EMBO/SourceData huggingface dataset:
Figure legend: "(E-F) expression levels of BomBc1, and BomS3 measured by RT-digital PCR 48 hours after challenge; BomBc1 PBST vs. Af, *p=0.015, PBST vs. restrictocin (R), *p=0.015; BomS3: PBST vs. Af, *p=0.02, PBST vs. R, *p=0.03 (pooled data of n=3 experiments, biological replicates)."
NCBI gene IDs:
"BomBc1: 37099
BomS3: 50209"
Figure legend: "(A-B) tremor rate (A) and survival (B) of flies (20 flies per condition) overexpressing Tl[10B] in neurons compared to wild-type after injection of verruculogen. (A) Each dot corresponds to the tremor rate measured in a batch of 20 flies; tremor rate wt vs. elav&gt; UAS-Toll10B, **p=0.002. (C-D) tremor rate (C) and survival (D) of flies (20 flies per condition) overexpressing Tl[10B] in glia compared to wild-type after injection of verruculogen. (C) Each dot corresponds to the tremor rate measured in a batch of 20 flies; tremor rate wt vs. repo&gt; UAS-Toll10B, **p=0.002. (D) Survival wt V vs. repo&gt; UAS-Toll10B V, **p=0.005."
NCBI gene IDs:
"elav: 31000
repo: 47285
Tl: 43222
Toll: 43222"
Figure legend: "(E-G) recovery time from tremor (E,F) and survival (G) of single flies overexpressing BomS6 ubiquitously (E,G) or in neurons (F-G) (biological replicates) compared to wild-type after injection of verruculogen; in (G) the inset represents the survival of vehicle control groups."
NCBI gene IDs:
"BomS6: 50206"
Figure legend: "(H-I) recovery time from tremor (H) and survival (I) of single flies overexpressing BomS6 in glia (pooled data from n=3 experiments, biological replicates) compared to wild-type after injection of verruculogen; in (I) the inset represents the survival of vehicle control groups. Recovery time (H) repo&gt;mCherry vs. repo&gt;BomS6, p=0.058, survival (I) repo&gt;mCherry V vs. repo&gt;BomS6 V, *p=0.016."
NCBI gene IDs:
"mCherry: 
BomS6: 50206
repo: 47285"
Figure legend: "(J-M) expression of BomS4 (J) and BomS6 (K) in head after verruculogen powder challenge, and BomS4 (L) and BomS6 (M) in head after A. fumigatus (Af), restrictocin or M. luteus injection (pooled data from n=3 experiments, biological replicates)."
NCBI gene IDs:
"BomS4: 37101
BomS6: 50206"
Figure legend: "a, Western blot analysis of yeast cell lysates with polyclonal anti-flag antibody to detect flag-tagged human Beclin 1 expression. Two-hundred micrograms of protein per lane was loaded. SEY6210, wild-type yeast; JCY3000, SEY6210 disrupted in apg6/vps30; (+) control, lysates of mammalian cells transfected with flag-beclin 1."
NCBI gene IDs:
"beclin 1: 8678
apg6: 855983
vps30: 855983"
Figure legend: "c, Quantitative effects of apg6/vps30 and beclin 1 transformation on autophagicbody formation in apg6/vps30-disrupted yeast in the presence of PMSF. Cells with one or more autophagic bodies within the vacuole were scored as positive (see arrows in b). A minimum of 100 cells was counted for each sample. Results represent the mean (±s.e.m.) percentage of cells with autophagic bodies within the vacuole for triplicate samples. Similar results were obtained in five independent experiments."
NCBI gene IDs:
"beclin 1: 8678
apg6: 855983
vps30: 855983"
Figure legend: "a-f, Electron micrographs of MCF7.control (clone 38) (a, b) and MCF7.beclin1 (clone 17) cells (c- f) grown in nutrient-rich media (a, c) or subjected to 4 h of serum and amino-acid deprivation (b, d-f). Asterisks in e and f denote autophagic vacuoles that would be counted in the experiment shown in g. Autophagic vacuoles were defined as double-membrane vacuolar structures containing recognizable cytoplasmic contents. Scale bars, 1 µm."
NCBI gene IDs:
"beclin1: 8678"
Figure legend: "g, Quantitative effects of beclin 1 on basal and nutrient-deprivation-induced autophagy of MCF7 cells. Bars indicate mean (±s.e.m.) number of autophagic vacuoles per cell for cells growing in normal media (black), for cells subjected to 4 h of serum and amino-acid deprivation (grey), and for cells pre-treated for 30 min with 10 mM 3-MA and subjected to 4 h of serum and amino-acid deprivation in the presence of 3-MA (open). Mean was determined by counting the total number of autophagic vacuoles in each cell for 100 cells per clone per treatment."
NCBI gene IDs:
"beclin 1: 8678"
Figure legend: "h, Comparison of the rates of degradation of long-lived proteins in MCF7.control cells (squares, clone 38), MCF7.beclin1 cells (circles, clone 17) and MCF7.beclin1stop cells (triangles, clone 70), in EBSS + 10% serum and complete amino acids (open symbols, solid lines) in EBSS alone (closed symbols, solid lines), and in EBSS + 10 mM 3-MA (closed symbols, dotted lines). Results are mean (±s.e.m.) of triplicate wells. Similar results were obtained in three independent experiments. Results shown with these clones are representative of results obtained with other clones analysed by electron microscopy in g."
NCBI gene IDs:
"beclin1: 8678"
Figure legend: "a, Western blot analysis of flag-tagged beclin-1-transfected MCF7 clones. C, MCF7.control cells (clone 38); St, MCF7.beclin1stop cells (clone 70). Mr, relative molecular mass."
NCBI gene IDs:
"beclin-1: 8678
beclin1: 8678"
Figure legend: "b, Western blot analysis of flag-tagged beclin1stop-transfected MCF7 clones. C, MCF.control cells (clone 38); B, MCF7.beclin1 cells (clone 1)."
NCBI gene IDs:
"beclin1: 8678"
Figure legend: "c, Photomicrographs of MCF7.control cells (left panel, clone 38), MCF7. beclin1 cells (middle panel, clone 17) and MCF7.beclin1stop cells (right panel, clone 70) 48 h after seeding at similar densities."
NCBI gene IDs:
"beclin1: 8678"
Figure legend: "d, Proliferation of MCF7.control cells (clones 37 and 38; closed squares and circles, respectively, solid lines), MCF7.beclin1 cells (clones 1, 6, 17; open squares, circles, triangles, respectively, solid lines) and MCF7.beclin1stop cells (clone 70, closed triangles, dotted line). Results represent mean Absorbance (A) (±s.e.m.) for six wells; similar results were obtained in three independent experiments."
NCBI gene IDs:
"beclin1: 8678"
Figure legend: "(B) Immunoblot analysis of SLC25A33 and SLC25A36 depletion in the indicated knockout (KO) and double knockout (DKO) HeLa cells (left) alongside the relative mtDNA levels of two monoclonal SLC25A33/SLC25A36 DKO cell lines calculated by qPCR (CYTB / ACTB ;right) (n=3 independent cultures)."
NCBI gene IDs:
"ACTB: 60
CYTB: 4519
SLC25A33: 84275
SLC25A36: 55186"
Figure legend: "(D) Representative images taken from the arrayed CRISPR-SpCas9 screen of SLC25A33/SLC25A36 DKO cells showing one field of view from wells transfected with non-targeting control (NTC) sgRNA or TFAM sgRNA (scale bar = 20 µm)"
NCBI gene IDs:
"CRISPR: 
Cas9: 69900935
SLC25A33: 84275
SLC25A36: 55186
TFAM: 7019"
Figure legend: "(G) Relative mtDNA levels in NME4 KO and NME4/SLC25A33/SLC25A36 triple KO HeLa (left) or NME6 KO and two clones of NME6/SLC25A33/SLC25A36 triple KO HeLa (right). MtDNA calculated by qPCR (CYTB / ACTB) and presented as log2 fold change compared to levels in WT HeLa cells (n = 4-5 independent cultures)."
NCBI gene IDs:
"ACTB: 60
CYTB: 4519
NME4: 4833
NME6: 10201
SLC25A33: 84275
SLC25A36: 55186"
Figure legend: "(A) The growth rate of NME6 KO and NME6 KO + NME6-MycFlag HeLa relative to WT HeLa cells incubated in DMEM containing 25 mM glucose (log2; n=13 independent cultures)."
NCBI gene IDs:
"Flag: 
Myc: 
NME6: 10201"
Figure legend: "(B) Violin plot of gene effects of NME3, NME4 or NME6 depletion in 1086 cell lines from the Cancer Cell Line Encyclopaedia (CCLE) determined by CRISPR screening (DepMap 22Q2 Public+Score, Chronos; solid line denotes median, dotted line denotes 25 % quartile)."
NCBI gene IDs:
"CRISPR: 
NME3: 4832
NME4: 4833
NME6: 10201"
Figure legend: "(B) Heat map representation of z-scores of log2-transformed protein intensities determined by quantitative mass spectrometry and filtered for mitochondrial proteins according to MitoCarta 3.0 The proteins shown clustered together due to their significant (permutation-based FDR &lt; 0.05, s0 = 0.1) depletion in NME6 KO HeLa cells compared to WT and NME6 KO + NME6-MycFlag HeLa cells. OXPHOS subunits are indicated in the right column (n=4 independent cultures)."
NCBI gene IDs:
"Flag: 
Myc: 
NME6: 10201"
Figure legend: "(E) Immunoblot analysis of WT HeLa cells, NME6 KO cells and NME6 KO cells expressing NME6-MycFlag (WT) or NME6H137N-MycFlag (H137N)."
NCBI gene IDs:
"Flag: 
Myc: 
NME6: 10201"
Figure legend: "(F) Immunoblot analysis of WT cells and two NME6 KO clones (#1, #2) generated in three different liver cancer cell lines: HLE, Huh6 and HepG2."
NCBI gene IDs:
"NME6: 10201"
Figure legend: "(H) The relative growth of WT and NME6 KO liver cancer cell lines monitored on each day (d) using an ATP luminescence assay. P-values for HLE cells: two-way ANOVA P-value (time) = &lt;0.0001, P-value (genotype) = &lt;0.0001, P-value (interaction) = &lt;0.0001; P-values for Huh6 cells: two-way ANOVA P-value (time) = &lt;0.0001, P-value (genotype) = 0.0005, P-value (interaction) = &lt;0.0001;p-values for genotype are shown (n=4 independent cultures)."
NCBI gene IDs:
"NME6: 10201"
Figure legend: "(E) MtDNA-encoded transcript levels analysed by qRT-PCR in NME6 KO and NME6 KO + NME6-MycFlag cells relative to WT HeLa cells. P-values for mtDNA-encoded transcripts: two-way ANOVA P-value (transcript) = &lt;0.0001, P-value (genotype) = &lt;0.0001, P-value (interaction) = &lt;0.0001 (log2; n=3 independent cultures)."
NCBI gene IDs:
"Flag: 
Myc: 
NME6: 10201"
Figure legend: "(F) Nuclear DNA-encoded transcript levels analysed by qRT-PCR in NME6 KO and NME6 KO + NME6-MycFlag HeLa cells relative to WT (log2; n=3 independent cultures)."
NCBI gene IDs:
"Flag: 
Myc: 
NME6: 10201"
Figure legend: "(A) Heat map of log2 transformed mean mitochondrial transcript levels of WT and NME6 KO HeLa cells incubated with 100 µM rNTPs or dNTPs for 48 h relative to untreated WT cells analysed by qRT-PCR (n=3 independent cultures)."
NCBI gene IDs:
"NME6: 10201"
Figure legend: "(B) Volcano plot representation of log2 fold change in proteins between NME6 KO cells treated with 100 µM rNTPs for 120 h and untreated NME6 KO HeLa cells determined by quantitative mass spectrometry. OXPHOS subunits are highlighted in teal (n=3 independent cultures)"
NCBI gene IDs:
"NME6: 10201"
Figure legend: "(D) Oxygen consumption rates (OCR) and extracellular acidification rates (ECAR) of WT and NME6 KO HeLa cells incubated with or without nucleosides (100 µM) for a minimum of 120 h. Mitochondrial stress test was performed as in Fig 3A (n=3 independent experiments). P-values for OCR: two-way ANOVA P-value (time) = &lt;0.0001, P-value (genotype) = 0.0011, P-value (interaction) = &lt;0.0001; P-values for ECAR: two-way ANOVA P-value (time) = &lt;0.0001, P-value (genotype) = 0.8994, P-value (interaction) = &lt;0.0001"
NCBI gene IDs:
"NME6: 10201"
Figure legend: "(G) CYTB (top) and ND5 (bottom) transcript levels analysed by qRT-PCR in WT and NME6 KO HeLa cells incubated with the indicated nucleoside species for 48 h. P-values were calculated using a one-way ANOVA (A, adenosine; G, guanosine; C, cytidine; U, uridine; log2; 100 µM; n=4 independent cultures)."
NCBI gene IDs:
"CYTB: 4519
ND5: 4540
NME6: 10201"
Figure legend: "(H) CTP (top) and dCTP (bottom) levels in the mitochondria enriched fraction of WT and NME6 KO HeLa cells incubated with the indicated nucleoside species for 120 h as determined by quantitative mass spectrometry. P-values for CTP: two-way ANOVA P-value (supplementation) = &lt;0.0001, P-value (genotype) = &lt;0.0001, P-value (interaction) = 0.3179; P-values for dCTP: two-way ANOVA P-value (supplementation) = &lt;0.0001, P-value (genotype) = &lt;0.0001, P-value (interaction) = 0.0569; P-values for supplementation are shown (C, cytidine; U, uridine; log2; 100 µM; n=4 independent cultures)."
NCBI gene IDs:
"NME6: 10201"
Figure legend: "(I) Basal (top) and maximal (bottom) oxygen consumption rates of WT and NME6 KO HeLa cells incubated with the indicated nucleoside species for a minimum of 120 h relative to untreated WT cells (A, adenosine; G, guanosine; C, cytidine; U, uridine; log2; 100 µM; n=4 independent experiments). P-values were calculated using a one-way ANOVA."
NCBI gene IDs:
"NME6: 10201"
Figure legend: "(C) Viremia progression in virus-infected mice was monitored over 2 weeks (n=11 per group). Viremia is detected with CHIKV nsP1 probe via qRT-PCR. Statistical"
NCBI gene IDs:
"nsP1: "
Figure legend: "Viremia were monitored over 2 weeks. Viremia is detected with CHIKV nsP1 probe via qRT-PCR."
NCBI gene IDs:
"nsP1: "
Figure legend: "Three-week-old WT C57BL/6 mice were infected with 1E6 PFU of WT-ONNV at the metatarsal region of the footpad. (A) Viremia progression in ONNV-infected mice were monitored over 2 weeks (n=5). Viremia is detected with ONNV nsP1 probe via qRT-PCR."
NCBI gene IDs:
"nsP1: "
Figure legend: "Three-week-old WT C57BL/6 mice were vaccinated subcutaneously with 1E6 PFU of WT-CHIKV or attenuated CHIKV (RH) at the metatarsal region of the footpad. Challenge with 1E6 PFU of WT-ONNV was performed via the same route at 3 months post-vaccination. Viremia progression of the mice were monitored over 2 weeks (n=5 per group). Viremia is detected with ONNV nsP1 probe via qRT-PCR."
NCBI gene IDs:
"nsP1: "
Figure legend: "S2 cells were transiently transfected with the indicated constructs and exposed to 1% O2 for 24h. (A, B) (A) Activities of Firefly (Fluc) and Renilla (Rluc) luciferase, produce from reporter genes under control of the Ldh gene promoter, were measured in total cell extracts by dual luciferase assay and the ratio of both measures was calculated for each transfection. (B) Relative FLuc and RLuc mRNA levels were measured by RT-qPCR."
NCBI gene IDs:
"Fluc: 
FLuc: 
luciferase: 
Rluc: 
RLuc: 
Ldh: 45880"
Figure legend: "S2 cells were transiently transfected with the indicated constructs and exposed to 1% O2 for 24h. (D) Indicated stably transfected cell lines were exposed to 21% or 1% O2 for 24h before fractionation of cell extracts by ultracentrifugation on linear sucrose gradients (15%-50% The distribution of FLuc mRNA, produced from reporter genes under control of the pMT promoter was measured by northern blot in each cell types. Fractions numbers from top to bottom of the gradient are indicated."
NCBI gene IDs:
"FLuc: "
Figure legend: "(A) Control (TM3&gt;UAS-eIF4EHP_RNAi) or eIF4EHP KD (Tub-GAL4&gt;UAS-eIF4EHP_RNAi) flies were maintained in either normoxia or hypoxia (1%O2, 24h). Protein extracts were prepared from whole flies and eIF4EHP, LDH and Actin were detected by western blot. (B) Quantification of LDH/Actin ratio in 3 independent experiments performed as in A. Values represent mean +/- SD, n=3 biological replicates, P-value of two-ways ANOVA."
NCBI gene IDs:
"eIF4EHP: 326255
GAL4: 855828
Tub: 40554"
Figure legend: "(C) S2 cells lines inactivated for Yellow or eIF4EHP genes were established by a CRISPR-Cas9 strategy as described in the methods section. After exposure to normoxic or hypoxic conditions, cells were lysed and Actin, LDH and eIF4EHP protein levels were detected by western blot. (D) Quantification of LDH/Actin ratio in 6 independent experiments performed as in C. Values represent mean +/- SD, P-values of two-way ANOVA."
NCBI gene IDs:
"CRISPR: 
Cas9: 69900935
eIF4EHP: 326255
Yellow: 30980"
Figure legend: "(E) Cell extracts from Yellow, eIF4EHP or eIF4E6 KO cells incubated at 21 or 1% O2 were separated by centrifugation on linear sucrose gradients and Ldh mRNA was detected by northern blot in the different fractions. Fractions numbers from top to bottom of the gradient are indicated."
NCBI gene IDs:
"eIF4E6: 43422
eIF4EHP: 326255
Ldh: 45880
Yellow: 30980"
Figure legend: "B) Polysome profiles of FLuc-Ldh 3'UTR and Fluc-CA-rich 3'UTR reporter mRNA in control (Yellow KO) and eIF4EHP KO S2 cells in hypoxia."
NCBI gene IDs:
"FLuc: 
Fluc: 
eIF4EHP: 326255
Ldh: 45880
Yellow: 30980"
Figure legend: "(D) WT and eIF4EHP KO cells were co-transfected with plasmids encoding V5-tagged D. persimilis eIF4EHP (Dp eIF4EHP) or GFP, along with FLuc-Ldh3'UTR and RLuc reporters. eIF4EHP proteins were detected by western blot using eIF4EHP antibody (cross-reacting to Dp eIF4EHP)."
NCBI gene IDs:
"FLuc: 
GFP: 
RLuc: 
V5: 
eIF4EHP: 326255
Ldh: 45880"
Figure legend: "(E, F) 24h after transfection, cells were cultivated in hypoxia (1%O2) for an additional 24h before measurement of luciferase activity by dual luciferase reporter assay (D) and luciferase mRNA levels by qPCR (E). Values represent mean ± SD, n=3 biological replicates, P-value of one-way ANOVA, *-P ≤ 0.05, ns- P&gt;0.05."
NCBI gene IDs:
"luciferase: "
Figure legend: "(C) Cross-Linking and Immunoprecipitation experiment (CLIP) was performed on cell extracts from normoxic and hypoxic (1% O2, 24h) UV irradiated WT or eIF4EHP KO S2 cells. eIF4EHP was immunoprecipitated with eIF4EHP antibody-coated protein G sepharose beads before Ldh and Rpl32 mRNA detection by RT-qPCR in total extract (input) or immunoprecipitation eluate. mRNA enrichment levels in eluate as compared to input from 3 independent experiments were calculated as described Data represent mean +/- SD. Statistical significance was tested by two-way ANOVA followed by Sidak's multiple comparisons test, * P&lt;0.05."
NCBI gene IDs:
"eIF4EHP: 326255
Ldh: 45880
Rpl32: 43573"
Figure legend: "(A) Female or male flies with chromosomal insertions of an UAS_eIF4EHP (BDSC 36876) RNAi construct were crossed with male or female Tub&gt;Gal4/Tm3 (BDSC 5138) driver flies. Two hours after mating, embryos were transferred to 6% O2 (lowest tolerated O2 concentration) or kept in normoxia until eclosion. Tub-Gal4/UAS-eIF4EHP_RNAi and Tm3/UAS-eIF4EHP_RNAi F1 individuals were counted based on the presence (control) or absence (eIF4EHP KD) of the Tm3 SB marker and results were expressed as % of total eclosions for each condition. Data represent mean +/-SD fro 2 independent biological replicates. Statistical significance was tested by two-way ANOVA followed by Sidak's multiple comparisons test. **** P&lt;0.0001; *** P&lt;0.001; ** P&lt;0.01; * P&lt;0.05."
NCBI gene IDs:
"eIF4EHP: 326255
Gal4: 855828
SB: 41958
Tub: 40554"
Figure legend: "(B) Mobility of age-matched Tub-Gal4/UAS-eIF4EHP_RNAi (eIF4EHPRNAi), TM3/UAS-eIF4EHP_RNAi (control) (upper panels) or Tub-Gal4/UAS-mCherry_RNAi (m-cherryRNAi) (lower panel) females was assessed by negative geotaxis assay in normoxic conditions (21% O2) or 40 min. and 48h after an initial exposure to 1% O2 for 24h. Flies climbing past threshold within 120s were counted and expressed as % of total flies. Each assay was performed in triplicate with 20 flies. Data are mean +/- SD."
NCBI gene IDs:
"m-cherry: 
mCherry: 
eIF4EHP: 326255
Gal4: 855828
Tub: 40554"
Figure legend: "A) Expression of PTGES in normal and tumor tissue."
NCBI gene IDs:
"PTGES: 9536"
Figure legend: "B) Kaplan-Meier analysis of overall (left) and progression-free (right) survival in patients with lung adenocarcinoma with high PTGES (top 10%) and low PTGES (bottom 90%) expression."
NCBI gene IDs:
"PTGES: 9536"
Figure legend: "D) IL15 gene expression analysis in high and low NK gene signature (NK GS)."
NCBI gene IDs:
"IL15: 3600"
Figure legend: "F) Overall survival in patients with high (top 50%) PTGES expression in relation to high (top 50%) and low (bottom 50%) NK cell gene expression signature."
NCBI gene IDs:
"PTGES: 9536"
Figure legend: "Death rates of wild-type and GlpK22 mutants plotted versus growth rates. Wild type is grown in glycerol minimal medium in batch cultures (black circle) and in 'chemostat' continuous cultures with growth rates coded in colors, see legend on the center right. GlpK22 mutants (white circle) are grown in glycerol minimal medium in batch culture. Data shown as mean ± (standard deviation) SD. Two replicates per condition."
NCBI gene IDs:
"GlpK22: 948423"
Figure legend: "Cell size during starvation. Length and width of the cells are measured with phase-contrast microscopy and the volume is computed considering cell shape as a cylinder with two semi-spheres, as described in the graphical synopsis at the top (see also Table EV3 and Methods). Each measurement is an average of 200 cells. (A) Measured length and width of wild type cells starved in batch cultures and previously grown in the chemostat at different steady-state growth rates and of GlpK22 cells starved and previously grown in batch culture at μ = 0.9 h − 1 (see upper color legend). Note that, as shown in Schink et al. (2019), cell widths do not change from steady state growth to starvation, while lengths decrease. Both length and width increase exponentially with growth rate. (B) Starvation volume of the cells described in panel A, computed as explained in the graphical synopsis (see also Methods). In agreement with literature (Schaechter et al., 1958), it increases exponentially with growth rate (black line)."
NCBI gene IDs:
"GlpK22: 948423"
Figure legend: "Death rates of ∆rpoS mutants versus the growth rate (grey symbols), compared to wild-type E. coli K-12 (white symbols, data from Fig. 1). Death rate increases with growth rate with a smaller slope (∆rpoS: 0.57±0.13 h) compared to wild-type (WT: 0.88±0.13 h). Black and grey lines show linear weighted least square fits to log-transformed data, which take uncertainty in data points into account (see Methods). Data shown as mean ± SD. Two or three replicates per condition."
NCBI gene IDs:
"rpoS: 947210"
Figure legend: "(D) Left panel, representative  high content microscopy  image of control and RIPK2  knockdown THP-1  cells infected with S. flexneri (MOI 1:25, 8 h). Right panel, the graph depicts an average number of RIPosomes/cell, which is calculated from 3 biological replicates, Mean ± SD. ***p &lt; 0.0005, Student's unpaired t-test."
NCBI gene IDs:
"RIPK2: 8767"
Figure legend: "(E-F) Western blot  analysis of soluble  and  insoluble fractions of S. flexneri  infected (E) control siRNA and RIPK2  siRNA transfected THP-1  cells (F) Control CRISPR  (RIPK2+/+) cells and RIPK2  CRISPR knockout (RIPK2-/-) HT-29 cells."
NCBI gene IDs:
"CRISPR: 
RIPK2: 8767"
Figure legend: "(I) Representative confocal  images of RIPosomes  in  THP-1 cells infected with RFP expressing Salmonella typhimurium (MOI 1:5, 4 h). Line profile: co-localization analysis using line intensity profile. Scale bar, 8 µm. Zoom panels are digital magnifications. DNA is stained  with DAPI."
NCBI gene IDs:
"RFP: "
Figure legend: "Representative confocal  images of (M) GFP  expressing M. tuberculosis (MOI 1:10, 8 h). Line profile: co-localization analysis using line intensity profiles. Scale bar, 5 µm. Zoom panels are digital magnifications. DNA is stained  with DAPI."
NCBI gene IDs:
"GFP: "
Figure legend: "(B) Left panel, representative  high-content microscopy  images of HEK293T  cells transfected with GFP-NOD1, GFP-NOD2, and GFP  -RIPK2  plasmids for 9 h. Right panel, the graph depicts the average number of RIPosomes  per GFP-positive cell. About 15000 cells were plated per well and RIPosomes  were screened in 35 fields per well. Mean ± SD, n=3 (biological replicates), ****p &lt; 0.00005, ordinary one-way ANOVA (Tukey's multiple comparisons test)."
NCBI gene IDs:
"GFP: 
NOD1: 10392
NOD2: 64127
RIPK2: 8767"
Figure legend: "(C) Western blot  analysis of soluble  and insoluble fractions  of HEK293T  cells transfected with the CARD domain-containing region of NOD1, NOD2, and RIPK2."
NCBI gene IDs:
"NOD1: 10392
NOD2: 64127
RIPK2: 8767"
Figure legend: "(F) Representative confocal images of immunofluorescence assays conducted with THP-1 cells infected with RFP expressing S. flexneri (pseudo-colored, blue) (MOI 1:25, 8h). Line profile: co-localization analysis using line intensity profiles. Scale bar, 5 µm. Zoom panels are digital magnifications."
NCBI gene IDs:
"RFP: "
Figure legend: "(G) Representative confocal  images of immunofluorescence  assays performed with HEK293T  cells transfected with GFP-RIPK2  and Flag-NOD2  (upper panel) or Flag-NOD1  (lower panel). Line profile: co-localization analysis using line intensity profiles. Scale bar, 5 or 10 µm as indicated in figures. Inset zoom panels are digital magnifications."
NCBI gene IDs:
"Flag: 
GFP: 
NOD1: 10392
NOD2: 64127
RIPK2: 8767"