EMBO/SourceData huggingface dataset:
Figure legend: "D) Substituting the Nter of Sen1 by Nrd1 CID but not Pcf11 CID partially suppresses the termination defects detected in the sen1∆Nter mutant. Northern blot assays performed in a Sen1-AID strain carrying an empty vector or a plasmid expressing the indicated versions of SEN1 upon depletion of the endogenous Sen1 protein as in figure 3B. Experiments performed in a ∆rrp6 background. Representative gel of one out of two independent experiments.The U4 RNA is used as a loading control."
NCBI gene IDs:
"U4: 
Nrd1: 855470
Pcf11: 851814
rrp6: 854162
SEN1: 851150
Sen1: 851150
sen1: 851150"
Figure legend: "E) Sen1 Nter interacts with the C-terminal domain (Cter) of Sen1 both in the presence and in the absence of the NIM in vitro. Pull-down experiments using either a wt or a ∆NIM version of recombinant Sen1 Cter immobilized on glutathione-sepharose beads and a TAP-tagged version of Sen1 Nter expressed in yeast. Representative gel of one out of three independent experiments."
NCBI gene IDs:
"TAP: 
Sen1: 851150"
Figure legend: "A-C) Comparison of the distribution of Sen1 and RNAPII (Rpb1) at mRNAs and CUTs. Values on the y axis correspond to the median coverage. Note that the scale of Sen1 and Rpb1 datasets have been modified to be able to visualize both in the same plot."
NCBI gene IDs:
"Rpb1: 
Sen1: 851150"
Figure legend: "G) Metagene analysis of the distribution of the different Sen1 variants at mRNAs using either the TSS or the PAS as reference point. Values correspond to the median of Sen1 data normalized by the RNAPII signal obtained in the corresponding background."
NCBI gene IDs:
"Sen1: 851150"
Figure legend: "H-I) Screenshots of two well-characterized protein-coding genes that are regulated by NNS-dependent premature termination. Values correspond to unnormalized Sen1 occupancy."
NCBI gene IDs:
"Sen1: 851150"
Figure legend: "J) Profile of Sen1 binding at CUTs calculated as for mRNAs."
NCBI gene IDs:
"Sen1: 851150"
Figure legend: "K-L) Examples of CUTs exhibiting differences in Sen1 occupancy upon deletion of the NIM or the Nter. Plots correspond to unnormalized data."
NCBI gene IDs:
"Sen1: 851150"
Figure legend: "M-O) Analysis of the distribution of the different Sen1 versions around snoRNAs performed as for CUTs."
NCBI gene IDs:
"Sen1: 851150"
Figure legend: "P) Comparison of the total levels of the different Sen1 variants at mRNAs, CUTs and the termination region of snoRNAs (i.e. a window of 200 nt downstream of the 3' end of the mature snoRNA, snoRNA-ter). Boxes in box-plots include all the values between the 25th and the 75th percentiles and the horizontal line indicates the median. The upper error bars indicate the distance between the largest value smaller than or equal to the upper limit of the box + 1.5 *IQR. The lower error bars indicate the distance between the lowest value greater than or equal to the lower limit of the box - 1.5 *IQR. Datasets for the different Sen1 versions were compared using a t-test (bilateral distributions, unpaired data). p-values≥ 0.05 are indicated as ns (not significant), one asterisk is used when 0.05&gt;p-value≥0.01, two asterisks when 0.01&gt;p-value≥0.001 and three asterisks for p-value &lt;0.001."
NCBI gene IDs:
"Sen1: 851150"
Figure legend: "A) Decreasing the elongation rate alleviates the termination defects associated with deletion of Sen1 Nter. Northern blot assays performed in a Sen1-AID, ∆rrp6 strain carrying a plasmid expressing the indicated versions of SEN1 upon depletion of the endogenous Sen1 protein as in former experiments. Where indicated, cells were treated with 50 mg/L of 6-azauracile (6AU) for 2h. Representative gel of one out of two independent biological replicates.The U4 RNA is used as a loading control."
NCBI gene IDs:
"U4: 
rrp6: 854162
SEN1: 851150
Sen1: 851150"
Figure legend: "(b-e) Induction of conventional macroautophagy in WT and Ulk1gt/gt, but not in Atg5−/−, embryonic erythroid cells. Ter119+ erythroid cells from WT, Atg5−/−, and Ulk1gt/gt embryonic mice (E18.5) were treated with 1 μM rapamycin (b,c) and 1 μM STS (d,e), and then harvested at the indicated times. (b,d) Representative protein expression of LC3 and p62 measured by western blot. Actin was a loading control. Uncropped images are shown in Supplementary Fig. 10. (c,e) Semi-quantitative analysis of LC3-II/LC3-I and p62 protein expression (n=3, mean±s.d.). Asterisks indicate a significant difference at P0.05 (analysis of variance (ANOVA)). #P0.05 versus value of WT 24 h (ANOVA). 'NS' indicates not significant (ANOVA)."
NCBI gene IDs:
"Atg5: 11793
Ulk1: 22241"
Figure legend: "(b-e) Induction of conventional macroautophagy in WT and Ulk1gt/gt, but not in Atg5−/−, embryonic erythroid cells. Ter119+ erythroid cells from WT, Atg5−/−, and Ulk1gt/gt embryonic mice (E18.5) were treated with 1 μM rapamycin (b,c) and 1 μM STS (d,e), and then harvested at the indicated times. (b,d) Representative protein expression of LC3 and p62 measured by western blot. Actin was a loading control. Uncropped images are shown in Supplementary Fig. 10. (c,e) Semi-quantitative analysis of LC3-II/LC3-I and p62 protein expression (n=3, mean±s.d.). Asterisks indicate a significant difference at P0.05 (analysis of variance (ANOVA)). #P0.05 versus value of WT 24 h (ANOVA). 'NS' indicates not significant (ANOVA)."
NCBI gene IDs:
"Atg5: 11793
Ulk1: 22241"
Figure legend: "(a) Induction of alternative macroautophagy in WT and Atg5−/−, but not Ulk1gt/gt and DKO, erythroid cells. Erythroblasts and reticulocytes from the liver of embryonic mice (E18.5) were incubated with or without STS (1 μM) for 24 h, followed by staining with anti-Lamp2 (red), anti-Ter119 (green) and DAPI (blue). DAPI-positive erythroblasts and DAPI-negative reticulocytes are shown. Lamp2 image and merged image (DAPI, Ter119 and Lamp2) are shown. Scale bar, 1 μm. Large dots for Lamp2 are observed in STS-treated WT and Atg5−/− cells, but not STS-treated Ulk1gt/gt or DKO cells."
NCBI gene IDs:
"Atg5: 11793
Ulk1: 22241"
Figure legend: "(b) Representative electron micrographs of EC incubated with or without STS. Erythroid cells were harvested from the liver of embryonic mice (E18.5), incubated with or without STS (1 μM) for 24 h, and analysed by electron microscopy (EM). Scale bar, 1 μm. Insets of WT and Atg5−/− cells show mitophagy (Scale bar, 0.5 μm). Inset of a Ulk1gt/gt cell showing mitochondria that have not been engulfed (Scale bar, 0.5 μm). Arrows point to non-engulfed mitochondria and the arrowheads indicate engulfed mitochondria. (c-e) Quantitative analysis of mitophagy after STS treatment, calculated from EM photos. Population of reticulocytes with mitophagy (c), number of mitochondria per reticulocytes (d) and population of reticulocytes showing macroautophagy (e) were calculated (n&gt;35 cells per mouse). The data are shown as mean±s.d. (n=3). *P0.05 versus value of WT (analysis of variance (ANOVA)); #P0.05 versus value of Atg5−/− (ANOVA); 'NS' indicates not significant versus value of WT (ANOVA)."
NCBI gene IDs:
"Atg5: 11793
Ulk1: 22241"
Figure legend: "(c) The percentage of CD71−Ter119+ cells without mitochondria was determined by gating the mitochondrialow fraction, as shown in (b) (mean±s.d., n=6). *P0.05 versus value of WT (analysis of variance (ANOVA)); #P0.05 versus value of Atg5−/− (ANOVA); 'NS' indicates not significant versus value of WT (ANOVA)."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "(d) Percent mitochondrialow cells in the CD71−Ter119+ EC of Atg7F/FCre embryo. Erythroid cells from the liver and peripheral blood of WT and Atg7F/FCre embryo (E18.5) were stained with anti-Ter119, anti-CD71, and Mitotracker Deep Red (mean±s.d., n=3). *P0.05 versus value of WT (Student's t-test)."
NCBI gene IDs:
"Cre: 
Atg7: 74244"
Figure legend: "(e) Percentage of mitochondrialow cells in Syto16low cells. Liver erythroid cells (E18.5) were stained with Syto16 (DNA) and Mitotracker Deep Red. Representative dot plots of the mitochondrial content of Syto16low cells are demonstrated in Supplementary Fig. 5, the percentage of Syto16low cells without mitochondria was determined by gating the mitochondrialow fraction (mean±s.d., n=6). *P0.05 versus value of WT (ANOVA); #P0.05 versus value of Atg5−/− (ANOVA); 'NS' indicates not significant versus value of WT (ANOVA)."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "(f) Immunofluorescent analysis of mitochondrial and lysosomal proteins. Liver Ter119+ cells (E18.5) of the indicated mice were stained with anti-Tom20 (mitochondrial marker) and anti-Lamp2 (lysosomal marker) antibodies, and observed by fluorescent microscopy. Scale bar, 2 μm. Green, red, white, and blue indicate Tom20, Lamp2, Ter119 and DAPI (DNA), respectively. Mitochondrial and lysosomal markers have separate distributions in Ulk1gt/gt cells and DKO cells."
NCBI gene IDs:
"Ulk1: 22241"
Figure legend: "(a-f) Representative EM of WT (a), ATG5−/− (b), Ulk1gt/gt (c,d) and DKO (e,f) reticulocytes from embryonic liver (E14.5). (a,b) Mitophagy was detected in WT and ATG5−/− cells (scale bar, 1 μm). Insets indicate mitophagy (scale bar, 0.2 μm). (c,e) In Ulk1gt/gt and DKO cells, numerous mitochondria were in contact with membrane structures (scale bar, 1 μm). Enlarged images are shown on the right side (scale bar, 0.2 μm). (d,f) Some Ulk1gt/gt and DKO cells showed plasma membrane blebs containing mitochondria (scale bar, 1 μm). (g,h) Quantitative analysis of mitophagy calculated from EM photos in the embryonic liver at E18.5. Population of reticulocytes with mitophagy (g), and number of mitochondria per reticulocytes (h) were calculated (n&gt;35 cells per mouse). The data are shown as mean±s.d. (n=3). *P0.05 versus value of WT (analysis of variance (ANOVA)); #P0.05 versus value of Atg5−/− (ANOVA); 'NS' indicates not significant versus value of WT (ANOVA)."
NCBI gene IDs:
"ATG5: 11793
Ulk1: 22241"
Figure legend: "(b) Semi-quantitative analysis of the expression level of each protein and the LC3-II/LC3-I ratio (mean±s.d., n=3). *P0.05 versus value of WT EC (analysis of variance (ANOVA)); #P0.05 versus value of Atg5−/− EC (ANOVA); 'NS' indicates not significant versus value of WT EC (ANOVA)."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "(c,d) Percentage of Syto16low cells without mitochondria. Differentiated cells were stained with Syto16 and Mitotracker Deep Red. Representative histograms of mitochondrial content in Syto16low cells on day 6 are shown in (c). Numbers indicate the population of mitochondrialow cells. Representative dot plots are also available in Supplementary Fig. 13. (d) Percentage of Syto16low cells lacking mitochondria determined by gating the mitochondrialow fraction as shown in (c) (mean±s.d., n=6). *P0.05 versus value of WT (analysis of variance (ANOVA)); #P0.05 versus value of Atg5−/− (ANOVA); 'NS' indicates not significant versus value of WT (ANOVA)."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "(i)Impact of various drugs on mitochondrial clearance during in vitro differentiation.with cells from Atg5−/− embryos exposed to wortmannin or 3-MA (mean±s.d., n=3). *P0.05 versus value of no drug (ANOVA)."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "(e) Representative electron micrographs of bone marrow reticulocytes in 10 week-old WT and Ulk1gt/gt mice (scale bar, 1 μm). Insets indicate mitophagy (scale bar, 0.2 μm)."
NCBI gene IDs:
"Ulk1: 22241"
Figure legend: "(h,i) The impact of Ulk1 on mitochondrial clearance during stress erythropoiesis. (h) Representative images of erythrocyte in PHZ-treated WT and Ulk1gt/gt mice (14 weeks old). Blood cells were stained with anti-Ter119 (erythroid cell marker) and anti-Tom20 (mitochondrial marker) antibodies and observed by fluorescence microscopy. Green and red indicate Ter119 and Tom20, respectively. Scale bar, 10 μm. (i) Percentage of mitochondrialow cells among Syto16low cells. Erythroid cells were stained with Syto16 (DNA) and Mitotracker Deep Red (mean±s.d., n=3). *P0.05 versus value of WT (Student's t-test). Mitochondrial retention was observed in Ulk1gt/gt mice."
NCBI gene IDs:
"Ulk1: 22241"
Figure legend: "(B) Assessment of exogenous DDX60  expression. HEK293T  cells transfected with DDX60  wild type (wt), or DDX60  mutants and analyzed by  western blot for DDX60, ß-actin and GAPDH (loading controls), and RFP  (reporter). DDX60  and RFP  quantification relative to GAPDH from one representative blot  are shown below."
NCBI gene IDs:
"DDX60: 55601"
Figure legend: "(C) HCV antiviral assays with DDX60  wt or mutant panel. Huh-7  cells transfected with an RFP  containing plasmid backbone encoding either Firefly luciferase  (Fluc, negative, and transfection control), IRF1  (positive antiviral control), DDX60  wt, or DDX60  mutants and infected with HCV-Ypet, a bicistronic reporter HCV  where Ypet  reporter protein is driven by HCV  IRES  and HCV  polyprotein consisting of C, E1, E2, p7, NS2, NS3, 4A, 4B, NS5A, and NS5B  is driven by EMCV  IRES. Data information: For (C) percent of Ypet+ cells in RFP+ cells is scaled to one replicate of Fluc  control. Data shows mean ± SD for at least n=3 biological replicates; ns = not significant, *p &lt; 0.05, ****p &lt; 0.0001, ns, non-significant using ANOVA and Dunnett's multiple comparison test against Fluc."
NCBI gene IDs:
"Fluc: 
luciferase: 
RFP: 
Ypet: 
DDX60: 55601
IRF1: 3659"
Figure legend: "(D) Effect of DDX60  on replication of bicistronic or monocistronic infectious reporter HCVs. Huh-7 cells transfected as in (C) and infected with either bicistronic HCV-Ypet   (left) or monocistronic HCV  J6/JFH-5AB-YPet. Ypet  reporter in monocistronic HCV  is placed in between NS5A  and NS5B. Data information: For (D), percent of Ypet+ cells in RFP+ cells is scaled to one replicate of Fluc  control. Data shows mean ± SD for at least n=3 biological replicates; ns = not significant, *p &lt; 0.05, ****p &lt; 0.0001, ns, non-significant using ANOVA and Dunnett's multiple comparison test against Fluc."
NCBI gene IDs:
"Fluc: 
YPet: 
Ypet: 
DDX60: 55601"
Figure legend: "(A) Plasmid-based dual luciferase bicistronic reporter assays. HEK293T  cells co-transfected with  dual luciferase bicistronic reporter plasmid  (Renilla luciferase  (Rluc) translationally driven by a 5' cap, and Firefly luciferase  (Fluc) translationally driven by different IRESs  as indicated) and GFP  plasmid (negative control) or increasing amounts of IRF1  (positive control), DDX60  wt, or DDX60  E890A mutant. Total amount of DNA transfected was kept constant by supplementing transfection mixes with GFP  plasmid. Luciferase  units after cell lysis is plotted as a percentage of GFP   transfected cells (left) and ratio of IRES Fluc  units over 5' cap Rluc  units (middle). Diagram to the right of ratios plot depicts expected ratios of IRES-driven Fluc  units to 5' cap-driven Rluc  units given either: equal translation of 5' cap-driven Rluc  and IRES-driven Fluc  (top), greater translation of IRES-driven Fluc  (middle), or greater translation of 5' cap-driven Rluc  (bottom). Data information: Data shows mean ± SD for at least n=3 biological replicates; *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001, ****p &lt; 0.0001, ns, non-significant using ANOVA and Dunnett's multiple comparison test against GFP."
NCBI gene IDs:
"DDX60: 55601
IRF1: 3659"
Figure legend: "(B) RNA-based monocistronic  luciferase reporter assays. HEK293T  cells transfected with GFP  (negative control), IRF1  (positive control), DDX60  wt, or DDX60  E890A and subsequently transfected with in vitro transcribed 5' cap or different IRES  driven Fluc  mRNA constructs as indicated. Luciferase  units after cell lysis is plotted as a percentage of GFP  transfected cells. Data information: Data shows mean ± SD for at least n=3 biological replicates; *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001, ****p &lt; 0.0001, ns, non-significant using ANOVA and Dunnett's multiple comparison test against GFP."
NCBI gene IDs:
"Fluc: 
GFP: 
DDX60: 55601
IRF1: 3659"
Figure legend: "(A-E) (A, B, E) Multi-cycle infection  assays with type I and type II IRES containing viruses. HeLa  cells stably expressing Firefly luciferase  (Fluc) (negative control), IRF1  (positive control), DDX60  wt, or DDX60  E890A and infected with (A) encephalomyocarditis virus, (B) poliovirus, or (E) a chimeric poliovirus  with the poliovirus  IRES replaced with the IRES of EMCV  (EMCV-IRES-PV) at MOI 0.001. Supernatants were collected 24 hours post infection  (hpi) (EMCV) or 48 hpi (poliovirus  and EMCV-IRES-PV) and titers determined via plaque assay on HeLa  cells. (C, D) Single-cycle infection  assays  with type I and type II IRES containing viruses. BHK-J cells stably expressing empty vector (negative control), IRF1  (positive control), DDX60  wt, or DDX60  E890A and infected with (C) foot and mouth disease virus, or (D) bovine enterovirus-1 at MOI 1. Supernatants were collected 5 hours post infection  (hpi) and titers determined via plaque assay on BHK-21  clone 13  cells. Data information: Data shows mean ± SEM percent infectious  titers relative to Fluc  from at least n=3 biological replicates; *p &lt; 0.05, **p &lt; 0.01, ***p &lt;0.001, ****p&lt;0.0001, ns, non-significant using ANOVA and Dunnett's multiple comparison test against DDX60  E890A."
NCBI gene IDs:
"Fluc: 
luciferase: 
DDX60: 55601
IRF1: 3659"
Figure legend: "B) HEK293T  cells transfected with DDX60  wt or DDX60  E890A (negative control) and transfected with in vitro transcribed 5' cap- or IRES-driven Fluc  mRNA constructs as indicated and lysed 16 hours later. (B) IRES- or cap-driven translation from the same samples assayed in parallel using luciferase assay. Data information: B) Mean ± SD from at least n=3 biological replicates; ****FDR &lt; 0.01% (p&lt;0.0001) using unpaired t-test with Welch correction and Benjamini and Yekutieli correction for multiple testing comparing DDX60  wt versus DDX60  E890A transfected cells. ns, non-significant."
NCBI gene IDs:
"Fluc: 
DDX60: 55601"
Figure legend: "(C, HEK293T  cells stably expressing a  type I IFN  sensitive response element (ISRE) driven Fluc  gene were transfected with increasing amounts of RIG-I, RIG-I in combination with DDX60  wt, or RIG-I  in combination with DDX60  E890A while supplementing with GFP  plasmid to equalize the total amount of DNA transfected. Transfected cells were then treated with either PBS  (negative control) or transfected with LMW poly(I:C). In parallel, untransfected cells were treated with either PBS  (mock), transfected with LMW poly(I:C), or treated with IFN-ß (positive control). Cells were subsequently used for a luciferase assay  to assess ISRE activity (C) Data information: (C) Mean ± SD from at least n=3 biological replicates; *p &lt; 0.05 using unpaired t-test with Welch's correction, ns, not significant using repeated measures one-way ANOVA with Geisser-Greenhouse correction comparing RIG-I transfected vs RIG-I + DDX60  wt or RIG-I + DDX60  E890A transfected cells."
NCBI gene IDs:
"Fluc: 
GFP: 
DDX60: 55601
RIG-I: 23586"
Figure legend: "D) HEK293T  cells stably expressing a  type I IFN  sensitive response element (ISRE) driven Fluc  gene were transfected with increasing amounts of RIG-I, RIG-I in combination with DDX60  wt, or RIG-I in combination with DDX60  E890A while supplementing with GFP  plasmid to equalize the total amount of DNA transfected. western blot  for analysis of DDX60, RIG-I, ß-actin (loading control), or GAPDH  (loading control) protein products (D). Quantification of DDX60  and RIG-I band intensities relative to ß-actin  are shown below each respective lane in (D). Data information: (D) representative western blot  from (C)."
NCBI gene IDs:
"Fluc: 
GFP: 
DDX60: 55601
RIG-I: 23586"
Figure legend: "(B) Effect of DDX60  on 5' cap (left) or EMCV  IRES (right) driven Fluc  mRNA polysomes. Data information: Mean percent ± SEM of Fluc  mRNA of each fraction relative to Fluc  mRNA in all fractions, from n=3 biological replicates."
NCBI gene IDs:
"Fluc: 
DDX60: 55601"
Figure legend: "(C) Representative results of RNA electrophoresis  analysis of individual fractions. Shown are results from one replicate of DDX60-transfected, EMCV-IRES-PV-infected cells. RNA  was analyzed by Bioanalyzer to visualize 28S, and 18S ribosome   subunit distribution. RIN, RNA  integrity number."
NCBI gene IDs:
"DDX60: 55601"
Figure legend: "(D) Effect of DDX60  expression on parental poliovirus (type I IRES, purple circles) versus chimeric poliovirus  (type II IRES, red squares) VP4  mRNA polysomes  (left) and cellular GAPDH   mRNA polysomes  in the same samples. Data information: Mean percent ± SEM of poliovirus VP4  or GAPDH  mRNA in each fraction relative to VP4  or GAPDH   mRNA in all fractions from n=3 replicate plates per condition."
NCBI gene IDs:
"VP4: 
DDX60: 55601
GAPDH: 2597"
Figure legend: "SUD binds to Paip1 and Paip1M with the same binding intensity. n. s.: not significant."
NCBI gene IDs:
"Paip1: 10605"
Figure legend: "The Mac2 subdomain is crucial for interacting with Paip1M."
NCBI gene IDs:
"Paip1: 10605"
Figure legend: "Δ16-Mac2 cannot bind Paip1M, Mac1−2 binds to Paip1M in the split-YFP assay. Scale bars represent 50 µM."
NCBI gene IDs:
"Paip1: 10605"
Figure legend: "SUD and PABP do not compete with each other for interacting with Paip1. (A) Excess expression of SUD-RFP does not impair the split-YFP signal between PABP and Paip1 (lower images), compared to the control (upper images). (B) Co-expression of excess RFP-PABP does not result in an impaired interaction between Paip1 and SUD either. RFP: red fluorescent protein. Scale bars represent 50 µM."
NCBI gene IDs:
"Paip1: 10605"
Figure legend: "Left image: SUD generally stimulates protein translation level detected by the luciferase-pcDNA3 reporter (n=6). Middle image: SUD does not increase the amounts of total protein synthesis (host and viral proteins) in the replicon-transfected cells. Right image: SUD augments viral protein synthesis (n=8). HEK-293 cells growing in 12-well plates were transfected with the indicated plasmids and replicon DNA. Twenty-four hours post-transfection, cells were harvested for Renilla luciferase activity measurement (left and right image). For the ribopuromycylation assay, 24 hours post-transfection cells were pulsed with 3 µM puromycin for 1 hour at 37°C before harvesting for western blot analysis (middle image)."
NCBI gene IDs:
"luciferase: "
Figure legend: "(B) Quantitative polymerase chain reaction  (qPCR) analysis of Mmps including Mmp2, Mmp9, Mmp10, Mmp12 and Mmp13 mRNA from mouse peritoneal macrophages stimulated with AG (1 μg/ml) for indicated times. (C) Immunoblots of cell supernatants to analyze secreted MMP2, MMP9, MMP10, MMP12 and MMP13 by mouse peritoneal macrophages stimulated with AG (1 μg/mL) for indicated  times; GADPH of cell lysates served as a loading control. Data information: Data are means + SD averaged from 3 independent experiments performed with technical triplicates and each symbol represents the mean of technical triplicates. Two-way ANOVA followed by Tukey's post hoc test was used for statistical analysis. *, p&lt;0.05; **, p&lt;0.01; ***, p&lt;0.001; ****, p&lt;0.0001."
NCBI gene IDs:
"Mmp10: 17384
Mmp12: 17381
Mmp13: 17386
Mmp2: 17390
Mmp9: 17395"
Figure legend: "(H) qPCR analysis of Mmps including Mmp9, Mmp10, Mmp12, and Mmp13 from mouse peritoneal macrophages infected with H37Rv for 24h (MOI=5) in absence or presence of AG  aptamers (1 μg/ml). (I) Immunoblots  of cell supernatants to analyze secreted MMP9, MMP10, MMP12 and MMP13 by mouse peritoneal macrophages infected with H37Rv for indicated times (MOI=5) in the absence or presence of AG  aptamers (0.5 μg/ml); GADPH of cell lysates served as the loading control. Data information: Data are means + SD averaged from 3 independent experiments performed with technical triplicates and each symbol represents the mean of technical triplicates. Two-way ANOVA followed by Tukey's post hoc test was used for statistical analysis. *, p&lt;0.05; **, p&lt;0.01; ***, p&lt;0.001; ****, p&lt;0.0001."
NCBI gene IDs:
"Mmp10: 17384
Mmp12: 17381
Mmp13: 17386
Mmp9: 17395"
Figure legend: "(I) Immunoblot of lysates of shCtrl and shGalectin-9 THP-1  cells stimulated with AG (1 μg/ml) for indicated  times. Data are representative of n=3 independent experiments."
NCBI gene IDs:
"Galectin-9: 3965"