EMBO/SourceData huggingface dataset:
Figure legend: "C-F Quantification of the percent of lysosomes moving in the anterograde  or  retrograde direction. C, E, F Cultured  hippocampal neurons  were infected with AAV  expressing either shLAMTOR1 or shSc; they were treated with vehicle control or ML-SI1 (20 µM, C, n = 16-49 neurons from 3-10 independent experiments), or  ML-SA1 (20 µM, E, n = 13-49  neurons from 3-10 independent experiments), or  CilioD (20 µM, F, n = 12-49  neurons from 3-10 independent experiments), and imaged with  LysoTracker to visualize lysosomal  trafficking in dendrites. D Neurons  were infected with shLAMTOR1 or shSc AAV and Accell TRPML1 siRNA or control siRNA; they were imaged as described above. N = 7-31 neurons from 3-6 independent experiments. Data information: Data with error bars are represented as means ± SEM. ***P &lt; 0.001 compared with shSc or shSc/Accell siControl; ##P &lt; 0.01, ###P &lt; 0.001 compared with shLAMTOR1 or shLAMTOR1/Accell siControl; &amp;&amp;P &lt; 0.01, &amp;&amp;&amp;P &lt; 0.001 compared with shSc/Accell siLyspersin; n.s., not significant; two-way ANOVA with Tukey's post-test."
NCBI gene IDs:
"Lyspersin: 71923
LAMTOR1: 66508
TRPML1: 94178"
Figure legend: "D  TAT-2031 treatment (10 µM) increased ML-SA1-induced   TRPML1 Ca2+  release in both control and  LAMTOR1 KD cells. Data information: traces represent the mean values of each group."
NCBI gene IDs:
"LAMTOR1: 55004"
Figure legend: "I Both LAMTOR1 KD and TAT-2031  treatment (10 µM) increased ML-SA1-induced TRPML1-GCaMP6m responses in neurons. J Quantification of peak responses as shown in I. N = 6-13 cells from 3 independent experiments. Data information: Data with error bars are represented as means ± SEM. Statistical significance was assessed by two-way ANOVA with Tukey's post hoc analysis *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001, ###P &lt; 0.001, n.s., not significant. traces represent the mean values of each group."
NCBI gene IDs:
"LAMTOR1: 66508"
Figure legend: "K LAMTOR1 KD increased PI(3,5)P2 (0.5 µM)-induced  TRPML1-GCaMP6m responses and the blocking effect of ML-SI1  treatment (20 µM). L Quantification of peak  TRPML1-GCaMP6m responses as shown in K. N = 6-16 cells from 3 independent experiments. Data information: Data with error bars are represented as means ± SEM. Statistical significance was assessed by two-way ANOVA with Tukey's post hoc analysis *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001, ###P &lt; 0.001, n.s., not significant. traces represent the mean values of each group."
NCBI gene IDs:
"LAMTOR1: 66508"
Figure legend: "A-D Effects of  LAMTOR1 KD and ML-SI1 treatment on TBS-induced LTP (A) or  LFS-induced  LTD (C) in CA1. B, D Means ± SEM of fEPSPs measured 40 min after TBS (B, n = 4-5 slices from 4-5 mice) or LFS (D, n = 4-8 slices from 4-8 mice) in different groups. Data information: Slopes of fEPSPs  were normalized to the average values recorded during the first 10 min baseline Statistical significance was assessed by two-way ANOVA with Tukey's post-test *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001 compared with shSc P &lt; 0.05, ##P &lt; 0.01, ###P &lt; 0.001 compared with shLAMTOR1. Insets show representative traces of evoked fEPSPs before and 40 min after TBS/LFS. Scale bar 0.5 mV/10 ms."
NCBI gene IDs:
"LAMTOR1: 66508"
Figure legend: "K Effects of LAMTOR1 KD and treatment with a calcineurin  inhibitor, FK506, on LFS-induced  LTD in  CA1. L Means ± SEM of fEPSPs measured 45 min after LFS in different groups (n = 3-4 slices from 3-4 mice). Data information: Slopes of fEPSPs were normalized to the average values recorded during the first 10 min baseline Statistical significance was assessed by two-way ANOVA with Tukey's post-test *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001 compared with shSc, Vehicle, or TAT, #P &lt; 0.05, ##P &lt; 0.01, ###P &lt; 0.001 compared with shLAMTOR1. Insets show representative traces of evoked fEPSPs before and 40 min after  LFS. Scale bar 0.5 mV/10 ms."
NCBI gene IDs:
"LAMTOR1: 66508"
Figure legend: "LAMTOR1  KD significantly reduced levels of GluA1 phosphorylation and total GluA1 as well as the ratio of p-GluA1 to GluA1 in hippocampal neurons, and this effect was reversed by ML-SI1 treatment. A Representative images of CA1 pyramidal neurons stained with anti-p-GluA1  S845 (magenta), anti-GluA1 (red), and anti-GFP (green) antibodies. Scale bar = 20 µm."
NCBI gene IDs:
"LAMTOR1: 66508"
Figure legend: "A  Mice received 10 min of training in an environment with two identical objects and received a retention test 24 h later in which one object was replaced with a novel one. LAMTOR1 shRNA-injected mice  exhibited a significant deficit 24 h after training, which was reversed by ML-SI1 treatment (N = 7-18 mice). B % freezing for different experimental groups in context memory (N = 7-19 mice). Data information: Data with error bars are represented as means ± SEM. Statistical significance was assessed by two-way ANOVA with Tukey's post-test. *P &lt; 0.05, ***P &lt; 0.001, as compared to shSc; #P &lt; 0.05, ###P &lt; 0.001, as compared to shLAMTOR1."
NCBI gene IDs:
"LAMTOR1: 66508"
Figure legend: "Paneth cell quantification on Lgr5-DTReGFP duodenum (Duo) and Ileum (Ile). Left panel: Representative images of Lendrum's staining that evidence Paneth cell granules. Arrows show differentiated Paneth cells. Right panel: quantification of the Paneth cells per 10 intervilli regions. Each symbol indicates the value for a given embryo."
NCBI gene IDs:
"eGFP: 
DTR: 1839
Lgr5: 14160"
Figure legend: "Expression analysis by qRT-PCR of the indicated Paneth cell markers in Lgr5-DTReGFP ileums (n= 8 WT, 12 HE, 10 KO)."
NCBI gene IDs:
"eGFP: 
DTR: 1839
Lgr5: 14160"
Figure legend: "X-gal staining in Axin2Lac/+-Lgr5-GFP-CreERT2 WT or KO ileums."
NCBI gene IDs:
"GFP: 
Lac: 
Axin2: 12006
Cre: 2777477
ERT2: 2099
Lgr5: 14160"
Figure legend: "Gene expression analysis by qRT-PCR of stem cell markers in Lgr5-DTReGFP ileums (n= 3 WT, 6 HE, 6 KO)."
NCBI gene IDs:
"eGFP: 
DTR: 1839
Lgr5: 14160"
Figure legend: "FACS quantification of the number of eGFP+ve (ISC) cells per small intestine at the indicated developmental stages in Lgr5 HEs and Lgr5 KOs. Each symbol indicates the value for a given embryo. Mean value for each group is depicted on the graph."
NCBI gene IDs:
"Lgr5: 14160"
Figure legend: "Influence of mouse Rspondin 1 concentration on growth of replated Lgr5-DTReGFP WT and Lgr5 KO organoids after 5 days of culture."
NCBI gene IDs:
"eGFP: 
DTR: 1839
Lgr5: 14160"
Figure legend: "Paneth cell quantification on Lgr5-DTReGFP ileums. Each symbol indicates the value for a given embryo."
NCBI gene IDs:
"eGFP: 
DTR: 1839
Lgr5: 14160"
Figure legend: "Immunofluorescence showing Olfm4+ve cells in Lgr5-DTReGFP duodenums. Cell membranes are shown with b-catenin and nuclei were counterstained with DAPI. Quantification of Olfm4+ve cells per intervilli regions in duodenum and ileum. Each symbol indicates the value for a given embryo."
NCBI gene IDs:
"eGFP: 
DTR: 1839
Lgr5: 14160"
Figure legend: "Axin2 expression levels detected by RNAscope on Lgr5-DTReGFP proximal intestine."
NCBI gene IDs:
"eGFP: 
Axin2: 12006
DTR: 1839
Lgr5: 14160"
Figure legend: "Gene expression analysis by qRT-PCR of stem cell and differentiation markers in Lgr5-DTReGFP ileums (vehicle-treated: 7 WT and 7 KO; LGK974-treated: 3 WT and 7 KO)."
NCBI gene IDs:
"eGFP: 
DTR: 1839
Lgr5: 14160"
Figure legend: "Representative pictures of lineage tracing in Lgr5-expressing or Lgr5 cKO intestine after 10 days of chase and quantification of the number of traced clones per recombined surface at PN18 (ileum). Each symbol indicates the value for a given mouse."
NCBI gene IDs:
"Lgr5: 14160"
Figure legend: "Representative immunofluorescence pictures showing Paneth cells (Plyz+ve) in traced clones (RFP+ve) from control (Lgr5Cre/+) and cKO (Lgr5Cre/flox) PN18 and adult ileums. Arrow heads point to Plyz+ve cells in traced clones. Quantification of the number of Paneth cell number per recombined RFP+ve crypt on control and cKO ileums in PN18. Each symbol indicates the value for a given mouse."
NCBI gene IDs:
"Cre: 2777477
Lgr5: 14160"
Figure legend: "ISC (eGFP+ve) cells were FACS-sorted from Lgr5-DTReGFP embryos at E16.5 and subjected to RNAseq analysis. Heatmap of differentially regulated genes in HE and KO ISCs at E16.5. Biological replicates for RNAseq experiments on ISC Lgr5-DTReGFP E16.5 independent embryonic pools, each obtained from independent litters (n= 2 HE, 2 KO)"
NCBI gene IDs:
"eGFP: 
DTR: 1839
Lgr5: 14160"
Figure legend: "Compared Hallmarks for upregulated and downregulated genes in the transcriptome of E16.5 Lgr5 KOs vs E16.5 HEs, adult HEs vs E18.5 HE embryos and adult Lgr5-Cre cKO vs HEs. * Asterisks refer to given pathways for which differentially modulated genes were found upregulated and downregulated. Right panels: GSEA showing enrichment of the epithelial to mesenchymal transition (EMT) data set in E16.5 Lgr5 KOs vs E16.5 HEs, adult HEs vs E18.5 HE embryos, and adult Lgr5 cKO vs adult HE modulated genes. NES: Normalized Enrichment Score. Biological replicates for RNAseq experiments on ISC Lgr5-DTReGFP E16.5 independent embryonic pools, each obtained from independent litters (n= 2 HE, 2 KO); Lgr5-DTReGFP E18.5 individual embryos (n=2 HE) and Lgr5-DTReGFP adult individual animals (n=2 HE); Lgr5-Cre/flox adult individual animals (n= 2 HE, 3 cKO)."
NCBI gene IDs:
"eGFP: 
Cre: 2777477
DTR: 1839
Lgr5: 14160"
Figure legend: "Expression levels of genes commonly downregulated in ISCs of Lgr5 KOs vs Lgr5 HEs at E16.5 and Lgr5 adult vs E18.5 HEs. RPKM: reads per kilobase of transcript per million mapped reads. Below: GeneOntology analysis of downregulated genes identified in the Epithelial Mesenchymal Transition Gene Set (Hallmark MSigDB collection). Biological replicates for RNAseq experiments on ISC Lgr5-DTReGFP E16.5 independent embryonic pools, each obtained from independent litters (n= 2 HE, 2 KO); Lgr5-DTReGFP E18.5 individual embryos (n=2 HE) and Lgr5-DTReGFP adult individual animals (n=2 HE); Lgr5-Cre/flox adult individual animals (n= 2 HE, 3 cKO). Data are represented as means ± sem (C)."
NCBI gene IDs:
"eGFP: 
Cre: 2777477
DTR: 1839
Lgr5: 14160"
Figure legend: "Expression profile of Col1a1, Zeb2 and Cxcl10 genes detected by RNAscope in embryonic and adult intestines. Insets with higher magnification are depicted on the right of each corresponding picture, boundaries between epithelium and mesenchyme are shown with dotted lines and arrows point to epithelial expression."
NCBI gene IDs:
"Col1a1: 12842
Cxcl10: 15945
Zeb2: 24136"
Figure legend: "Expression of Axin2, Lgr5, Lgr4, Rspo1, Rspo2, Rspo3 and Rspo4 genes was analyzed on E15, E16.5 and adult stages by RNAscope. Arrows evidence expressing cells."
NCBI gene IDs:
"Axin2: 12006
Lgr4: 107515
Lgr5: 14160
Rspo1: 192199
Rspo2: 239405
Rspo3: 72780
Rspo4: 228770"
Figure legend: "Representative pictures showing the influence of mouse Rspondin type and concentration on growth of replated Lgr5-DTReGFP WT and Lgr5 KO organoids after 4 days of culture. Arrows show alive elements and arrow heads dead elements."
NCBI gene IDs:
"eGFP: 
DTR: 1839
Lgr5: 14160"
Figure legend: "Heatmap showing the impact of Rspondin type and concentration (ng/ml) on relative Wnt target gene expression (list from the Sansom APC data set) in Lgr5-DTReGFP WT and KO organoids analyzed by RNAseq (n= 3 WT and 2 organoid culture samples, each originating from a given embryo)."
NCBI gene IDs:
"eGFP: 
DTR: 1839
Lgr5: 14160"
Figure legend: "Gene expression analysis by qRT-PCR of stem cell markers in Lgr5-DTREeGFP WT and KO organoids after 5 days of culture (expression relative to reference genes). Each symbol indicates the value for an organoid culture originated from a given embryo."
NCBI gene IDs:
"EeGFP: 
DTR: 1839
Lgr5: 14160"
Figure legend: "Immunofluorescence showing Olfm4+ve cells in Lgr5-DTReGFP WT and KO organoids cultured in Rspo2 conditions. Epithelium is delineated with b-catenin and nuclei counterstained with DAPI (Merge). Insets: white arrowheads evidence Olfm4+ve cells concentrated in organoid protrusions. Quantification of Olfm4+ve area with respect to the total epithelial area. Each symbol indicates the value for an organoid culture originating from a given embryo."
NCBI gene IDs:
"eGFP: 
DTR: 1839
Lgr5: 14160"
Figure legend: "A-D J-Lat 8.4 cells were mock-treated or treated with increasing concentrations of 5-AzadC or 5-AzaC. At 72 h post-treatment; and initiated (primers TAR) or elongated (primers tat) transcripts were quantified by RT-qPCR (D)."
NCBI gene IDs:
"tat: 155871"
Figure legend: "E J-Lat 8.4 cells were mock-treated or treated with 5-AzadC (400nM) or TNFα (10ng/ml) as positive control. At 24 h, 48 h or 72 h post-treatment, initiated (primers TAR) or elongated (primers tat) transcripts were quantified by RT-qPCR."
NCBI gene IDs:
"tat: 155871"
Figure legend: "A-F J-Lat 8.4 (A, C, E) and 15.4 (B, D, F) cell lines were mock-treated or treated with 5-AzadC. At 48 h post-treatment, HDACIs were then added for 24 h. At 72 h 5-AzadC post-treatment samples were harvested and analysed as follows: initiated (primers TAR) or elongated (primers tat) transcripts were quantified by RT-qPCR and results were normalized using the β-actin gene primers and are presented as histograms representing fold-inductions compared to the mock-treated condition (E and F). Means and standard errors of the means from three independent biological duplicates (n=6) are indicated. The result obtained with mock-treated cells was arbitrarily set at a value of 1 (E, F)."
NCBI gene IDs:
"β-actin: 
tat: 155871"
Figure legend: "A. Representative confocal micrographs of HeLa cells transfected with a non-targeting siRNA pool (siNT - 40 nM) or a BNIP3L siRNA SMARTpool (siBNIP3L - 40 nM), infected or not (NI) with B. abortus 544 GFP (Red) for 48 h, then fixed and immunostained for BNIP3L (Alexa Fluor 568 - Magenta) and TOMM20 (Alexa Fluor 633 - Green). DNA was stained with Hoechst 33258 (Blue). B.,C. Quantification of the mitochondrial population morphology by assessing the AR (B) and EBR (C) of the mitochondria of HeLa cells from micrographs shown in (A). Data are presented as means ± SD from n=3 (biological replicates) independent experiments (the numbers indicated in the columns represent the number of cells analysed per condition). Statistical analyses were performed using a multiple Mann-Whitney test followed by a Holm-Šidàk's multiple comparisons test; asterisks indicate significant differences compared to the control (NI); *: p &lt;0.05; **: p &lt;0.01; hashtags indicate significant differences compared to the infected condition transfected with a siNT; #: p &lt;0.05."
NCBI gene IDs:
"BNIP3L: 665"
Figure legend: "D. Representative confocal micrographs of HeLa cells transfected with a FIS1-GFP(Green)-mCherry(Magenta) expression construct, infected or not (NI) with B. abortus 544 for 48 h while being transfected with a non-targeting siRNA pool (siNT - 40 nM) or a BNIP3L siRNA SMARTpool (siBNIP3L - 40 nM), then fixed and immunostained for B. abortus LPS (Alexa Fluor 633 - Red). DNA was stained with Hoechst 33258 (Blue). Arrows indicate FIS1-mCherry-positive-GFP-negative punctae. Scale bars: 20 µm. E. Quantification of the number of FIS1-mCherry-positive-GFP-negative punctae per cell of HeLa cells from micrographs t shown in (D). Data are presented as means ± SD from n=3 (biological replicates) independent experiments (the numbers indicated in the columns represent the number of cells analysed per condition). Statistical analyses were performed using a two-way ANOVA followed by a Šidàk's multiple comparisons test; asterisks indicate significant differences compared to the control (NI); ns: not significant; **: p &lt;0.01; hashtags indicate significant differences compared to the infected condition transfected with a siNT; #: p &lt;0.05."
NCBI gene IDs:
"BNIP3L: 665"
Figure legend: "A. Representative confocal micrographs of HeLa cells infected with B. abortus 544 GFP (Green) and transfected with a non-targeting siRNA pool (siNT - 40 nM) or a BNIP3L siRNA SMARTpool (siBNIP3L - 40 nM) for 48 h, then incubated under reinfection-permissive conditions for 24 h before analysis at 72 h pi. Cells were fixed and DNA was stained with Hoechst 33258 (Blue). Arrows indicate reinfected cells. B. Quantification of the percentages of reinfection foci per infected cell at 72 h pi of HeLa cells from micrographs shown in (A). Data are presented as means ± SD from n=3 (biological replicates) independent experiments (the numbers indicated in the columns represent the number of cells analysed per condition). Statistical analyses were performed using an unpaired two-tailed Student's t-test; **: p &lt;0.01 (p = 0.0032). C. CFU assay expressing Log (CFU/ml) from the supernatant of HeLa cells infected with B. abortus 544 GFP (Green) and transfected with a non-targeting siRNA pool (siNT - 40 nM) or a BNIP3L siRNA SMARTpool (siBNIP3L - 40 nM) for 48 h, then incubated under reinfection-permissive conditions for 24 h before collecting the supernatant at 72 h pi for analysis. Data are presented as means ± SD from n=5 (biological replicates) independent experiments; Statistical analyses were performed using an unpaired two-tailed Student's t-test; (p = 0.0042)."
NCBI gene IDs:
"BNIP3L: 665"
Figure legend: "D. Representative confocal micrographs of HeLa cells infected with B. abortus 544 GFP (Red) and transfected with a non-targeting siRNA pool (siNT - 40 nM) or a BNIP3L siRNA SMARTpool (siBNIP3L - 40 nM) for 72 h pi, then fixed and immunostained for LAMP-1 (Alexa Fluor 568 - Green). DNA was stained with Hoechst 33258 (Blue). Arrows indicate LAMP-1-positive BCVs (aBCVs). Scale bars: 20 µm. E. Quantification of the number of LAMP-1-positive BCVs (aBCVs) per infected HeLa cells from micrographs shown in (E). Data are presented as means ± SD from n=3 (biological replicates) independent experiments (the numbers indicated in the columns represent the number of cells analysed per condition). Statistical analyses were performed using an unpaired two-tailed Student's t-test; *: p &lt;0.05 (p = 0.0117)."
NCBI gene IDs:
"BNIP3L: 665"
Figure legend: "(A) A boxplot showing log2 TPM values of HSPA5 gene expression compared between tumors and matched normal samples across 23 tumor types from TCGA with normal tissue data available. The boxplot indicates the median (central band) and the interquartile range (boxes) of the expression value and whiskers indicates values that outside of the middle 50% (interquartile). The barplot on the top shows the number of normal tissue samples for each corresponding tumor type. Asterisks indicate significant differences by student's t-test after Benjamini-Hochberg multiple testing correction (FDR &lt; 0.05)."
NCBI gene IDs:
"HSPA5: 3309"
Figure legend: "(B) Analysis and quantification of Xbp1 splicing in DLD1 and SKOV3 cells treated with varying concentrations of Reversine (Rv) for 12, 24, 48, and 72 hours. Thapsigargin  (Tg) is shown as positive control."
NCBI gene IDs:
"Xbp1: 7494"
Figure legend: "(D)  Xbp1 splicing in B16 melanoma cells and eight B16:MEF fused clonal cell lines."
NCBI gene IDs:
"Xbp1: 22433"
Figure legend: "(E) Detection of mRNA  expression (by  RT-PCR) of UPR-associated genes (Ern1, Af4, Ddit3 and Atf6) in tumor cells treated with Reversine  (Rv) at 4µM (DLD1  cells) or 0.5µM (SKOV3  cells) for 6 hours. Data points refer to triplicate samples collected at the same time point, run in duplicate, and expressed as means ± SD."
NCBI gene IDs:
"Af4: 468
Atf6: 22926
Ddit3: 1649
Ern1: 2081"
Figure legend: "(A)  Xbp1 splicing analysis (left panel) and quantification (right panel) of bone marrow-derived macrophages (BMDM) cultured in conditioned medium (CM) of Rv-treated  DLD1 and SKOV3  cells or respective control medium (culture medium of cancer cells not treated with Rv), and CM of fused B16 melanoma  cells or their nonfused parental cells."
NCBI gene IDs:
"Xbp1: 7494"
Figure legend: "(B, C) mRNA expression (RT-PCR) of Il6 (B) and Arg1 (C) in BMDM  cultured in the CM of  Rv-treated  SKOV3  cells (0.5µM for 3 days) or control cells, and CM of fused B16 cells or their nonfused parental cells. Data points refer to triplicate experiments expressed as means ± SD."
NCBI gene IDs:
"Arg1: 383
Il6: 3569"
Figure legend: "(a) Mouse fibroblasts knockeddown for LAMP-2A and transfected with KFERQ-PS-CFP2 were photoconverted and maintained in media supplemented (+) or not (−) with serum for 16 h. Representative images of cells also immunostained for LAMP-1 are shown."
NCBI gene IDs:
"LAMP-2A: 16784"
Figure legend: "(A) Lung cancer cells PC-9, prostate cancer cells 22RV1, bladder cancer cells UMUC3, breast cancer cells MCF-7, colonic adenoma-derived non-cancerous cells AA/C1 (aka C1) and AA/C1/SB (aka SB), or cancerous cells AA/C1/SB/10C (aka 10C) were incubated with wild-type F. nucleatum 12230 (Fn), the fadA-deletion mutant US1 (US1), or E. coli DH5α (E. coli) at multiplicity of infection (MOI) of 1,000:1. Cells numbers are mean values ± SEM. The experiment was performed in triplicates and repeated three times. **p&lt;0.01, ***p&lt;0.001, compared to untreated controls; #p&lt;0.05, ### p&lt;0.001, compared to US1-treated cells (two-way ANOVA)."
NCBI gene IDs:
"fadA: 31730396"
Figure legend: "(B) Attachment (left panel) and invasion (right panel) of wild-type F. nucleatum 12230 (Fn) to the non-cancerous SB cells, either untreated or transfected with antisense or sense ANXA1, and to the cancerous 10C cells, either untreated or transfected with control or ANXA1- or CDH1-specific siRNA or both (MOI 50:1). F. nucleatum attachment and invasion to the untreated SB cells were designated as 100%, respectively; all other values were expressed as relative to those obtained with untreated SB. Data are mean values ± SEM. The experiment was performed in triplicates and repeated four times. *p&lt;0.05, **p&lt;0.01 and ***p&lt;0.001 (one-way ANOVA)."
NCBI gene IDs:
"ANXA1: 
ANXA1: 301
CDH1: 999"
Figure legend: "(C) Left panel: qPCR analysis of Villin1 (VIL1) mRNA levels in 10C cells treated with control siRNA or VIL1-specific siRNA, demonstrating knocking down of Villin1. Right panel: attachment of F. nucleatum 12230 to 10C cells treated with control siRNA or VIL1-specific siRNA. Data are mean values ± SD. The experiment was performed in triplicates and repeated twice. *p&lt;0.05 (student's t-test)."
NCBI gene IDs:
"VIL1: 7429
Villin1: 7429"
Figure legend: "Relationship between ANXA1 mRNA expression levels and disease-free survival (DFS) in colon cancer patients. The relationship between ANXA1 mRNA expression levels and DFS was investigated in a database of 466 primary colon carcinomas, assembled by pooling four independent gene-expression array datasets from the NCBI-GEO online repository (GSE14333, GSE17538, GSE31595, GSE37892) The association between ANXA1 expression levels and DFS was tested using Kaplan-Meier survival curves, after patient stratification in groups with high, medium and low ANXA1 expression, using three different methods: (A) based on the median of ANXA1 mRNA expression levels (high 50% vs. low 50%); (B) based on the quartile distribution of ANXA1 mRNA expression levels (high 25% vs. middle 50% vs. low 25%); and (C) based on ANXA1 mRNA expression thresholds calculated using the StepMiner algorithm (low vs. high) Overall, high ANXA1 mRNA expression levels were associated with a statistically significant reduction in DFS (p&lt;0.001, log-rank test), irrespective of the method used for the stratification. Differences in ANXA1 mRNA expression levels did not appear to correlate with differences in each tumor's relative content of epithelial cells in the analyzed biospecimens (i.e. tumor cell density) as revealed by the lack of visual correlations with the epithelial cell marker Desmoplakin (DSP)."
NCBI gene IDs:
"ANXA1: 301"
Figure legend: "(A) Real-time qPCR analysis of ANXA1 expression using mRNA extracted from the non-cancerous SB, cancerous 10C, and human CRC cell lines HCT116, DLD1 and RKO, each grown to 50% or 100% confluency. All results were normalized to the ANXA1 mRNA levels in SB cells of 100% confluency, which was designated as 1. Data are mean values ± SEM. The experiment was performed in triplicates and repeated twice. **p&lt;0.01 and ***p&lt;0.001 (student's t-test)."
NCBI gene IDs:
"ANXA1: 301"