EMBO/SourceData huggingface dataset:
Figure legend: "Western blot analysis performed with lysates of (I) Irgm1+/+ and Irgm1-/- mouse brain to determine levels of TBK1 protein."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "Western blot analysis performed with lysates of (J) IRGM+/+ and IRGM+/- HT29 cells"
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "Western blot analysis performed with lysates of (K-L) Irgm1+/+ and Irgm1-/- mouse brain to determine levels of IRF proteins."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "Western blot analysis performed with lysates of (M) IRGM+/+ and IRGM+/- HT29 cells"
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "Western blot analysis performed with lysates of (N) Irgm1+/+ and Irgm1-/- mouse brain to determine levels of STAT proteins (n=3 mice)."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "Western blot analysis performed with lysates of (O) IRGM+/+ and IRGM+/- HT29 cells. 2 biological replicates are shown."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "Western blot analysis performed with lysates of (P) Irgm1+/+ and Irgm1-/- mouse brain to determine levels of ISG proteins (n=2 mice)."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "(Q) Representative confocal image of immunofluorescence assay performed with IRGM+/+ and IRGM+/- HT29 cells stained with MX1 antibodies. Scale bar, 10 µm."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(F) Western blot analysis with the lysates of HT-29 cells stably transfected with control or Flag-IRGM plasmid and probed with the indicated antibodies."
NCBI gene IDs:
"Flag: 
IRGM: 345611"
Figure legend: "(J-K) The qRT-PCR analysis with RNA isolated from (J) control and Flag-IRGM stable HT-29 cells (K) THP-1 cells transiently transfected with control or Flag-IRGM plasmid."
NCBI gene IDs:
"Flag: 
IRGM: 345611"
Figure legend: "(O) Western blotting analysis with lysates of control and untreated or Bafilomycin A1 (300 nM; 4 h and 8 h) treated Flag-IRGM expressing HT29 stable cell lines."
NCBI gene IDs:
"Flag: 
IRGM: 345611"
Figure legend: "(P) Western blotting analysis with lysates of control and untreated or chloroquine (50 µM; 4 h and 8 h) treated Flag-IRGM expressing HT29 stable cell lines."
NCBI gene IDs:
"Flag: 
IRGM: 345611"
Figure legend: "(Q) The qRT-PCR analysis with RNA isolated from untreated or Bafilomycin A1 (300 nM; 4 h, 8 h, and 12 h) treated control or Flag-IRGM expressing HT-29 stable cells as indicated."
NCBI gene IDs:
"Flag: 
IRGM: 345611"
Figure legend: "(A) The cell lysates of control or BECLIN1 siRNA transfected THP-1 cells expressing GFP or GFP-IRGM were subjected to immunoblotting with indicated antibodies."
NCBI gene IDs:
"GFP: 
BECLIN1: 8678
IRGM: 345611"
Figure legend: "(B) The cell lysates of control or ATG5 siRNA transfected THP-1 cells expressing GFP or GFP-IRGM were subjected to immunoblotting with indicated antibodies."
NCBI gene IDs:
"GFP: 
ATG5: 9474
IRGM: 345611"
Figure legend: "(C-D) qRT-PCR analysis with RNA isolated from control or BECLIN1 siRNA transfected THP-1 cells expressing 3X-Flag epitope or Flag-IRGM as indicated."
NCBI gene IDs:
"Flag: 
BECLIN1: 8678
IRGM: 345611"
Figure legend: "qRT-PCR analysis with RNA isolated from control or ATG5 siRNA transfected THP-1 cells expressing 3X-Flag epitope or Flag-IRGM as indicated."
NCBI gene IDs:
"Flag: 
ATG5: 9474
IRGM: 345611"
Figure legend: "(G-H) qRT-PCR analysis with RNA isolated from control or p62 siRNA or BECLIN1 siRNA transfected HT29 cells expressing 3X-Flag epitope or Flag-IRGM as indicated."
NCBI gene IDs:
"Flag: 
BECLIN1: 8678
IRGM: 345611
p62: 8878"
Figure legend: "(K-M) Co-IP analysis of the interaction between GFP IRGM with (K) Flag-cGAS, (L) Flag-RIG-I, (M) Flag-TLR3 in control siRNA or p62 siRNA transfected HEK293T cell lysates."
NCBI gene IDs:
"p62: 8878"
Figure legend: "(N) The cell lysates of control or p62 siRNA transfected THP-1 cells expressing GFP or GFP- IRGM (as indicate) were subjected to immunoblotting with indicated antibodies."
NCBI gene IDs:
"p62: 8878"
Figure legend: "(O) The qRT-PCR analysis with RNA isolated from control or p62 transfected THP-1 cells expressing 3X-Flag epitope or Flag-IRGM as indicated."
NCBI gene IDs:
"Flag: 
IRGM: 345611
p62: 8878"
Figure legend: "(P-R) Co-IP analysis of the interaction between HA-p62 and (P) Flag-RIG-I, (Q) Flag-TLR3, (R) Flag-cGAS in the absence and presence of GFP or GFP-IRGM in HEK293T cell lysates."
NCBI gene IDs:
"GFP: 
IRGM: 345611"
Figure legend: "(A) Representative confocal images of Irgm1+/+ and Irgm1-/- mouse BMDMs processed for IF analysis with Tom20 antibody. Scale bar, 5 µm. Zoom panels are digital magnifications."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "(B) The graph depicts the percentage of cells with swollen/rounded mitochondria in Irgm1+/+ and Irgm1-/- mouse BMDMs."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "(C) Representative confocal (STED) images of Irgm1+/+ and Irgm1-/- mouse BMDMs processed for IF analysis with Tom20 and Parkin antibodies. Line profile: Co-localization analysis using line intensity profiles."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "(D) Representative confocal (STED) images of Irgm1+/+ and Irgm1-/- mouse BMDMs processed for IF analysis with Tom20 and Pink1 antibodies. Line profile: Co-localization analysis using line intensity profiles."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "(E) Representative confocal images of control siRNA and IRGM siRNA transfected THP-1 cells processed for IF analysis with Ubiquitin (green) and TOM20 (red) antibodies. Scale bar, 10 µm."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(F) Western blot analysis of mitochondrial fraction of control siRNA and IRGM siRNA transfected THP-1 cells, probed with indicated antibodies."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(G) Western blot analysis of mitochondrial fraction of Irgm1+/+ and Irgm1-/- mouse BMDM cells, probed with indicated antibodies (n=2 mice)."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "(H) Western blot analysis of mitochondrial fraction of Irgm1+/+ and Irgm1-/- mouse BMDM cells untreated or treated with Bafilomycin A1 (300 nM, 3 h), probed with indicated antibodies."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "(I) Western blot analysis of mitochondrial fraction of control siRNA and IRGM siRNA transfected THP-1 cells untreated or treated with Bafilomycin A1 (300 nM, 3 h), probed with indicated antibodies."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(J) Seahorse XF Cell Mito stress test for analysis of mitochondrial function in Irgm1+/+ and Irgm1-/- mouse BMDM cells. The experiments were performed using the XF24 extracellular flux analyzer, and the flow chart showed the measurement of oxygen consumption rate (OCR)"
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "(K) Representative confocal images of control and IRGM siRNA transfected THP-1 cells stained with CMXRos red dye."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(L) Flow cytometry analysis of control siRNA and IRGM siRNA transfected THP-1 cells stained with CMXRos red dye (10 nM, 30 mins). (M) Graph depicts the normalized mean fluorescent intensity of control and IRGM knockdown THP-1 cells stained with CMXRos."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(N) Representative dot plot showing flow cytometry analysis of control and IRGM siRNA knockdown THP-1 cells stained with JC-1 dye (2 µM, 30 mins). At low mitochondrial membrane potential, JC-1 is predominantly a monomer that yields green fluorescence, whereas at mitochondrial membrane potential the dye aggregates producing a red to orange colored emission."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(P) Representative flow cytometry analysis of control and IRGM siRNA transfected THP-1 cells stained with MitoSox red dye (1µM, 20 min). The percentage of control and IRGM knockdown cells with increased red fluorescence (mitochondrial ROS generation) is depicted."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(Q) Representative flow cytometry analysis of control and IRGM siRNA transfected THP-1 cells stained with CellRox-green and CellRox-orange dye (1µM, 30 min)."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(A) Representative confocal images of Irgm1+/+ and Irgm1-/- mouse BMDMs processed for IF analysis with Tom20 (red) and dsDNA (green) antibody."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "(B) Representative STED microscopy images of control THP-1 cells processed for IF analysis with cGAS (green), dsDNA (red), and Lamin B1 (cyan) antibodies. (C) The graph depicts the percentage of cells with micronuclei in control siRNA and IRGM siRNA knockdown THP-1 cells."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(D-E) Representative STED microscopy images of Irgm1-/- mouse BMDMs (D) transfected with mCherry-cGAS and immunostained with dsDNA (green) antibody. The white line depicts the periphery of the cells. Scale bar, 3 µm. (E) The graph depicts the percentage of cells with micronuclei in Irgm1+/+ and Irgm1-/- mouse BMDMs."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "(F) The qRT-PCR analysis with cytosolic DNA (minus mitochondria) isolated from Irgm1+/+ and Irgm1-/- mouse BMDMs."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "(G) The qRT-PCR analysis with cytosolic DNA (minus mitochondria) isolated from control and IRGM siRNA transfected HT-29 cells."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(H) The qRT-PCR analysis with cytosolic DNA (minus mitochondria) isolated from control or IRGM shRNA or EtBr treated IRGM shRNA HT-29 (Rho0) cells."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(I) The qRT-PCR analysis with total RNA isolated from control or IRGM shRNA or EtBr treated IRGM shRNA HT-29 (Rho0) cells."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(J) The qRT-PCR analysis with cytosolic DNA (minus mitochondria) isolated from Irgm1+/+ and Irgm1-/- mouse BMDMs transfected with DNase I (15 μg, 6hr)."
NCBI gene IDs:
"DNase I: 282217
Irgm1: 15944"
Figure legend: "(K) The qRT-PCR analysis with RNA isolated from control and IRGM siRNA knockdown THP-1 cells electroporated with DNase I (5 μg, 1hr) as indicated."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(L-M) Representative confocal images of Irgm1+/+ and Irgm1-/- mouse BMDMs processed for IF analysis with (L) dsRNA (green) and Tom20 (red) antibodies. (M) The graph depicts the percentage of Irgm1+/+ and Irgm1-/- mouse BMDMs with dsRNA aggregates."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "(N) Representative confocal images of Irgm1-/- mouse BMDMs processed for IF analysis with RIG-I (red) and dsRNA (green) antibodies. Line profile: Co-localization analysis using line intensity profiles."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "Representative confocal images of Irgm1-/- mouse BMDMs processed for IF analysis with (O) Mda5 (red) and dsRNA (green) antibodies Co-localization analysis using line intensity profiles."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "Representative confocal images of Irgm1-/- mouse BMDMs processed for IF analysis with (P) Mda5 (red), dsRNA (green) and Tia1 (blue) antibodies (Scale bar, 3 µm). Line profile: Co-localization analysis using line intensity profiles."
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "(A) qRT-PCR analysis with total RNA isolated from Irgm1+/+ and Irgm1-/- mouse BMDMs transfected with control siRNA or cGAS siRNA or RIG-I siRNA or cGAS siRNA and RIG-I siRNA as indicated."
NCBI gene IDs:
"cGAS: 214763
RIG-I: 230073
Irgm1: 15944"
Figure legend: "(B) qRT-PCR analysis with total RNA isolated from HT-29 cells transfected with control siRNA or IRGM siRNA or doubly transfected with IRGM siRNA and cGAS siRNA or IRGM siRNA and RIG-I siRNA or transfected with three siRNAs as indicated."
NCBI gene IDs:
"cGAS: 115004
RIG-I: 23586
IRGM: 345611"
Figure legend: "(C) qRT-PCR analysis with total RNA isolated from HT-29 cells transfected with control siRNA or IRGM siRNA or doubly transfected with IRGM siRNA and STING siRNA or IRGM siRNA and MAVS siRNA or transfected with all the three siRNAs as indicated."
NCBI gene IDs:
"IRGM: 345611
MAVS: 57506
STING: 340061"
Figure legend: "(D) qRT-PCR analysis with total RNA isolated from HT-29 cells transfected with control siRNA or IRGM siRNA or doubly transfected with IRGM siRNA and MDA5 siRNA as indicated."
NCBI gene IDs:
"MDA5: 64135
IRGM: 345611"
Figure legend: "(E) qRT-PCR analysis with total RNA isolated from HT-29 cells transfected with control siRNA or IRGM siRNA or doubly transfected with IRGM siRNA and IRF3 siRNA as indicated."
NCBI gene IDs:
"IRF3: 3661
IRGM: 345611"
Figure legend: "(F) qRT-PCR analysis with total RNA isolated from HT-29 cells transfected with control siRNA or IRGM siRNA or doubly transfected with IRGM siRNA and STAT1 siRNA or IRGM siRNA and STAT2 siRNA as indicated."
NCBI gene IDs:
"IRGM: 345611
STAT1: 6772
STAT2: 6773"
Figure legend: "(H) MLL-ENL-expressing  CB cells and MOLM13  cells were transduced with Cas9  together with non-targeting (NT) sgRNA or IMPDH2-targeting sgRNAs (IMPDH2-KO1 and KO2) co-expressing tRFP657. Changes in the frequency of tRFP657+ cells (sgRNA-transduced cells) in cell cultures are shown. Results are normalized to the frequency of tRFP657+ cells at day 4, set to 1."
NCBI gene IDs:
"tRFP657: 
Cas9: 69900935
IMPDH2: 3615"
Figure legend: "(I) The tRFP657+ cells in (H) were sorted and subjected to  western blotting. The depletion of IMPDH2  protein in MLL-ENL  cells and MOLM13  cells was confirmed by  western blotting."
NCBI gene IDs:
"ENL: 4297
MLL: 4297"
Figure legend: "(A) Immunoblotting  of the  cord blood cells  and those expressing RUNX1-ETO  or MLL-AF9. The cells were incubated with/without 1 μM MPA  (M) and 100 μM Guanosine  (G) for 24 h."
NCBI gene IDs:
"MLL: 4297
AF9: 4300
RUNX1: 861
ETO: 862"
Figure legend: "(B) CB-MLL-AF9#2 cells were transduced with a Non-targeting (NT) control and an shRNA targeting p21  (sh-p21). Cells were incubated with/without 1 μM MPA  (M) and 100 μM guanosine  (G) for 24 hours. Total cell lysates were analyzed by western blotting  using the antibodies for p21  and Tubulin."
NCBI gene IDs:
"p21: 1026
MLL: 4297
AF9: 4300"
Figure legend: "(C) CB-MLL-AF9#2 cells transduced with NT or sh-p21  shRNAs were incubated with MPA  at the indicated concentration for 72 hours. Cell viability assays  were performed using  WST-1 in three technical replicates."
NCBI gene IDs:
"p21: 1026"
Figure legend: "(D) CB-MLL-AF9#2 cells were transduced by vector control or p53DD (dominant-negative) and were incubated with/without 1 μM MPA  (M) and 100 μM guanosine  (G) for 24 h. Total cell lysates were analyzed by  western blotting  using the antibodies for p53  and Tubulin. Note the elevated levels of endogenous p53  protein (upper arrow) in p53DD (lower arrow)-expressing cells."
NCBI gene IDs:
"MLL: 4297
AF9: 4300
p53: 7157"
Figure legend: "(F) Mouse bone marrow c-Kit+ cells derived from Trp53-/- mice  were transduced with MLL-AF9-GFP  and were transplanted into mice  to generate p53-deficient (p53-/-) leukemia  cells. GFP+ MLL-AF9 leukemia  cells  were collected from  bone marrows  of vehicle- or  FF-10501-01-treated wild-type and p53-/- leukemic mice. Expression levels of p53  and Tubulin  were assessed by western blotting 24 hours after the treatment."
NCBI gene IDs:
"GFP: 
MLL: 214162
AF9: 70122
p53: 22059
Trp53: 22059"
Figure legend: "(H) Kaplan-Meier survival curves of p53-/- MLL-AF9 leukemia mice  treated with vehicle or FF-10501-01or  DS-5272 (n = 6 per group). Statistical significance was evaluated by the log-rank test (left). Frequency of GFP+ leukemia  cells in peripheral blood at day 19 (right, n = 6 per group). A two-tailed unpaired t-test was used for the comparison. Data information: All data are shown as mean ± SEM."
NCBI gene IDs:
"MLL: 214162
AF9: 70122
p53: 22059"
Figure legend: "(B) The TLR-expressing BaκB cells were stimulated with the corresponding TLR ligands (100 ng/mL Pam3CSK4   for TLR2, 100 ng/mL LPS  for TLR4, 10 ng/mL Flagellin      for TLR5, 100 ng/ml R848  for TLR7) with titrating doses of MPA  (1 - 10 μM). GFP  expression was assessed 24 hours after the stimulation."
NCBI gene IDs:
"TLR2: 24088
TLR4: 21898
TLR5: 53791
TLR7: 170743"
Figure legend: "(C) 293T  cells were transfected with FLAG-tagged TRAF6  and HA-tagged K63-ubiquitin. After 24 hours, these cells were treated with 3 or 10 μM MPA  (M-3 μM or M-10 μM) with/without 100 μM guanosine  (G). IRAK1/4 inhibitor (IRAK1/4 i) was also used as a control. Whole-cell extracts were immunoprecipitated  with anti-FLAG  antibody, and ubiquitinated TRAF6  was detected with anti-HA  antibody."
NCBI gene IDs:
"FLAG: 
HA: 
ubiquitin: 
TRAF6: 22034"
Figure legend: "(D, Murine bone marrow-derived macrophages (BMDMs) were treated with vehicle, 10 μM MPA  alone (D) N=3 (technical replicates) per group. mRNA levels of TNF-α and  IL-1β were measured by qPCR. Two-tailed unpaired t-tests were used for the comparison in (D). Data information: All data are shown as mean ± SEM."
NCBI gene IDs:
"IL-1β: 16176
TNF-α: 21926"
Figure legend: "E) Murine bone marrow-derived macrophages (BMDMs) were treated with vehicle, 10 μM MPA  alone or co-treated with vehicle, 10 μM MPA  (M), 100 ng/mL Pam3CSK4  and 100 μM Guanosine  (G) for 4 hours (E), as indicated. N=3 (technical replicates) per group. mRNA levels of TNF-α and IL-1β  were measured by qPCR. Ordinary one-way ANOVA was used for the comparison in (E). Data information: All data are shown as mean ± SEM."
NCBI gene IDs:
"IL-1β: 16176
TNF-α: 21926"
Figure legend: "(G) MLL-AF9-expressing CB  cells (CB-MLL-AF9#1) were pretreated with 10 μM MPA  for 2 hours and then treated with 1000 ng/mL Pam3CSK4  for 0, 30, 60 Cells were lysed and subjected to SDS-PAGE. Levels of total IκBα, phosphate-p38, total p38  were evaluated by western blotting."
NCBI gene IDs:
"MLL: 4297
AF9: 4300"
Figure legend: "(E) Example images of brightfield and fluorescently labelled EU (Alexa Fluor 488) of hENT1 and hsvTK cells (PN10567) assayed for global cellular transcription. Scale bars represent 5 µm. (F) Change in EU labelling signal with different lengths of EU incubations, measured by flow cytometry (in PN10597). The mean and standard deviation (SD) of the population medians of at least 200,000 cells in experimental triplicates are shown in black. The dark green line is the OLS linear regression fitted on the mean data between 2 and 12 minutes."
NCBI gene IDs:
"ENT1: 2030
TK: 24271467"
Figure legend: "(H) Medians of global translation (solid black line) and IQR (shaded area) of cdc25-22 (PN143) cells grown at 30 °C and grouped in length bins of 2 µm. Bins containing more than 30 cells are shown. The solid red lines represent a locally estimated scatterplot smoothing (LOESS) function fitted on the single-cell data."
NCBI gene IDs:
"cdc25: 2542632"
Figure legend: "(F) Example images of brightfield and EGFP-PCNA fluorescence in CCP∆ EGFP-pcn1 cells (PN6001). The dashed lines in the EGFP-PCNA channel delimit the cell masks generated from the brightfield image. Cells with visible foci in the EGFP-PCNA channel are highlighted in yellow and marked with arrows. Scale bars represent 5 µm."
NCBI gene IDs:
"EGFP: 
pcn1: 2540020"
Figure legend: "Human brain  slices were infected with HSV-1-GFP  (1˟106 PFU/ml) and  HSV-2-GFP (1˟106 PFU/ml) for 72 h, visualized microscopically"
NCBI gene IDs:
"GFP: "
Figure legend: "Human brain  slices were infected with HSV-1-GFP  (1˟106 PFU/ml) and HSV-2-GFP  (1˟106 PFU/ml) for 72 h, and lysed for analysis of GSDME  and vinculin."
NCBI gene IDs:
"GFP: "
Figure legend: "(C, SH-SY5Y cells were transfected with CASP2  gRNA-Cas9 RNPs  or AAVS1  gRNA-Cas9 RNPs  and infected with HSV-2. Lysates were isolated 16 h post infection and immunoblotted  for GSDME, CASP2, cleaved caspase 3 (CL-CASP3), cleaved PARP  (CL-PARP) and vinculin  (C)."
NCBI gene IDs:
"AAVS1: 17
Cas9: 69900935
CASP2: 835"
Figure legend: "(H) SH-SY5Y  cells transfected with AAVS1  or CASP2  gRNA-Cas9 RNPs  and infected with HSV-2  for 16 h and examined for morphological  changes by microscopy. Boxes indicate areas highlighted in the zoomed images. Arrows indicate ballooning or syncytial cells."
NCBI gene IDs:
"AAVS1: 17
Cas9: 69900935
CASP2: 835"
Figure legend: "(B, SH-SY5Y cells transfected with AAVS1  or BID  gRNA-Cas9 RNPs  were infected with HSV-2. Lysates were isolated 16 h post infection and immunoblotted  for GSDME, CL-CASP3  and CL-PARP  (B)"
NCBI gene IDs:
"AAVS1: 17
BID: 637
Cas9: 69900935"
Figure legend: "C) SH-SY5Y cells transfected with AAVS1  or BID  gRNA-Cas9 RNPs  were infected with HSV-2. Lysates were isolated 16 h post infection and assayed for CASP3  activity (C). Data information: All data shown are representative of at least 3 independent experiments. Data are presented as mean ± s.d. in all graphs. ∗∗∗p ≤ 0.001 two-way ANOVA in C"
NCBI gene IDs:
"AAVS1: 17
BID: 637
Cas9: 69900935"
Figure legend: "B) SH-SY5Y cells were infected with HSV-2  (MOI=1) for the indicated time  intervals, and analyzed for mRNA levels of the ER  stress response genes BIP, ATF6  and CHOP  by RT-qPCR (B). Data information: All data shown are representative of at least 3 independent experiments. Data are presented as mean ± s.d. in all graphs. ∗∗p ≤ 0.01; ∗∗∗p ≤ 0.001; ∗∗∗∗p ≤ 0.0001 (Mann-Whitney test, two-tailed in B"
NCBI gene IDs:
"ATF6: 22926
CHOP: 1649
BIP: 3309"
Figure legend: "(L) SH-SY5Y cells transduced with lenti-plasmid BIP  or empty vector control were infected with HSV-2  (MOI=1, 16 h). Lysates were isolated and immunoblotted  for GSDME  and tBID."
NCBI gene IDs:
"BIP: 3309"
Figure legend: "SH-SY5Y cells were infected with HSV-2 for the indicated time  intervals. Total RNA was analyzed for spliced XBP1  (XBP1s) by  RT-qPCR  Data information: All data shown are representative of at least 3 independent experiments. Data are presented as mean ± s.d. in all graphs. ∗∗p ≤ 0.01; ∗∗∗p ≤ 0.001 (Mann-Whitney test, two-tailed in B"
NCBI gene IDs:
"XBP1: 7494"
Figure legend: "(E) SH-SY5Y  cells transfected with AAVS1  or IRE1A  gRNA-Cas9 RNPs  were infected with HSV-2 (MOI=1, 16 h). Lysates  and supernatant  were isolated and immunoblotted  for IRE1α, GSDME, cytochrome c  and HMGB1  release."
NCBI gene IDs:
"AAVS1: 17
Cas9: 69900935
IRE1A: 2081"
Figure legend: "(B-D) iPSC-derived microglia  cells were treated with the conditioned medium from HSV-2-infected control and GSDME-depleted SH-SY5Y  cells for 8 h. Total RNA was isolated and analyzed for expression of IL6, TNFA, and CXCL10  by RT-qPCR. Data information: All data shown are representative of at least 3 independent experiments. Data are presented as mean ± s.d. in all graphs. ∗∗∗p ≤ 0.001; ∗∗∗∗p ≤ 0.0001 (Two-way ANOVA in B-D"
NCBI gene IDs:
"CXCL10: 3627
GSDME: 1687
IL6: 3569
TNFA: 7124"
Figure legend: "(E-G) Conditioned medium from SH-SY5Y cells with HSV-2  infection (MOI=1, 24 h) was transferred to THP1  cells (WT, STING-/-, MYD88-/-, TRIF-/- and MAVS-/-). Total RNA was isolated 8h later and analyzed for expression of IL6  (E), TNFA  (F), and CXCL10  (G) by  RT-qPCR. Data information: All data shown are representative of at least 3 independent experiments. Data are presented as mean ± s.d. in all graphs. ∗∗∗p ≤ 0.001; ∗∗∗∗p ≤ 0.0001 Wilcoxon matched-pairs test in E-G)."
NCBI gene IDs:
"CXCL10: 3627
IL6: 3569
MAVS: 57506
MYD88: 4615
STING: 340061
TRIF: 148022
TNFA: 7124"
Figure legend: "B. Quantification of PLAs  between BRCA2  and DPP9  in control HeLa  WT cells treated with non-targeting siRNA (siNT) or silenced with the indicated oligos. 300 ng / mL MMC  was added for 24 h. Each dot represents the number of PLA  events in a single cell, from two to seven biological replicates (siNT-MMC  (n = 6), siNT+MMC  (n = 7), siDPP9-MMC  (n = 4), siDPP9+MMC (n = 5), siBRCA2-MMC  (n = 2), siBRCA2+MMC  (n = 3), siFLNA-MMC  (n = 5), siFLNA+MMC  (n = 6), NgtCntrl-MMC  (n = 3), NgtCntrl+MMC  (n = 6)). The number of foci are shown based on their cellular localisation. Data were analysed by a two-way ANOVA, with Tukey's Multiple Comparison test. Shown are Mean ± SEM (* = p ≤ 0.05, **** = p ≤ 0.0001). C. Representative PLA  images showing close proximity between endogenous DPP9  and endogenous BRCA2  in HeLa WT cells. Exposure of cells to MMC  triggers more PLA  events (white). Phalloidin  (green) stains actin filaments, DAPI  (blue) stains  the nucleus. Scale bar 10 µm. Anti-BRCA2: RRID:AB_2259370, anti-DPP9: RRID:AB_2889071"
NCBI gene IDs:
"BRCA2: 675
DPP9: 91039
FLNA: 2316"