EMBO/SourceData huggingface dataset:
Figure legend: "b, Shift in phase durations of RPE cells overexpressing Myc. boxplots representing the distributions of phase durations in untreated cells are underlaid for comparison. *, P &lt; 1 × 10-5; **, P &lt; 1 × 10-10; ***, P &lt; 1 × 10-20, 2-sided Kolmogorov-Smirnov test. Number of cells: Myc, n = 116"
NCBI gene IDs:
"Myc: 4609"
Figure legend: "c, Pairwise correlation between cell cycle phase durations of RPE cells overexpressing Myc. Number of cells: Myc, n = 116"
NCBI gene IDs:
"Myc: 4609"
Figure legend: "j, Shifts in phase durations for RPE cells overexpressing cyclin D. A boxplot representing the distributions of durations in untreated cells is underlaid for comparison. *, P &lt; 1 × 10-5, 2-sided Kolmogorov-Smirnov test. (n = 113 cells)."
NCBI gene IDs:
"cyclin D: 595"
Figure legend: "k, Pairwise correlation between cell cycle phase durations upon overexpression of cyclin D. P indicates P-value."
NCBI gene IDs:
"cyclin D: 595"
Figure legend: "Representative images of LINC00115 expression in clinical GBM tumors and adjacent tissue using RNAscope analysis. Images are representative of two independent experiments. Scale bars: 50 μm."
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "Kaplan-Meier analysis of patients with high versus low LINC00115-expressing GBM tumors from B. Median survival (in months): low, 13.9; high, 8.1. Black bars, censored data. Data information: , *, p &lt; 0.05, by log-rank test."
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "Expression levels of LINC00115 are higher in LGG (low grade gliomas) versus normal brain tissues and GBM versus LGG. Expression data of LINC00115 were downloaded from the REMBRANDT dataset. Data are presented as mean ± SEM. **, p &lt; 0.01, ***, p &lt; 0.001, by two-tailed t test."
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "E to G. Kaplan-Meier analysis of patients with high versus low LINC00115-expressing Grade III and GBM tumors from the REMBRANDT (E) or the TCGA (G) 26[], and GBM from GSE83300 50[] (F) datasets. Median survival (in months) in E: low, 20.2; high, 15.9; in F: low, 19.4; high, 13.0; in G: low, 33.2; high, 25.4. Black bars, censored data. Data information: , *, p &lt; 0.05, by log-rank test."
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "qRT-PCR analysis of LINC00115 knockdown using two different shRNAs, shL115-1 and shL115-2 in 1123 and 528 GSCs. Data information: data are representative of three independent experiments. Error bars, ± SD. *, p &lt; 0.05, **, p &lt; 0.01, by One-way ANOVA"
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "Effects of LINC00115 knockdown on GSC proliferation (B) data are representative of three independent experiments. Error bars, ± SD. *, by two-tailed t-test in B."
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "C. Effects of LINC00115 knockdown on neuro-like sphere formation (C). Data information: data are representative of three independent experiments. Error bars, ± SD. *, p &lt; 0.05, **, p &lt; 0.01, by One-way ANOVA in"
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "H. Immunofluorescence (IF) analysis of Nestin expression in 1123 GSC control and LINC00115 knockdown xenograft tumors from F. Images are representative of two independent experiments. Scale bars: 50 μm."
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "B and C. MS2-RIP followed by qRT-PCR analysis of endogenous microRNAs association with LINC00115. 12XMS2 empty vector, LINC00115-12XMS2, or LINC00115-mut- 12XMS2 with Flag-tagged MS2 were co-transfected into 1123 GSCs. Data information data are representative of three independent experiments. Error bars, ± SD. , ***, p &lt; 0.001, by two-tailed t-test."
NCBI gene IDs:
"Flag: 
MS2: 
LINC00115: 79854"
Figure legend: "E. RNA pull-down and qRT-PCR assays of LINC00115 binding with miR-200s. GSC1123 cell lysates were incubated with biotin-labeled LINC00115. Data information data are representative of three independent experiments. Error bars, ± SD. p &lt; 0.05, **, p &lt; 0.01, by One-way ANOVA."
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "F. Luciferase activity analysis of 1123 GSCs co-transfected with miR-200s and luciferase reporters containing LINC00115 WT, mutant, or empty vector (EV). Data information: data are representative of three independent experiments. Error bars, ± SD. p &lt; 0.05, **, p &lt; 0.01, by One-way ANOVA."
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "A and B. Correlation of expression between LINC00115 and ZEB1 from TCGA GBM RNA-Seq dataset (A) and REMBRANDT GBM array dataset (B). ***, p &lt; 0.001, by two-tailed t-test."
NCBI gene IDs:
"LINC00115: 79854
ZEB1: 6935"
Figure legend: "C. LINC00115 knockdown reduced ZEB1 mRNA expression in 1123 and 528 GSCs. Data information: , data are representative of three independent experiments. Error bars, ± SD. **, p &lt; 0.01, by One-way ANOVA"
NCBI gene IDs:
"LINC00115: 79854
ZEB1: 6935"
Figure legend: "D. Effects of LINC00115 knockdown on ZEB1, vimentin, and E-cadherin protein expression. Data information: data are representative of three independent experiments. Error bars, ± SD. **,"
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "E. Effects of re-expression of shRNA-resistant LINC00115 WT (L115-WT), miR-200 binding mutant (L115-mut) with or without miR-200b on ZEB1 signaling activation. Data information data are representative of three independent experiments. Error bars, ± SD."
NCBI gene IDs:
"LINC00115: 79854
miR-200: 406984
miR-200b: 406984"
Figure legend: "F. Neuro-like sphere formation assay of effects of re-expression of shRNA-resistant LINC00115 WT and mutant with or without miR-200b. Data information: data are representative of three independent experiments. Error bars, ± SD. **, p &lt; 0.01, by two-tailed t-test in F."
NCBI gene IDs:
"LINC00115: 79854
miR-200b: 406984"
Figure legend: "H and I. GSEA of EMT signature genes using ranked gene expression changes in TGF-β1-treated 1123/shLINC00115 GSCs versus the control (H) or in 1123 GSCs with ectopic expression of LINC00115 or an empty vector (EV) (I). NES, normalized enrichment score."
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "LINC00115 knockdown reduced ZNF596 mRNA expression. Data information: In data are representative of three independent experiments. Error bars, ± SD. *, p &lt; 0.05, by One-way ANOVA"
NCBI gene IDs:
"LINC00115: 79854
ZNF596: 169270"
Figure legend: "LINC00115 knockdown reduced ZNF596 protein (D) expression. Data information: data are representative of three independent experiments. Error bars, ± SD."
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "E. Effects of exogenous ZNF596 expression on LINC00115 knockdown-inhibited ZNF596 protein expression. Data information: data are representative of three independent experiments. Error bars, ± SD."
NCBI gene IDs:
"LINC00115: 79854
ZNF596: 169270"
Figure legend: "F. ZNF596 overexpression had no effect on LINC00115 expression. Data information data are representative of three independent experiments. Error bars, ± SD. *, p &lt; 0.05, by One-way ANOVA"
NCBI gene IDs:
"LINC00115: 79854
ZNF596: 169270"
Figure legend: "G. Expression of exogenous ZNF596 rescued LINC00115 knockdown-inhibited cell proliferation. Data information: data are representative of three independent experiments. Error bars, ± SD. *, p &lt; 0.05 , by two-tailed t-test in G."
NCBI gene IDs:
"LINC00115: 79854
ZNF596: 169270"
Figure legend: "H. Representative H&amp;E staining images of mouse brain sections with 1123/shC and 1123/shL115 GSC tumor xenografts with empty vector (EV) or ectopic ZNF596 expression. Images represent results of five mice per group of two independent experiments. Scale bars: 1 mm. I. Quantification of tumor size in H. "
NCBI gene IDs:
"ZNF596: 169270"
Figure legend: "J and K. Correlation of expression between LINC00115 and ZEB1 from TCGA GBM RNA-Seq dataset (J) and REMBRANDT GBM array dataset (K). **, p &lt; 0.01, by two-tailed t-test."
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "Expression of shRNA-resistant LINC00115 WT but not mutant or empty vector (EV) rescued LINC00115 shRNA-inhibited ZNF596 mRNA (A) expression in 1123 GSCs."
NCBI gene IDs:
"LINC00115: 79854
ZNF596: 169270"
Figure legend: "Expression of shRNA-resistant LINC00115 WT but not mutant or empty vector (EV) rescued LINC00115 shRNA-inhibited ZNF596 protein (B) expression in 1123 GSCs."
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "D. MS2-RIP followed by qRT-PCR for endogenous microRNAs association with ZNF596. 12XMS2 empty vector, ZNF596-5'-UTR-WT-12XMS2, or ZNF596-5'-UTR-mut -12XMS2 with Flag-tagged MS2 were co-transfected into 1123 GSCs."
NCBI gene IDs:
"Flag: 
MS2: 
ZNF596: 169270"
Figure legend: "F. Luciferase activity in 1123 GSCs co-transfected with miR-200s and luciferase reporters containing ZNF596 5'-UTR WT, mutant, or empty vector (EV)."
NCBI gene IDs:
"ZNF596: 169270"
Figure legend: "GSEA of EZH2-targeted signature genes using ranked gene expression changes in 1123 GSCs with ZNF596 sgRNA or a control sgRNA. NES, normalized enrichment score."
NCBI gene IDs:
"EZH2: 2146
ZNF596: 169270"
Figure legend: "qRT-PCR analysis of effect of ZNF596 knockout on EZH2 expression. Data information: data are representative of three independent experiments. Error bars, ± SD. *, p &lt; 0.05, **, p &lt; 0.01, ***, p &lt; 0.001, by One-way ANOVA"
NCBI gene IDs:
"EZH2: 2146
ZNF596: 169270"
Figure legend: "ZNF596 knockout impaired EZH2 expression, its downstream H3K27me3, and STAT3 phosphorylation in 1123 and 528 GSCs. Data information , data are representative of three independent experiments. Error bars, ± SD."
NCBI gene IDs:
"ZNF596: 169270"
Figure legend: "LINC00115 regulated ZNF596/EZH2/STAT3 signaling. 1123 and 528 GSCs were treated with or without EZH2 inhibitor GSK343 (3 μM) for 6 Data information: data are representative of three independent experiments. Error bars, ± SD."
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "LINC00115 and ZNF596 regulate EZH2 promoter activity. Data information: data are representative of three independent experiments. Error bars, ± SD. , by two-tailed t-test"
NCBI gene IDs:
"LINC00115: 79854
ZNF596: 169270"
Figure legend: "ChIP-qPCR analysis of ZNF596 binding with the EZH2 promoter. Data information: data are representative of three independent experiments. Error bars, ± SD. *, p &lt; 0.05, **, p &lt; 0.01, ***, p &lt; 0.001, by One-way ANOVA"
NCBI gene IDs:
"EZH2: 2146
ZNF596: 169270"
Figure legend: "EZH2 inhibitor GSK343 impaired ZNF596 overexpression-reversed and LINC00115 knockdown-inhibited neuro-like sphere formation. 1123 and 528 GSCs with an inducible ZNF596 shRNA were treated with or without Dox (2 μg/ml) and/or EZH2 inhibitor GSK343 (1 μM) for 7 days. Data information: data are representative of three independent experiments. Error bars, ± SD. by two-tailed t-test"
NCBI gene IDs:
"LINC00115: 79854
ZNF596: 169270"
Figure legend: "Representative images of RNAscope for LINC00115 and IHC for ZEB1 and ZNF596 expression in two GBM specimens, Sample #1 (positive) and Sample #2 (negative). Scale bar, 50 μm. Images are representative of two independent experiments."
NCBI gene IDs:
"LINC00115: 79854"
Figure legend: "Correlation of detected expression between ZEB1 or ZNF596, and LINC00115 from a separate cohort of a total of 75 paraffin-embedded clinical GBM samples. Statistical analysis was performed by Chi-square test."
NCBI gene IDs:
"ZEB1: 
LINC00115: 79854
ZNF596: 169270"
Figure legend: "Kaplan-Meier survival analysis of patients with GBM tumors expressing high or low levels of LINC00115 with high or low levels of ZEB1 or ZNF596 expression. Median survival (in months): LINC00115hi/ZEB1hi, 5.4; LINC00115lo/ZEB1lo, 27.9; LINC00115hi/ZNF596hi, 4.2; LINC00115lo/ZNF596lo, 23.8. Statistical analysis was performed by log-rank test."
NCBI gene IDs:
"LINC00115: 79854
ZEB1: 6935
ZNF596: 169270"
Figure legend: "(C) Heatmaps showing changes in expression of key myogenic (MYOD, MYOGENIN), perivascular (PDGFRB, NG2, CD146, ALPL) and NOTCH target (HEY1, HES1) genes upon treatment with DLL4 &amp; PDGF-BB in mMuSC-derived myoblasts (left), human myoblasts (middle) and hiMPs (right). Clustering was performed by genes/probes with Pearson correlation. Colour scale based on z-scores: red regions indicate high expression whilst blue regions indicate low expression. Dendrograms indicate the similarity of clusters as well as the orders in which clusters were assembled."
NCBI gene IDs:
"ALPL: 11647
NG2: 121021
HES1: 15205
HEY1: 15213
CD146: 84004
MYOD: 17927
MYOGENIN: 17928
PDGFRB: 18596"
Figure legend: "B, CSF-1 mRNA expression was measured in MC38 and KPC cells exposed to 10Gy IR compared with mock irradiated cells. Cells were harvested at 24, 48 and 72 hours after irradiation and RNA expression was analysed by RT-qPCR. Data are presented as mean ± SEM and analysed by Kruskal-Wallis test with Dunn's multiple comparison (n=3)."
NCBI gene IDs:
"CSF-1: 12977"
Figure legend: "HEp-2 cells remained untreated or were incubated with 20 µg/ml of whole cell extract of Y. pseudotuberculosis expressing full-length CNF1, CNFY or the N- or C-terminally deleted toxin variants at 37°C for 4 h. The cells were thoroughly washed, pelleted, lysed and the toxin variants bound to the cells were identified by western blotting using an anti-Flag antibody."
NCBI gene IDs:
"CNFY: "
Figure legend: "Left upper and right panel: HEp-2 cells re­mained untreated or were incubated with 20 µg/ml of whole cell extract of Y. pseudotuberculosis expressing full-length CNFY or the N- or C-terminally deleted toxin variants for 4 h. Cells were lysed and the de­amidation of RhoA was analyzed by the shift of the modified Rho GTPase band in SDS PAGE gels; left lower panel: HEp-2 cells were lysed and the cell extracts were incubated with full-length CNFY or the N-ter­minally deleted toxin variants for 4 h. The de­amidation of RhoA in the cell extracts was analyzed by the mobility shift of the modified Rho GTPase on SDS PAGE after detection with anti-RhoA antibodies."
NCBI gene IDs:
"CNFY: "
Figure legend: "HEp-2 cells were incubated with 20 µg/ml of whole cell extract of Y. pseudotuberculosis expressing full-length CNFY or the N- or C-terminally deleted toxin variants for 24 h. The cell nuclei were strained with DAPI (blue) and the actin cytoskeleton was stained using FITC-phalloidin (green). The formation of large, multinuclear cells was ob­served by fluorescence micro­­scopy and the formation of thick actin stress fibers and membrane actin folding were only observed with CNFY-treated cells. The white scale bar is 40 µm. Cells incubated with extracts of YP147 (ΔcnfY) harboring the empty expression vector were used as negative controls."
NCBI gene IDs:
"cnfY: 
CNFY: "
Figure legend: "HEp-2 cells were incubated with 20 µg/ml of whole cell extract of Y. pseudotuberculosis expressing full-length CNFY, N- or C-terminal deletion variants fused to GFP (green) for 90 or 180 min. Cells were fixed and processed for fluorescence microscopy. The red fluorescent signal represents late endosomes (CellLight Late Endosomes-RFP (Rab7a)). Nuclei were stained with DAPI (blue). A merged image of the different channels is shown, and smaller images are magnified views of boxed areas. White scale bar is 10 µm."
NCBI gene IDs:
"CNFY: "
Figure legend: "Nitrocefin (2 mM) was added to the supernatant from 25°C overnight Yersinia cultures expressing the indicated CNFY derivatives to determine β-lactamase activity by measuring changes in absorbance at 390 nm (yellow) and 486 nm (red). The data represent the mean ± SD of three independent experiments, carried out in triplicates."
NCBI gene IDs:
"CNFY: "
Figure legend: "The viability of Y. pseudotuberculosis YPIII expressing the indicated CNFY derivatives was assessed in equalized bacterial cultures using the BacTiter-Glo Microbial Cell Viability Assay kit (Promega). The data represent the mean ± SD of three independent experiments, carried out in triplicates."
NCBI gene IDs:
"CNFY: "
Figure legend: "Comparative analysis of RhoA activation in HEp-2 cell lysate by CNFY and the recombinant D4-5 protein. Purified CNFY or the D4-5 fragment (1 µM) was added to extracts of HEp-2 cells and incubated for 10, 20, 30 or 60 min. De­amidation of RhoA was analyzed by the shift of the modified Rho GTPase band in SDS PAGE gels after detection with anti-RhoA antibodies."
NCBI gene IDs:
"CNFY: "
Figure legend: "(J) IgM-BCR immunoprecipitation to investigate recruitment of endophilin A2 to activated BCRs. Anti-endophilin A2 blots detect overexpressed endophilin A2-GFP in streptavidin immunoprecipitates and total supernatants from anti-IgM-biotin-stimulated Ramos and DG75  cells. Representative experiment and quantification from 3 independent pulldowns in WT, BLNK- or GRB2-knockout (KO)  DG75 cells.  Pulldown  intensity is calculated as a percentage of total endophilin A2 protein and normalized to WT in each experiment. Data show mean and SEM; p values calculated using one-way ANOVA."
NCBI gene IDs:
"GFP: 
BLNK: 29760
GRB2: 2885
endophilin A2: 6455"
Figure legend: "(C) Surface levels of MHCII, BAFFR, CD40  and LPAM1 in Sh3gl1-/- and WT littermates. N = 4-5 mice. P, statistical significance from unpaired t tests. Data show mean ± SEM."
NCBI gene IDs:
"Sh3gl1: 20405"
Figure legend: "(A) Soluble anti-IgM internalization in CRISPR-targeted follicular B cells. N = 11- 12  mice. Data show mean ± SEM. P, statistical significance from two-way ANOVA. (B) Soluble anti-IgD internalization. N = 3  mice. Data show mean ± SEM. P, statistical significance from two-way ANOVA. (C) Soluble anti-IgG internalization in GC B cells from  SRBC-immunized mice. N = 4 mice. Data show mean ± SEM. P, statistical significance from two-way ANOVA. "
NCBI gene IDs:
"CRISPR: "
Figure legend: "(C-D) Isolated naïve B cells from CRISPR-targeted chimeras after 3-day culture in stated cytokines. (C)  mCherry percentage in targeted primary cell cultures. N = 15  mice. *p&lt;0.05, **p&lt;0.01, ****p&lt;0.0001 using two-way ANOVA. (D) AnnexinV  surface stain in targeted cells. N = 3-4 mice. Data information: All data show means ± SEM."
NCBI gene IDs:
"CRISPR: "
Figure legend: "(G) Oxygen consumption rate (OCR) in CRISPR-targeted Ramos cells. N = 2 independent infections. P, two-way ANOVA of basal and maximum OCR. (H)  OCR in  B cells isolated from Sh3gl1-/- and WT littermates. N = 9 mice. P, two-way ANOVA of basal and maximum OCR. "
NCBI gene IDs:
"CRISPR: 
Sh3gl1: 20405"
Figure legend: "Cell cultures with full RPMI media supplemented with 50 μg/ml  FeSO4 or 5 μM hemin chloride. (J) SH3GL1-targeted Ramos cells. N = 4 independent infections. P, statistical significance from two-way ANOVA from both treatments versus RPMI. (K) Control sgRNA-targeted Ramos cells."
NCBI gene IDs:
"SH3GL1: 6455"
Figure legend: "(O) TfR internalization assay in Ramos cells using biotinylated  anti-CD71. 4 independent CRISPR infections in 2 experiments. P, significance calculated using two-way ANOVA and indicated in corresponding color."
NCBI gene IDs:
"CRISPR: "
Figure legend: "(P,Q) Mouse transferrin internalization in B cells  from SRBC-immunized WT and Sh3gl1-/- littermates. N = 7 mice per genotype in 2 experiments. P, statistical significance analyzed using two-way ANOVA. (P) Naïve B cells. (Q) GC B cells."
NCBI gene IDs:
"Sh3gl1: 20405"
Figure legend: "AGS cells were infected with H. pylori P1 wild‑type or isogenic ∆HP0857 (mutated in the gmhA gene) strains. Total cell lysates were analyzed by immunoblotting using the indicated antibodies."
NCBI gene IDs:
"gmhA: 56917658"
Figure legend: "Parental AGS, ALPK1‑KO and TIFA‑KO cells were infected with H. pylori for the times shown. Total cell lysates were analyzed by immunoblotting using the indicated antibodies. CagA demonstrated a similar infection rate of the different cells. Asterisk denotes an unspecific band and the arrow indicates the band corresponding to phosphorylated p100."
NCBI gene IDs:
"ALPK1: 80216
TIFA: 92610"
Figure legend: "Total RNA was isolated from ALPK1‑KO cells and analyzed using quantitative RT‑PCR for the ALPK1 transcript. Data shown depict the average of triplicate determinations normalized to the RPL13A housekeeping gene. Error bars denote RQ ± RQmin/RQmax."
NCBI gene IDs:
"ALPK1: 80216
RPL13A: 23521"
Figure legend: "TIFA-KO cells were transfected with His‑tagged recombinant TIFA protein 24 h prior to H. pylori infection. Co‑IP with an anti‑His antibody was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies. Asterisk denotes an unspecific band and the arrow indicates the TRAF2 band."
NCBI gene IDs:
"TIFA: 92610"
Figure legend: "AGS and ALPK1-KO cells were infected with H. pylori for the times shown. Co‑IP with an anti‑TRAF6 antibody or isotype‑matched antibody (IgG) was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies."
NCBI gene IDs:
"ALPK1: 80216"
Figure legend: "AGS and TIFA-KO cells were infected with H. pylori for the times shown. Co‑IP with an anti‑TRAF6 antibody or isotype‑matched antibody (IgG) was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies."
NCBI gene IDs:
"TIFA: 92610"
Figure legend: "AGS and TIFA-KO cells were treated with 30 ng/ml IL-1β for the times shown. Co‑IP with an anti‑TRAF6 antibody or isotype‑matched antibody (IgG) was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies."
NCBI gene IDs:
"TIFA: 92610"
Figure legend: "TIFA-KO cells were transfected with His‑tagged recombinant TIFA protein 24 h prior to H. pylori infection or treatment with 30 ng/ml LTα1β2. Co‑IP with an anti‑His antibody was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies."
NCBI gene IDs:
"TIFA: 92610"
Figure legend: "AGS and ALPK1-KO cells were infected with H. pylori for the times shown. Co‑IP with an anti‑TIFA antibody or isotype‑matched antibody (IgG) was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies."
NCBI gene IDs:
"ALPK1: 80216"
Figure legend: "AGS and TIFA-KO cells were infected with H. pylori for the times shown. Co‑IP with an anti‑TRAF2 antibody or isotype‑matched antibody (IgG) was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies."
NCBI gene IDs:
"TIFA: 92610"
Figure legend: "AGS cells were transfected with siRNA against cIAP1. Co‑IP with an anti‑TIFA antibody or isotype‑matched antibody (IgG) was performed. Eluates and total cell lysates were analyzed by immunoblotting using the indicated antibodies."
NCBI gene IDs:
"cIAP1: 329"
Figure legend: "TIFA-KO cells were transfected with empty vector plasmid (pCMV6), wild‑type human (phTIFA), phosphorylation‑defective mutant (pT9A) or TRAF6 binding‑defective mutant (pE178A) FLAG‑tagged TIFA plasmids. Total cell lysates were analyzed by immunoblotting using the indicated antibodies."
NCBI gene IDs:
"TIFA: 92610
TRAF6: 7189"
Figure legend: "TIFA-KO cells were transfected with empty vector plasmid (pCMV6), wild‑type human (phTIFA), phosphorylation‑defective mutant (pT9A) or TRAF6 binding‑defective mutant (pE178A) FLAG‑tagged TIFA plasmids. Total cell lysates were separated by native gel electrophoresis under non-reducing conditions."
NCBI gene IDs:
"TIFA: 92610
TRAF6: 7189"
Figure legend: "In TIFA‑KO cells transiently expressing TIFA‑tdTomato, co-localization of TRAF6 (A), TRAF2 (B), cIAP1 (C) and TRAF3 (D) with TIFA-tdTomato, which formed TIFAsomes upon infection with H. pylori P1 wild‑type strain, were detected by immunofluorescence staining. The nuclei were counterstained with DAPI. Scale bar = 10 µm. TIFA‑KO cells transiently expressing TIFA‑tdTomato were infected with H. pylori P1 strain mutated in the gmhA gene (∆HP0857). Scale bar = 10 µm."
NCBI gene IDs:
"gmhA: 56917658
TIFA: 92610"
Figure legend: "Colonic organoids grown from Lgr5-EGFP-IRES-CreERT2 mice were treated with an AhR agonist (10 nM TCDD) or antagonist (10 µM CH223191) for 3 d. (A) Induced Cyp1a1 mRNA expression in response to different treatments (n=3 per group)."
NCBI gene IDs:
"EGFP: 
Cre: 2777477
Cyp1a1: 13076
ER: 2099
Lgr5: 14160"