and the nuclei dye Hoechst. Scale bar 20 μm. Plots of the DCF fluorescence signal from NCAM positive controls- and PKAN humanneurons, infected or not with Ngn2-PANK2-LV. Data presented as means + SEM of at least three independent experiments (One-way ANOVA)."
NCBI gene IDs:
"Ngn2: 63973"
Figure legend: "mRNA and protein expression of CiTLR5a-HA   (D),  CiTLR5b-HA   (D), CiTLR5a-GFP  (E), and  CiTLR5b-GFP  (E) plasmids in FHM  cells were examined by  qRT-PCR (upper panel) with EF1α  gene as an internal control and by immunoblotting  (IB) (lower panel) with β-tubulin as a reference (n = 4). Data information: All data are presented as mean ± SD. The two-tailed Mann-Whitney U-test was used for (D) and (E). n represents biological replicates. ***P &lt; 0.001."
NCBI gene IDs:
"HA: 
TLR5a: 
TLR5b: 
EF1α: 120485211"
Figure legend: "Lysates of FHM   cells overexpressing CiTLR5a   were respectively incubated with FlaA, FlaB, FlaC, at pH  5.0 or pH  7.4 for 1 h at 4 °C, mixed with HA  Ab-coupled beads or streptavidin agarose  beads for 2 h at 4 °C, then analyzed by immunoblotting  (IB) with anti-HA  or anti-His  antibodies."
NCBI gene IDs:
"TLR5a: "
Figure legend: "Lysates of FHM  cells overexpressing CiTLR5b  were respectively incubated with FlaA, FlaB, FlaC, at pH  5.0 or pH  7.4 for 1 h at 4 °C, mixed with HA  Ab-coupled beads or streptavidin agarose  beads for 2 h at 4 °C, then analyzed by immunoblotting  (IB) with anti-HA  or anti-His  antibodies."
NCBI gene IDs:
"TLR5b: "
Figure legend: "Lysates of FHM  cells overexpressing CiTLR5a and CiTLR5b were respectively incubated with biotin-poly(I:C), biotin-ssRNA  (1 μg/mL) at pH  5.0 or pH  7.4 for 1 h at 4 °C, mixed with HA  Ab-coupled beads for 2 h at 4 °C, then analyzed by immunoblotting  (IB) with anti-HA  antibodies."
NCBI gene IDs:
"TLR5a: 
TLR5b: "
Figure legend: "N, O CiUNC93B1-Myc  and CiTLR5a-HA  (M) or CiTLR5b-HA  (N) were transfected into FHM  cells. Co-IP and immunoblotting  were conducted to test the interactions  between CiUNC93B1-Myc  and CiTLR5a-HA  or CiTLR5b-HA."
NCBI gene IDs:
"HA: 
Myc: 
TLR5a: 
TLR5b: 
UNC93B1: "
Figure legend: "Lysates of FHM  cells overexpressing  CiTLR5a  and CiTLR5b   (including region deletants) were incubated with biotin-poly(I:C). Vector was used as a control. Pull-down  and immunoblotting  (IB) were performed."
NCBI gene IDs:
"TLR5a: 
TLR5b: "
Figure legend: "H-K Lysates of FHM  cells overexpressing  CiTLR5a  and CiTLR5b  site mutants were incubated with biotin-poly(I:C). Vector and wild type were used as controls. Pull-down and immunoblotting  were carried out (H, J). (I, K) Relative band intensity ratios of (H) and (J) were analyzed by ImageJ, respectively (n = 3). Data information: All data are presented as mean ± SD. The two-tailed Mann-Whitney U-test was used for (I), and (K). n represents biological replicates. *P &lt; 0.05, **P &lt; 0.01."
NCBI gene IDs:
"TLR5a: 
TLR5b: "
Figure legend: "Lysates of FHM  cells overexpressing CiTLR5a   or CiTLR5b  were respectively treated with Endo H  and analyzed by immunoblotting  (IB) with anti-HA  antibody."
NCBI gene IDs:
"TLR5a: 
TLR5b: "
Figure legend: "Lysates of FHM  cells overexpressing CiTLR5a or CiTLR5b  mutants were respectively incubated with biotin-poly(I:C) (I) Vector and wild type were used as controls. Pull-down and immunoblotting  assays were conducted (I, (J, Relative band intensity ratios of (I) were analyzed by ImageJ (n = 3). Data information: All data are presented as mean ± SD. The two-tailed Mann-Whitney U-test was used for (J), n represents biological replicates. *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001."
NCBI gene IDs:
"TLR5a: 
TLR5b: "
Figure legend: "Lysates of FHM  cells overexpressing CiTLR5a or CiTLR5b  mutants were respectively incubated with FlaC  (K). Vector and wild type were used as controls. Pull-down and immunoblotting  assays were conducted K). L) Relative band intensity ratios of (K) were analyzed by ImageJ (n = 3). Data information: All data are presented as mean ± SD. The two-tailed Mann-Whitney U-test was used for (L). n represents biological replicates. *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001."
NCBI gene IDs:
"TLR5a: 
TLR5b: "
Figure legend: "Lysates of FHM  cells overexpressing LoTLR5 (A),  DrTLR5a (B), DrTLR5b  (B),  IpTLR5-1  (C),  IpTLR5-2 (C), IpTLR5S (C),  OmTLR5M (D), OmTLR5S (D), were respectively incubated with FlaC-His  (1 μg/mL) at pH  5.0 or pH  7.4. Complexes were pulled down  by Anti-GFP  antibody coupling beads and analyzed by immunoblotting  (IB) with anti-His  antibody."
NCBI gene IDs:
"TLR5-2: 108275971
TLR5-1: 108275978
TLR5S: 100304981
TLR5: 102693268
TLR5S: 100135812
TLR5a: 403138
TLR5b: 403139
TLR5M: 100137014"
Figure legend: "Lysates of FHM  cells overexpressing HsTLR5 (E) were respectively incubated with FlaC-His  (1 μg/mL) at pH 5.0 or pH  7.4. Complexes were  pulled down  by Anti-GFP  antibody coupling beads and analyzed by immunoblotting  (IB) with anti-His  antibody."
NCBI gene IDs:
"TLR5: 7100"
Figure legend: "Lysates of FHM  cells overexpressing LoTLR5 (F), DrTLR5a (G),  DrTLR5b (G),  IpTLR5-1 (H),  IpTLR5-2 (H), IpTLR5S (H), were respectively incubated with biotin-poly(I:C) (1 μg/mL) at pH  5.0 or pH 7.4. Complexes were pulled down by streptavidin  beads and analyzed via immunoblotting with anti-GFP  antibody."
NCBI gene IDs:
"TLR5-2: 108275971
TLR5-1: 108275978
TLR5S: 100304981
TLR5: 102693268
TLR5a: 403138
TLR5b: 403139"
Figure legend: "Lysates of FHM cells overexpressing OmTLR5M  (I), OmTLR5S (I), and HsTLR5 (J) were respectively incubated with biotin-poly(I:C) (1 μg/mL) at pH  5.0 or pH  7.4. Complexes were pulled down by streptavidin  beads and analyzed via immunoblotting  with anti-GFP  antibody."
NCBI gene IDs:
"TLR5: 7100
TLR5S: 100135812
TLR5M: 100137014"
Figure legend: "Lysates of FHM  cells overexpressing  DrTLR5a and DrTLR5b mutants were incubated with biotin-poly(I:C) and analyzed by immunoblotting  (N), and relative band intensity ratios were analyzed by ImageJ (O) (n = 3). Vector and wild type (WT) were used as controls. Data information: All data are presented as mean ± SD. The two-tailed Mann-Whitney U-test was used for (O). n represents biological replicates. *P &lt; 0.05, **P &lt; 0.01."
NCBI gene IDs:
"TLR5a: 403138
TLR5b: 403139"
Figure legend: "Representative femur sections from 8-day-old wild-type and Dnmt2−/− mice. The staining of perivascular cells (GLS, green) is strongly reduced in Dnmt2−/− bone marrow. Nuclei are counterstained with DAPI. Scale bar: 100 μm."
NCBI gene IDs:
"Dnmt2: 13434"