EMBO/SourceData huggingface dataset:
Figure legend: "(J-O) Impaired granulation tissue formation and angiogenesis in αSMA-TK mice. (J) Representative H&amp;E images of wound tissue sections at day 17 post-wounding. Granulation areas are marked by black lines, triangles (open: incomplete closure, filled: closed wounds) denote the epithelial tongues. Epi, epidermis; derm, dermis regions denoted. Scale bar: 200 μm. (K) Granulation tissue thickness measured on digital images and normalized to the average values in the WT control (set to 100%). NA (not assessed) reflects the lack of granulation in αSMA-TK mice. WT, N=5; TK, N=4 biological replicates. (L) Immunofluorescent staining for CD31 (red) and nuclei (blue) on wound tissue sections at day 17 post-wounding. White boxes denote zoomed regions depicted in right panels. Scale bar, 100 μm. (M) Quantification of CD31+ cells per visual field normalized to WT mice. WT, N=3; TK, N=5 biological replicates. (N) IHC for hypoxyprobe (brown) on wound tissue sections at day 17 post-wounding. Black boxes denote zoomed regions depicted in right panels. Scale bar, 100 μm. (O) Quantification of hypoxyprobe area per visual field normalized to WT mice. WT, N=5; TK, N=6 biological replicates."
NCBI gene IDs:
"αSMA: 11475
TK: 24271467"
Figure legend: "(D) Representative FACS plots of digested skin from bone marrow (BM) transplanted αSMA-RFP mice 17 days post-wounding. (E) FACS quantification of αSMA-RFP+ cells in wounds of BM transplanted mice. αSMA-RFP with αSMA-RFP BM, N=2; WT with αSMA -RFP BM, N=3; αSMA-RFP with WT BM, N=4 biological replicates. One-way ANOVA with Tukey's multiple comparison test performed comparing WT with αSMA-RFP BM and αSMA-RFP with WT BM to αSMA-RFP with αSMA-RFP BM. ("
NCBI gene IDs:
"RFP: 
αSMA: 11475"
Figure legend: "(L) Representative H&amp;E images of wound tissue sections at day 17 post-wounding. Granulation areas are marked by black lines. Scale bar, 200 μm. (M) Granulation tissue thickness measured on digital images and normalized to the average values in the WT control. WT, N=3; FAP-TK, N=3; WT, N=17, FSP1-TK, N=9 biological replicates. (N) Immunofluorescent staining for CD31 (red) and nuclei on wound tissue sections at day 17 post-wounding. White boxes denote zoomed regions depicted in right panels. Scale bar, 100 μm. (O) Quantification of CD31+ cells per visual field normalized to WT mice. WT, N=4; FAP-TK, N=4; WT, N=3; FSP1-TK, N=3 biological replicates. (P) IHC for hypoxyprobe (brown) on wound tissue sections at day 17 post-wounding. Black boxes denote zoomed regions depicted in right panels. Scale bar, 100 μm. (Q) Quantification of hypoxyprobe area per visual field normalized to WT mice. WT, N=3; FAP-TK, N=3; WT, N=3; FSP1-TK, N=4 biological replicates. (R) W"
NCBI gene IDs:
"FSP1: 71361
FAP: 14089
TK: 24271467"
Figure legend: "(C) Enrichment plot of genes in αSMA C1 (left panel). Violin plots for genes enriched in αSMA C1 (right panels). (D) Enrichment plot of genes in αSMA C2 (left panel). Violin plots for genes enriched in αSMA C2 (right panels). (E) Enrichment plot of genes in αSMA C3 (left panel). Violin plots of enriched genes in the αSMA C3 cluster (right panels). Raw scRNA-seq data are derived from (Haensel et al., 2020, Data ref: Haensel et al 2020). Da"
NCBI gene IDs:
"αSMA: 11475"
Figure legend: "(A) IHC for collagen I on wound tissue sections at day 17 post-wounding (brown stain). Black boxes denote zoomed regions depicted in bottom panels. Scale bar: 50 μm. (B) Quantification of collagen I positive area normalized to the average area in WT controls. WT, N=5; TK, N=5 biological replicates. (C) Polarized light images of picrosirius red stained wound tissues at day 17 post-wounding. Red: collagen fibers. White boxes denote zoomed regions depicted in bottom panels. Scale bar, 50 µm. (D) Quantification of collagen fiber (picrosirius red) percent area normalized to the average area in WT controls. WT, N=3; TK, N=3 biological replicates. (E-"
NCBI gene IDs:
"TK: 24271467"
Figure legend: "(E-H) Reduced collagen deposition in Col1α1cKO wounds. (E) IHC for collagen I on wound tissue sections at day 14 post-wounding (brown stain). Black boxes denote zoomed regions depicted in bottom panels. Scale bar: 25 μm. (F) Quantification of collagen I positive area normalized to the average area in WT controls. WT, N=7; Col1α1cKO, N=4 biological replicates. (G) Polarized light images of picrosirius red stained wound tissues at day 14 post-wounding. Red: collagen fibers. White boxes denote zoomed regions depicted in bottom panels. Scale bar, 50 µm. (H) Quantification of collagen fiber percent area and fiber width normalized to the average area and width, respectively, in WT controls. WT, N=4; Col1α1cKO, N=5 biological replicates."
NCBI gene IDs:
"Col1α1: 12842"
Figure legend: "(J-M) Reepithelization and vascularization in WT and Col1α1cKO mice. (J) Representative images of keratin 5 (Krt5, red) stained wounds at day 14 post-wounding. White boxes denote zoomed regions depicted in right panels. Scale bar, 500 µm. (K) Quantification of epidermal thickness. WT, N=6; Col1α1cKO, N=5 biological replicates. (L) Immunofluorescent staining for CD31 (red) and nuclei (blue) on wound tissue sections at day 14 post-wounding. White boxes denote zoomed regions depicted in right panels. Scale bar, 20 μm. (M) Quantification of CD31+ area per visual field normalized to WT mice. WT, N=6; Col1α1cKO, N=5 biological replicates."
NCBI gene IDs:
"Col1α1: 12842"
Figure legend: "(F-K) Reepithelization, granulation tissue formation, and vascularization in WT and Itgb1cKO mice. (F) Representative images of keratin 5 (Krt5, red) stained wounds at day 14 post-wounding. White boxes denote zoomed regions depicted in right panels. Scale bar, 500 µm. (G) Quantification of epidermal thickness. WT, N=4; Itgb1cKO, N=6 biological replicates. (H) Immunofluorescent staining for CD31 (red) and nuclei (blue) on wound tissue sections at day 14 post-wounding. White boxes denote zoomed regions depicted in right panels. Scale bar, 20 μm. (I) Quantification of CD31+ area per visual field normalized to WT mice. WT, N=6; Itgb1cKO, N=6 biological replicates. (J) Polarized light images of picrosirius red stained wound tissues at day 14 post-wounding. Red: collagen fibers. White boxes denote zoomed regions depicted in right panels. Scale bar, 50 µm. (K) Quantification of collagen fiber percent area normalized to the average area in WT controls. WT, N=6; Itgb1cKO, N=6 biological replicates. (L) Quantification of collagen fiber width normalized to the average width in WT controls. WT, N=6; Itgb1cKO, N=6 biological replicates. D"
NCBI gene IDs:
"Itgb1: 16412"
Figure legend: "(D) Growth rate  in rich medium (LB) under different levels of overexpression of a gratuitous  protein from a T5-lac   promoter; overexpression burden is controlled by IPTG  concentration Data information: Error bars in D, show standard deviation from 6, 12, and 18 biological replicates, respectively; day-to-day reproducibility of growth rate  measurements is high"
NCBI gene IDs:
"lac: "
Figure legend: "(B) Growth rate as a function of TMP  concentration for different paths through IPTG-TMP  concentration space Constant FolA   is shown in black and inverted FolA   regulation in red. Wild-type  dose-response curve  (blue line; is shown for comparison. (C) Steepness of the  dose response curve  (quantified as dose-sensitivity n) for the three cases in B. Inset: Normalized FolA expression  level as a function of TMP  concentration for the three cases in B; WT (blue) colors as in the bar chart and in B. Data information: Error bars in B show standard deviation of the measured growth rates  used for interpolating the values shown; the entire experiment was replicated once Error bars in C show standard deviation of parameter estimates from Hill function fit."
NCBI gene IDs:
"FolA: 944790"
Figure legend: "(D) Quantification of EGFP-LC3 puncta in MCF7-EGFP-LC3 cells 56 h after transfection with the indicated siRNAs. When indicated, cells were exposed to 100 nM rapamycin for the last 3 h. RPTOR (raptor) and BECN1 (beclin1) siRNAs served as positive and negative controls, respectively."
NCBI gene IDs:
"BECN1: 8678
RPTOR: 57521"
Figure legend: "(E) Autophagic flux was measured as the ratio between luciferase activities in MCF7-RLuc-LC3WT and MCF7-RLuc-LC3G120A cells transfected with the indicated siRNAs 56 h earlier and left untreated or treated with 100 nM rapamycin for the last 3 h. Error bars are SDs for a representative (n = 5) triplicate experiment with a minimum of 4 × 10 randomly chosen areas/sample analyzed (D) or three independent experiments (F). *, P &lt; 0.05; **, P &lt; 0.01; ***, P &lt; 0.001, as compared with similarly treated control siRNA-transfected samples."
NCBI gene IDs:
"LC3: 440738///81631///84557"
Figure legend: "(B) Representative immunoblots of the indicated proteins from whole-cell lysates of MCF7-EGFP-LC3 cells stably infected with control or CIP2Ar (siRNA-resistant CIP2A)-encoding lentivirus, transfected with the indicated siRNAs for 53 h, and treated with 100 nM rapamycin (Rapa) for 0-20 min."
NCBI gene IDs:
"CIP2A: 57650
LC3: 440738///81631///84557"
Figure legend: "(C) MCF7-EGFP-LC3 cells stably infected with control or CIP2Ar-encoding lentivirus were transfected with indicated siRNAs for 48 h and analyzed for EGFP-LC3 puncta formation."
NCBI gene IDs:
"CIP2A: 57650"
Figure legend: "(D) MCF7-EGFP-LC3 cells transfected with control (−) and CIP2A siRNAs together with an empty vector (−) or MYC-S62A cDNA as indicated were analyzed 56 h later for EGFP-LC3 puncta (left) and expression of indicated proteins (right)."
NCBI gene IDs:
"CIP2A: 57650"
Figure legend: "(E) Representative immunoblots (left) of indicated proteins from whole-cell lysates of MCF7 cells treated with the control (C), RPTOR (RP), or CIP2A (CIP) siRNAs for 56 h and densitometric quantification of three independent experiments (right). Error bars show SDs for three independent experiments. *, P &lt; 0.05; **, P &lt; 0.01; ***, P &lt; 0.001, compared with Student's t test as indicated (C and D) or with control siRNA-transfected samples (E). Black lines indicate that intervening lanes have been spliced out."
NCBI gene IDs:
"CIP2A: 57650
RPTOR: 57521"
Figure legend: "(A, top left) Quantification of EGFP-LC3 puncta in MCF7-EGFP-LC3 cells infected with control or CIP2A lentiviral shRNAs. Representative immunofluorescence images (right) and immunoblots (bottom) are shown. (B) Mean cell diameters of MCF7-EGFP-LC3 cells infected as in A were measured with a cytometer (NucleoCounter NC-3000; Chemometec AS) equipped with Via1-Cassettes (Chemometec AS)."
NCBI gene IDs:
"CIP2A: 57650"
Figure legend: "(E) Light microscopy pictures of MCF10A cells at passage 8 after infection with control or CIP2A-encoding lentivirus."
NCBI gene IDs:
"CIP2A: 57650"
Figure legend: "(A and B) In vitro translated full-length CIP2A was incubated with purified human PP2A complex and HA-Raptor (A) or HA-S6K1 (B) purified from transiently transfected MCF7 cells. Protein complexes were immunoprecipitated with anti-HA antibody and analyzed by immunoblotting as indicated. Nonspecific IgG served as a control. Note that human reticulocyte (RC) lysate used for in vitro translation of CIP2A contained detectable amounts of PP2Ac."
NCBI gene IDs:
"CIP2A: 57650
S6K1: 6198
Raptor: 57521"
Figure legend: "(D) Endogenous raptor protein complexes immunoprecipitated from MCF7 cells stably infected with control (Ctr) or CIP2A shRNA lentiviruses (Fig. 3 A) and starved for amino acids for 20 min when indicated were analyzed by immunoblotting and PP2A activity assay. Immunoblots of corresponding cell lysates are shown on the right."
NCBI gene IDs:
"CIP2A: 57650"
Figure legend: "(E) Raptor protein complexes immunoprecipitated from MCF7 cells treated with control (C) or PPP2R1A (R1A) siRNAs for 56 h were analyzed by immunoblotting with the indicated antibodies. Immunoblots of corresponding cell lysates are shown on the left."
NCBI gene IDs:
"PPP2R1A: 5518"
Figure legend: "(F) HA-S6K1 protein complexes immunoprecipitated from MCF7 cells stably infected with control or CIP2A shRNA lentiviruses (Fig. 3 A), transiently transfected with HA-RPS6K1 cDNA and starved for amino acids for 20 min when indicated, were analyzed by immunoblotting. Immunoblots of corresponding cell lysates are shown on the right."
NCBI gene IDs:
"CIP2A: 57650
RPS6K1: 6198"
Figure legend: "(G) Enzymatic activity of a purified PP2A holoenzyme incubated with human reticulocyte lysate with or without in vitro translated full-length CIP2A. Error bars are SDs for four (D) independent experiments or a representative triplicate experiment (C and G)."
NCBI gene IDs:
"CIP2A: 57650"
Figure legend: "(B) qPCR analysis of CIP2A and MYC mRNA levels in MCF7 cells treated as in A. AA-starv, amino acid starvation; a.u., arbitrary unit. Error bars show SDs for three independent experiments."
NCBI gene IDs:
"CIP2A: 57650
MYC: 4609"
Figure legend: "(C) Representative immunoblots of the indicated proteins from whole-cell lysates of MCF7 cells treated with ULK1 or SQSTM1 siRNAs for 54 h before the exposure to fresh medium (0) or amino acid starvation (−AA) for 12 h. Ctr, control."
NCBI gene IDs:
"SQSTM1: 8878
ULK1: 8408"
Figure legend: "(F) Representative immunoblots of an endogenous CIP2A protein complex immunoprecipitated from lysates of MCF7 cells left untreated or treated for 4 h with 100 nM rapamycin (Rapa) and 2 nM ConA as indicated. Mouse IgG served as a negative control."
NCBI gene IDs:
"CIP2A: 57650"
Figure legend: "(G) MCF7 cells were treated with 100 nM rapamycin, 2 nM ConA, and 2 µM MG132 for 24 h as indicated. Endogenous CIP2A was immunoprecipitated (IP) in stringent conditions (no coimmunoprecipitation of p62) and analyzed by immunoblotting using antibodies against CIP2A, monoubiquitin, and polyubiquitin. Short (&lt;100 kD), medium (&gt;150 kD), and long (100-130 kD) exposures are shown."
NCBI gene IDs:
"CIP2A: 57650"
Figure legend: "(J) Lysates from MCF7 cells transfected with the CIP2A-FLAG construct (Junttila et al., 2007) and the indicated ubiquitin-HA constructs were subjected to anti-FLAG immunopurification in denaturing conditions with 0.1% SDS followed by immunoblotting with the indicated antibodies. Black lines indicate that intervening lanes have been spliced out. Ub, ubiquitin; WT, wild type."
NCBI gene IDs:
"ubiquitin: 6232///7314///7311///7316"
Figure legend: "(B) Fraction of unlabeled nucleosides, nucleic bases and PPP intermediates as a function of starvation time, in wild‐type and autophagy deficient (atg7 deletion) yeast. The x axis represents minutes after carbon starvation, and the y axis represents fraction of unlabeled metabolites (mean±range of N=2 biological replicates)."
NCBI gene IDs:
"atg7: 856576"
Figure legend: "(C) Ratio of metabolite levels in atg7 strain versus wild‐type strain in carbon starvation."
NCBI gene IDs:
"atg7: 856576"
Figure legend: "(D) Ratio of metabolite levels in bcy1 strain and snf1 strain versus wild‐type strain in carbon starvation."
NCBI gene IDs:
"bcy1: 854778
snf1: 852088"
Figure legend: "(A) Ratio of metabolite levels in sdt1 and phm8 strains versus wild‐type strain in carbon starvation. All reported values are log2 transformed ratios; data are mean of duplicate samples at each time point."
NCBI gene IDs:
"phm8: 856759
sdt1: 852648"
Figure legend: "(B) Summary of transcripts data of PHM8, SDT1 and other enzymes in the pathway (Gasch et al, 2000; Bradley et al, 2009; Klosinska et al, 2011). All values are log2 transformed fold changes."
NCBI gene IDs:
"PHM8: 856759
SDT1: 852648"
Figure legend: "(C) Screening of Phm8's phosphatase activity against 90 phosphorylated compounds. Phosphatase activity was measured in the presence of 0.5 mM substrate and 5 mM Mg2+ (pH=7.0, 30°C). Compounds with specific activity higher than 0.1 μmol/mg/min are shown. The x axis represents specific phosphatase activity (μmol of phosphate produced per minute per mg of enzyme, mean±range of N=2 replicates)."
NCBI gene IDs:
"Phm8: 856759"
Figure legend: "(D) Top table: absolute intracellular concentration of nucleotide monophosphates in carbon starvation. Bottom plots: Phosphatase activity of Phm8 and Sdt1 as a function of CMP concentration. The x axis represents CMP concentration and the y axis represents specific phosphatase activity (μmol of phosphate produced per minute per mg of enzyme, mean±range of N=2 replicates)."
NCBI gene IDs:
"Phm8: 856759
Sdt1: 852648"
Figure legend: "Confirmation that Pnp1 is the physiological purine nucleoside phosphorylase, Urh1 is the pyrimidine hydrolase, and Prm15 (Pgm3) is the phosphoribomutase. Ratio of metabolite levels in pnp1/urh1, pnp1, urh1 and prm15 (pgm3) strains versus wild‐type strain during carbon starvation. Data are shown in heat map format, with each line reflecting the dynamics of the ratio of the metabolite levels in a particular strain versus wild‐type strain. All reported values are log2 transformed ratios; data are mean of duplicate samples at each time point."
NCBI gene IDs:
"pnp1: 850906
pgm3: 855321
prm15: 855321
urh1: 852009"
Figure legend: "(B‐E) DHAP, SBP and S7P levels in wild type, tkl1/tkl2 (B), tal1/nqm1 (C) and pfk1 (E) strains upon carbon starvation, and wild‐type strain upon abruptly switching from glucose to no carbon (WT) versus to dihydroxyacetone (WT+DHA) as the sole carbon source (D). The x axis represents hours after carbon starvation, and the logarithmic y axis represents absolute intracellular concentration (mean±range of N=2 biological replicates)."
NCBI gene IDs:
"nqm1: 852934
pfk1: 853155
tal1: 851068
tkl1: 856188
tkl2: 852414"
Figure legend: "(A) Level of hallmark metabolites and energy charge in wild type, phm8 and pnp1/urh1 strains in starvation. The x axis represents hours after starvation, and the logarithmic y axis represents energy charge ([ATP]+0.5[ADP]/([ATP]+[ADP]+[AMP]) or absolute intracellular concentration (mean±range of N=2 biological replicates)."
NCBI gene IDs:
"phm8: 856759
pnp1: 850906
urh1: 852009"
Figure legend: "(B and C) Growth and viability of wild type, phm8 and pnp1/urh1 strains in starvation."
NCBI gene IDs:
"phm8: 856759
pnp1: 850906
urh1: 852009"
Figure legend: "(D) Growth of wild type, phm8 and pnp1/urh1 strains in the switch from glucose to glycerol+ethanol. The x axis represents hours after starvation and the logarithmic y axis represents optical density (A600) in (B and D) and percentage of live cells calculated by dividing the number of colonies formed after starvation by the number of colonies formed before starvation in (C) (mean±range of N=2 biological replicates)."
NCBI gene IDs:
"phm8: 856759
pnp1: 850906
urh1: 852009"
Figure legend: "(C and D) DHAP, S7P, G6P, and glutathione levels and NADPH/NADP+ ratio in wild type, phm8 and pnp1/urh1 strains in the experiment shown in (A) The x axis represents minutes after oxidative stress, and the y axis represents absolute intracellular concentration or ratio of intracellular concentration (mean±range of N=2 biological replicates)."
NCBI gene IDs:
"phm8: 856759
pnp1: 850906
urh1: 852009"
Figure legend: "(E) Viability of wild type, phm8 and pnp1/urh1 strains in oxidative stress. The y axis represents percentage of survived cells calculated by dividing the number of colonies formed after oxidative stress by the number of colonies formed under the same starvation condition but without H2O2 treatment (mean±range of N=2 biological replicates)."
NCBI gene IDs:
"phm8: 856759
pnp1: 850906
urh1: 852009"
Figure legend: "Two-class comparison of genetic dependencies from a publically available genome-scale CRISPR-Cas9 screen of HNSCC (12 cell line) versus SQCLC (10 cell lines) identified a subset of differentially expressed proteins that were also differential dependencies in these tumor types. The x-axis represents the effect size of the mean difference of dependency scores in HNSCC compared to SQCLC cell lines. Positive effect size indicates a greater mean dependency in HNSCC; negative effect size indicates a greater mean dependency in SQCLC. The y-axis represents the statistical significance of differential enrichment calculated as -log10(p-value) from a two-sided t-test. The p-values used for this plot are uncorrected for multiple hypothesis testing. Highlighted in green are genetic dependencies that were also identified as differentially expressed proteins in our study."
NCBI gene IDs:
"CRISPR: "
Figure legend: "Using CRISPR/Cas9, MyD88 knock-out (KO) and AAVS1KO (control) pDCs  were generated. MyD88 protein levels in KO and control pDCs were analyzed by western blotting"
NCBI gene IDs:
"CRISPR: 
AAVS1: 17
Cas9: 69900935
MyD88: 4615"
Figure legend: "C-D: MyD88KO and control pDCs were either mock treated (mock) or exposed to  SARS-CoV-2  (SARS-2, 1 MOI), supernatants were collected at indicated time points  and analyzed for type I IFNα (C) and CXCL10 (D). Done with n=4 Data information: Bars represent mean values and equal symbols represent equal donors. Statistical significance was determined using Mann-Whitney one-tailed T test in (C) as MyD88-KO data had no variance and values of 0. For (D) a Mann-Whitney two-tailed T test was used for comparison between conditions of mock and MyD88 KO donors."
NCBI gene IDs:
"MyD88: 4615"
Figure legend: "E-F: Type I  IFNα production was then determined in cell culture supernatant from SARS-CoV-2  exposed TRIFKO or TRIG+MyD88KO (E) and RIG-IKO or RIG-I+MyD88KO (F)  pDCs. Done with n=2"
NCBI gene IDs:
"RIG-I: 23586
MyD88: 4615
TRIF: 148022
TRIG: 148022"
Figure legend: "(C) TNFemARE/ARE mice  show significantly elevated serum  levels of TNF  (wild-type n=5, TNFemARE/+ n=5, TNFemARE/ARE n=5). Data information: data are represented as Mean +/- SEM, n=biological replicates. one-way ANOVA test was used with Tukey's multiple comparisons test, ns= p-value &gt; 0.05, * = p-value ≤ 0.05, ** = p-value ≤ 0.01, *** = p-value ≤ 0.001, **** = p-value ≤ 0.0001."
NCBI gene IDs:
"TNF: 21926"
Figure legend: "(D) Histologic  H&amp;E sections of ileum  and hind paw indicate severe ileitis  and arthritis  in 20-30 w/o SPF TNFemARE/ARE mice  (Scale bars upper panel: 100 μm, scale bars lower panel: 500 μm)."
NCBI gene IDs:
"TNF: 21926"
Figure legend: "(H) Ileal flow cytometry  data of 25 w/o TNFemARE mice  show a highly activated innate immune system (n=5/genotype). Data information: data are represented as Mean +/- SEM, n=biological replicates. one-way ANOVA test was used with Tukey's multiple comparisons test, ns= p-value &gt; 0.05, * = p-value ≤ 0.05, ** = p-value ≤ 0.01, *** = p-value ≤ 0.001, **** = p-value ≤ 0.0001."
NCBI gene IDs:
"TNF: 21926"
Figure legend: "(D) Quantitative real-time PCR  reveals increased expression of the tnf  gene in the ileum  in homozygous SPF  and GF mice  (SPF  wild-type n=10, SPF TNFemARE/+ n=10, SPF TNFemARE/ARE n=13; GF  wild-type n=3, GF TNFemARE/+ n=4, GF TNFemARE/ARE n=4). Data information: data are represented as Mean +/- SEM, n=biological replicates, two-way ANOVA test used with Tukey's multiple comparisons test, ns= p-value &gt; 0.05, * = p-value ≤ 0.05, ** = p-value ≤ 0.01, *** = p-value ≤ 0.001, **** = p-value ≤ 0.0001."
NCBI gene IDs:
"tnf: 21926
TNF: 21926"
Figure legend: "(F) Comparing SPF  versus GF  H&amp;E sections of the ileum  shows complete rescue of gut inflammation  under axenic conditions in 20-30 w/o TNFemARE/ARE mice  (Scale bars: 100 μm)."
NCBI gene IDs:
"TNF: 21926"
Figure legend: "(C) 20-30 w/o SPF TNFemARE/ARE mice  clearly suffer from inflammation  in the synovio-entheseal complex, which is not rescued in age-matched GF mice. (Scale bars: 200 μm)"
NCBI gene IDs:
"TNF: 21926"
Figure legend: "(F) &lt;em&gt;μ&lt;/em&gt;CT images of tails  of wild-type versus SPF  and GF TNFemARE/ARE mouse  display fusion of  sacral vertebrae in homozygous SPF  and GF mice, as indicated by yellow arrows."
NCBI gene IDs:
"TNF: 21926"