EMBO/SourceData huggingface dataset:
Figure legend: "A- HEI-OC1 cells containing a Tlr4 deletion (Tlr4-/-) were compared to HEI-OC1 non-targeting (NT) control cells and assessed for cell viability (A), AnnexinV/propidium iodide staining (B), following cisplatin treatment at the indicated concentrations (n=3 independent biological replicates). Data Information: In all panels data are presented as mean and standard deviation. Statistical comparisons to NT at the same cisplatin concentration were assessed by 2-way (A, B) *, P&lt;.05; **, P&lt;.0001(Bonferroni test)."
NCBI gene IDs:
"Tlr4: 21898"
Figure legend: "A IL-6 secretion in HEI-OC1 cells treated with 100 pg/mL LPS or 20μM cisplatin (n=3 or 4 independent biological replicates). B IL-6 secretion in TLR4-/- cells transfected with empty vector (EV) or mouse Tlr4 (mTlr4) following treatment with 20μM cisplatin (n=6 independent biological replicates). Data information: In all panels data are presented as mean and standard deviation. Statistical comparisons to 0 hr time point were assessed by 2-way ANOVA. ns, not significant; *, P&lt;.05; **, P&lt;.01; ***, P&lt;.001; ****, P&lt;.0001 (Dunnett's test)."
NCBI gene IDs:
"TLR4: 21898
Tlr4: 21898"
Figure legend: "C Il6 and Tlr4 transcript levels in HEI-OC1 cells following treatment with 20μM cisplatin for the indicated times (n=3 independent biological replicates). Data information: In all panels data are presented as mean and standard deviation. Statistical comparisons to 0 hr time point were assessed by 2-way ANOVA. ns, not significant; *, P&lt;.05; **, P&lt;.01; ***, P&lt;.001; ****, P&lt;.0001 (Dunnett's test). "
NCBI gene IDs:
"Il6: 16193
Tlr4: 21898"
Figure legend: "B Hair cell viability in larval zebrafish pre-treated with control-, tlr4ba- and/or tlr4bb-targeting morpholino oligonucleotides (MO) and subsequently treated with 15 μM cisplatin. Data information: In both panels each data point represents a score of hair cell integrity in an individual animal (taken from multiple samples per animal) with lines representing mean and standard deviation. Statistical comparisons to control morpholino (B, except as indicated in blue) were assessed by one-way ANOVA. *, P&lt;.05; **, P&lt;.01; ****, P&lt;.0001 (Tukey test)."
NCBI gene IDs:
"tlr4ba: 403131
tlr4bb: 403132"
Figure legend: "(A)  QRT-PCR assay of  PAX6, SOX1,   NKX2-1,  NKX2-2, TBR1  and TBR2  during dorsal (up) and  ventral (down)  neural  differentiation. (B) QRT-PCR assay of SOX1-OT V1 during dorsal (up) and ventral  (down) neural  differentiation Data information: Data are presented as mean ±SEM from three independent experiments (n=3). *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001 (unpaired two-tailed Student's t-test)."
NCBI gene IDs:
"TBR2: 8320
NKX2-1: 7080
NKX2-2: 4821
PAX6: 5080
SOX1: 6656
TBR1: 10716"
Figure legend: "(C and D) Immunostaining assay of MAP2 (green) in control and SOX1KO cells on day 35 of dorsal neural  differentiation (C), and quantiﬁcation of MAP2+ cells (D), p=0.0001. Scale bar, 100 μm. Data information: Data are presented as mean ±SEM from three independent experiments (n=3). ***p&lt;0.001 versus Ctrl group (unpaired two-tailed Student's t-test)."
NCBI gene IDs:
"SOX1: 6656"
Figure legend: "(F and G)  Immunostaining assay of GABA (green) in control and SOX1KO cells on day 35 of  ventral neural differentiation (F), and quantiﬁcation of GABA+ cells (G), p=0.0001. Scale bar, 100 μm. Data information: Data are presented as mean ±SEM from three independent experiments (n=3). ***p&lt;0.001 versus Ctrl group (unpaired two-tailed Student's t-test)."
NCBI gene IDs:
"SOX1: 6656"
Figure legend: "(H and I)  Immunostaining assay of MAP2 (green) after SOX1 overexpression in V1-PAKI cells on day 35 of dorsal neural  differentiation (H), and quantiﬁcation of MAP2+ cells (I), p=0.0001 (V1-PAKI), p=0.0001 (V1-PAKI+ptSOX1+dox). Scale bar, 100 μm. Data information: Data are presented as mean ±SEM from three independent experiments (n=3). ***p&lt;0.001 versus Ctrl group ; ###p&lt;0.001 versus -dox group (one-way ANOVA)."
NCBI gene IDs:
"SOX1: 6656"
Figure legend: "(J and K) Immunostaining assay  of GABA (green) after SOX1 overexpression in V1-PAKI cells on day 35 of  ventral neural differentiation (J), and quantiﬁcation of GABA+ cells (K), p=0.0001 (V1-PAKI), p=0.0002 (V1-PAKI+ptSOX1+dox). Scale bar, 100 μm. Data information: Data are presented as mean ±SEM from three independent experiments (n=3). ***p&lt;0.001 versus Ctrl group ; ###p&lt;0.001 versus -dox group (one-way ANOVA)."
NCBI gene IDs:
"SOX1: 6656"
Figure legend: "(A and B) Enrichment of H3K14Ac (left) and H3K27Ac (right) on SOX1  promoter region in control and  V1-PAKI  cells on day 16 of dorsal neural differentiation (A), p=0.0046 (H3K14Ac), p=0.0223 (H3K27Ac) and  ventral neural differentiation (B), p=0.0499 (H3K14Ac), p=0.0022 (H3K27Ac). Data information: Data are presented as mean ±SEM from three independent experiments (n=3). *p&lt;0.05, **p&lt;0.01 versus Ctrl group (unpaired two-tailed Student's t-test)."
NCBI gene IDs:
"SOX1: 6656"
Figure legend: "(L) Enrichment of   RNA polymerase Ⅱ   on  SOX1 promoter region after Bufexamac treatment in V1-PAKI  cells on day 16 of  dorsal  (left, p=0.0007 (V1-PAKI), p=0.0002 (+Buf)) and ventral (right, p=0.0083 (V1-PAKI), p=0.0276 (+Buf)) neural  differentiation. Data information: Data are presented as mean ±SEM from three independent experiments (n=3). *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001 versus Ctrl group ; #p&lt;0.05, ##p&lt;0.01, ###p&lt;0.001 versus V1-PAKI group ; (one-way ANOVA)."
NCBI gene IDs:
"SOX1: 6656"
Figure legend: "(B and C)  RIP  analysis for endogenous  interaction between  HDAC10 and SOX1-OT V1 on day 16 of dorsal neural  differentiation (B), p=0.0085 and ventral neural differentiation (C), p=0.0152. Data information: Data are presented as mean ±SEM from three independent experiments (n=3). *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001 versus IgG group (unpaired two-tailed Student's t-test)."
NCBI gene IDs:
"SOX1: 6656"
Figure legend: "(D and E) Enrichment of HDAC10 on SOX1 promoter region in control and V1-PAKI cells on day 16 of  dorsal neural  differentiation (D), p=0.0052 and ventral neural  differentiation (E), p=0.0001. Data information: Data are presented as mean ±SEM from three independent experiments (n=3). *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001 versus Ctrl group (unpaired two-tailed Student's t-test)."
NCBI gene IDs:
"SOX1: 6656"
Figure legend: "(G and H)  Immunostaining assay of SOX1  (red) after SOX1-OT V1, SOX1-OT V1-5P or SOX1-OT V1-3P overexpression in V1-PAKI cells on day 16 of  dorsal neural differentiation (G), and quantiﬁcation of SOX1+ cells (H), p=0.0001 (V1-PAKI), p=0.0001 (ptV1+dox), p=0.0001 (pt5P+dox). Scale bar, 100 μm. (I and J) Immunostaining assay of SOX1 (red) after  SOX1-OT V1, SOX1-OT V1-5P or SOX1-OT V1-3P overexpression in V1-PAKI cells on day 16 of ventral neural  differentiation (I), and quantiﬁcation of SOX1+ cells (J), p=0.0001 (V1-PAKI), p=0.0001 (ptV1+dox), p=0.0001 (pt5P+dox). Scale bar, 100 μm. Data information: Data are presented as mean ±SEM from three independent experiments (n=3). *p&lt;0.05, ***p&lt;0.001 versus Ctrl group ; #p&lt;0.05, ##p&lt;0.01, ###p&lt;0.001 versus -dox group (one-way ANOVA)."
NCBI gene IDs:
"SOX1: 6656"
Figure legend: "(A and B) Immunostaining assay of ASCL1 (green) in control, V1-PAKI and SOX1KO cells on day 25 of dorsal neural differentiation (A), and quantiﬁcation of ASCL1+ cells (B), p=0.0021 (V1-PAKI), p=0.0024 (SOX1KO). Scale bar, 100 μm. (C and D)  Immunostaining assay  of ASCL1 (green) in control, V1-PAKI  and SOX1KO cells on day 25 of ventral neural differentiation (C), and quantiﬁcation of ASCL1+ cells (D), p=0.0003 (V1-PAKI), p=0.0004 (SOX1KO). Scale bar, 100 μm. Data information: Data are presented as mean ±SEM from three independent experiments (n=3). **p&lt;0.01, ***p&lt;0.001 versus Ctrl group (unpaired two-tailed Student's t-test)."
NCBI gene IDs:
"SOX1: 6656"
Figure legend: "(E and F) Immunostaining assay  of ASCL1  (green) after SOX1 overexpression in V1-PAKI cells on day 25 of  dorsal neural differentiation (E), and quantiﬁcation of ASCL1+ cells (F), p=0.0001 (V1-PAKI), p=0.0001 (ptSOX1+dox). Scale bar, 100 μm. (G and H)  Immunostaining assay  of  ASCL1 (green) after SOX1 overexpression in V1-PAKI cells on day 25 of ventral neural differentiation (G), and quantiﬁcation of  ASCL1+ cells (H), p=0.0001 (V1-PAKI), p=0.0001 (ptSOX1+dox). Scale bar, 100 μm. (I and J)  Immunostaining assay of MAP2 (green) after  ASCL1 overexpression in V1-PAKI cells on day 35 of dorsal neural  differentiation (I), and quantiﬁcation of MAP2+ cells (J), p=0.0001 (V1-PAKI), p=0.0001 (ptASCL1+dox). Scale bar, 100 μm. (K and L)  Immunostaining assay  of GABA (green) after  ASCL1  overexpression in V1-PAKI  cells on day 35 of ventral neural differentiation (K), and quantiﬁcation of GABA+ cells (L), p=0.0001 (V1-PAKI), p=0.0001 (ptASCL1+dox). Scale bar, 100 μm. Data information: Data are presented as mean ±SEM from three independent experiments (n=3). ***p&lt;0.001 versus Ctrl group ; ###p&lt;0.001 versus -dox  group (one-way ANOVA)."
NCBI gene IDs:
"ASCL1: 429
SOX1: 6656"
Figure legend: "(A and B) Immunostaining assay  of SOX1 (red) in control, V1-PAKI  and  SOX1KO cells on day 40 of dorsal (A) and  ventral (B) organoids differentiation. Scale bar, 100 μm. (C) Immunostaining assay of MAP2  (green) in control, V1-PAKI  and SOX1KO cells on day 40 of dorsal organoids differentiation. Scale bar, 100 μm. (D)  Immunostaining assay  of GABA (green) in control, V1-PAKI and SOX1KO cells on day 40 of  ventral organoids  differentiation. Scale bar, 100 μm."
NCBI gene IDs:
"SOX1: 6656"
Figure legend: "(E and F) Immunostaining assay  of SOX1  (red) after SOX1-OT V1 overexpression in V1-PAKI cells on day 40 of dorsal (E) and ventral (F) organoids differentiation. Scale bar, 100 μm. (G)  Immunostaining assay of MAP2  (green) after SOX1-OT V1 overexpression in V1-PAKI cells on day 40 of  dorsal organoids differentiation. Scale bar, 100 μm. (H) Immunostaining assay  of GABA (green) after SOX1-OT V1 overexpression in V1-PAKI  cells on day 40 of  ventral organoids differentiation. Scale bar, 100 μm."
NCBI gene IDs:
"SOX1: 6656"
Figure legend: "B) Representative IRM and TIRF microscopy images showing microtubule positions and Tau-meGFP intensities for different PTM variants (grey: wild type; blue: Ttll1-/-; yellow: Ttll7-/-; green: Ttll1-/-Ttll7-/-; pink: Atat1‑/‑). In the last column, false-coloured TIRF images highlight differences of Tau-meGFP intensities on different types of microtubules (Movie EV1). C) Quantification of integrated intensity of Tau-meGFP on GMPCPP microtubules in three independent sets of experiments performed with independently purified tubulin samples. Single assays (Fig EV2A) of one experiment were combined after normalisation to the wild-type microtubule values (A.U. = arbitrary units). Each data point represents the normalised fluorescence intensity value of one microtubule. D) Summary quantification the three independent experiments shown in (C). Each point is a normalised mean of the triplicates, error bars represent standard deviation."
NCBI gene IDs:
"Atat1: 73242
Ttll1: 319953
Ttll7: 70892"
Figure legend: "E) Saturation curve of increasing concentration Tau-mCherry binding to GMPCPP wild-type and Ttll1-/-Ttll7-/- microtubules. Each data point is shown as mean ± standard deviation of the raw integrated intensity values (A.U. ×104) of three experiments with independently purified tubulin samples (Fig EV2D). Dissociation constants Kd and R2 coefficient from non-linear fits of each microtubule type are indicated below the plot."
NCBI gene IDs:
"Ttll1: 319953
Ttll7: 70892"
Figure legend: "Confirmation of ALDH1A3 mRNA levels of gene expression in pro-invasive (Ren13 and Ren86) and non-pro-invasive (Ren28 and Ren50) tumors. Average ± SD of 4-6 independent replicates per group were analyzed by Mann-Whitney test *p &lt; 0.05 **p &lt; 0.01."
NCBI gene IDs:
"ALDH1A3: 220"
Figure legend: "(a) MDCK/pGFP-LC3 cells infected with a wild-type or ΔactA2 strain of L. monocytogenes were stained with an anti-Listeria antibody (red) and rhodamine phalloidin (stains F-actin; light blue). Scale bars, 10 μm. Arrowheads indicate GFP-LC3-positive bacteria. (b) High magnification of framed images in a, and graphs show intensity of the fluoresence signal along the arrow. (c) Quantification of the number of GFP-LC3-positive bacteria shown in a. Data are mean ± s.e.m. At least 500 bacteria were counted in each experiment (n = 7 and 6 experiments at 2 and 4 h, respectively)."
NCBI gene IDs:
"actA2: 17175811
LC3: 84557"
Figure legend: "(d) LC3 levels in infected MDCK cells. MDCK cells were infected with wild-type or ΔactA2 bacteria for the indicated times. EBSS (Earle's balanced salt solution, a starvation medium) and rapamycin (100 μg ml−1) were used as controls."
NCBI gene IDs:
"actA2: 17175811
LC3: 84557"
Figure legend: "(e-f) Intracellular survival of wild-type or ΔactA2 bacteria in MDCK cells (e; n = 8), MDCK cells treated with 10 mM 3-MA (f; n = 4),"
NCBI gene IDs:
"actA2: 17175811"
Figure legend: "(e-h) Intracellular survival of wild-type or ΔactA2 bacteria in atg5+/+ MEF cells (g; n = 8 and 7 for wild-type and ΔactA2, respectively) or atg5−/− MEF cells (h; n = 4 and 3 for wild-type and ΔactA2, respectively). Data are presented as the number of colony-forming units (CFU) relative to that at 30 min after infection, and are mean ± s.e.m. WT, wild type."
NCBI gene IDs:
"actA2: 17175811
atg5: 11793"
Figure legend: "(b, c) Quantification of the number of GFP-LC3-positive bacteria (b) or actin-accumulating bacteria (c). Data are mean ± s.e.m., at least 500 bacteria were counted in each experiment (n = 3 experiments)."
NCBI gene IDs:
"LC3: 84557"
Figure legend: "(d) Colocalization of ubiquitin with ΔactA2. MDCK/pGFP-LC3 cells infected with ΔactA2 bacteria were stained with an anti-Listeria antibody (blue) and anti-ubiquitin antibody (red). Scale bars, 10 μm. Arrowheads indicate GFP-LC3-positive or ubiquitin-positive bacteria. (e) High magnification of framed image in d, and the graph shows the intensity of the fluorescence signal along the arrow. (f) Quantification of the number of GFP-LC3-positive, ubiquitin-positive or GFP-LC3- and ubiquitin-positive bacteria. Data are mean ± s.e.m., at least 500 bacteria were counted in each experiment (n = 3 experiments)."
NCBI gene IDs:
"actA2: 17175811
LC3: 84557"
Figure legend: "(g) Immunogold electron micrograph of MDCK/pGFP-LC3 cells infected with ΔactA2. Gold particles of 5 nm (arrowheads) indicate GFP-LC3, and gold particles of 10 nm (arrows) indicate ubiquitin. Scale bars, 0.5 μm."
NCBI gene IDs:
"actA2: 17175811
LC3: 84557"
Figure legend: "(h) Kinetics of the generation of GFP-LC3-positive or ubiquitin-positive bacteria. Data are mean ± s.e.m., at least 500 bacteria were counted in each experiment (n = 3 experiments). *P 0.001. (i) Quantification of the number of ubiquitin-positive or GFP-LC3-positive bacteria. MDCK/pGFP-LC3 cells infected with wild-type or ΔactA2 bacteria were untreated or treated with 3-MA (10 mM). Data are mean ± s.e.m., at least 500 bacteria were counted in each experiment (n ≥ 3 experiments). Ub, ubiquitin. WT, wild type."
NCBI gene IDs:
"actA2: 17175811
LC3: 84557"
Figure legend: "(a) Quantification of the number of ubiquitin-positive, p62-positive or GFP-LC3-positive bacteria. MDCK/pGFP-LC3/pp62-3×Myc cells were infected with a wild-type or ΔactA2 strain of L. monocytogenes for 2 h. Data are mean ± s.e.m., at least 500 bacteria were counted in each experiment (n = 6 experiments)."
NCBI gene IDs:
"p62: 
actA2: 17175811
LC3: 84557"
Figure legend: "(b) Colocalization of p62 with ΔactA2. MDCK/pGFP-LC3/pp62-3×Myc cells were stained with an anti-ubiquitin antibody (light blue), anti-Myc antibody (red), DAPI (white) and anti-GFP-LC3 (green). Scale bar, 10 μm. Arrowheads indicate GFP-LC3-, ubiquitin- or p62-positive bacteria."
NCBI gene IDs:
"p62: 
actA2: 17175811
LC3: 84557"
Figure legend: "(c) Quantification of the number of ubiquitin-positive, p62-positive or GFP-LC3-positive bacteria. p62−/−/p62 cells were infected with ΔactA2 bacteria for 2 h. Data are mean ± s.e.m., at least 500 bacteria were counted in each experiment (n = 6 and 3 experiments for p62−/− and p62−/−/p62, respectively)"
NCBI gene IDs:
"p62: 
actA2: 17175811
LC3: 84557"
Figure legend: "(d, e) Intracellular survival of wild-type or ΔactA2 bacteria in p62−/− cells (d) or p62−/−/p62 cells (e; colony-forming units, CFU, relative to CFU 30 min after infection). Data are presented as mean ± s.e.m. (n ≥ 4 experiments)."
NCBI gene IDs:
"p62: 
actA2: 17175811"
Figure legend: "(g) Generation of p62-3×Myc mutants in p62−/− cells."
NCBI gene IDs:
"p62: "
Figure legend: "(h) Quantification of the number of GFP-positive or GFP-LC3-positive bacteria. p62−/−/p62 (wild type, ΔLIR, ΔUBA, ΔLIR-ΔUBA or K7AD69A) cells were infected with ΔactA2 bacteria and stained with anti-bacteria and anti-Myc antibodies (Supplementary Information, Fig. S4e). Data are mean ± s.e.m., at least 500 LC3 were counted in each experiment (n = 3 experiments). P 0.001 versus p62-positive LC3 in p62−/−/p62 wild-type cells, P 0.001 versus GFP-p62-positive bacteria in p62−/−/ubiquitinwild-type cells. Ub, ubiquitin. WT, wild type. A full scan of g is shown in Supplementary Information, Fig. S7."
NCBI gene IDs:
"p62: 
actA2: 17175811
LC3: 84557"
Figure legend: "(b-e) The series of pEGFP-ActA-Q79C constructs was transfected into COS-7 cells. Cells were fixed with 4% Paraformaldehyde after 18 h and stained with an anti-Arp2 antibody (b), an anti-VASP antibody (c), an anti-ubiquitin antibody (d) or an anti-p62 antibody (e; red). Scale bars, 10 μm. Arrowheads indicate Arp2-, VASP-, ubiquitin- or p62-positive Q79C. Ub, ubiquitin."
NCBI gene IDs:
"ActA: 17175811"
Figure legend: "(b-e) The series of pEGFP-ActA-170 constructs was transfected into COS-7 cells. Cells were fixed with 4% Paraformaldehyde after 14 h and stained with an anti-Arp2 antibody (b), an anti-VASP antibody (c), an anti-ubiquitin antibody (d) or an anti-p62 antibody (e; red). Scale bars, 10 μm. Arrowheads indicate Arp2-, VASP-, ubiquitin- or p62-positive 170. Ub, ubiquitin."
NCBI gene IDs:
"ActA: 17175811"
Figure legend: "Ala/Phe substitutions of aa 239-244 were introduced in the NCT ectodomain to evaluate the role of this region in the regulation of GSEC processivity. Aβ38, Aβ40, and Aβ42 levels present in the conditioned medium collected from KO NCT MEF cells rescued with WT or respective mutant NCT GSECs and transiently expressing with APPC99 were quantified by ELISA. Aβ(38+40)/42 ratio was calculated to determine GSEC processivity towards APPC99. DKO PSEN1/PSEN2 MEFs rescued with the indicated FAD PSEN1 mutant and transduced with APPC99 were used as references."
NCBI gene IDs:
"PSEN1: 5663
PSEN2: 5664"
Figure legend: "Aβ profiles (% contribution of individual Aβ37, Aβ38, Aβ40, and Aβ42 peptides to the total Aβ levels (Aβ37+38+40+42)) in the conditioned medium collected from WT or mutant (NCT) MEF cells lines co-expressing WT or mutant APPC99 substrates were assayed by ELISA. Schematic models of the tested GSEC-APP complexes are shown."
NCBI gene IDs:
"NCT: 59287"
Figure legend: "(b) Images of MCF10A cells expressing GFP-LC3G120A and mCherry-LC3; note no recruitment of GFP-LC3G120A to the entotic vacuole. Scale bar, 15 μm. (c) LC3 is recruited from the host-cell cytosol onto the entotic vacuole membrane. Data points are the mean fluorescence intensity of GFP-LC3 on vacuoles versus cytoplasm for two independent cell-in-cell structures (see Supplementary Movie S2)."
NCBI gene IDs:
"LC3: 440738///81631///84557"
Figure legend: "(c,d) Quantification of LC3 recruitment (c), and cell fate (d), of mixed cell-in-cell structures for which host or internalized cells were treated with ATG5 siRNA. Data represent mean±s.e.m.from three separate experiments; n, total number of structures analysed; *P0.01, **P0.004."
NCBI gene IDs:
"ATG5: 9474"
Figure legend: "(a) The fate of internalized cells (control MCF10A and MCF10A expressing E7 and Bcl2) was measured with and without autophagy inhibition. Data show the percentage of internalized cell release with autophagy inhibition, compared with each control without autophagy inhibition; mean±s.e.m. from at least three independent experiments (total cell numbers analysed: ATG5 siRNA, 261 cells; Bcl2 ATG5 siRNA, 97 cells; 3-MA, 170 cells; Bcl2 3-MA, 112 cells); *P0.05, **P0.02."
NCBI gene IDs:
"ATG5: 9474
Bcl2: 596
E7: 1489445"
Figure legend: "(b) Effects of Y27632, 3-MA and VPS34 and ATG5 siRNA on MCF10A cell-in-cell formation in suspension for 7 h; &gt;300 cells per condition were scored for cell-in-cell formation; ±s.e.m.from three independent experiments; **P0.004."
NCBI gene IDs:
"ATG5: 9474
VPS34: 5289"
Figure legend: "(c) Representative images of an MCF10A E7+Bcl2 cell-in-cell structure formed in soft agar. The arrow marks LC3 recruitment around internalized cells. Scale bar, 5 μm."
NCBI gene IDs:
"Bcl2: 596
E7: 1489445"
Figure legend: "(d) Quantification of MCF10A E7+Bcl2 cell-in-cell structures 48 h after seeding into soft agar (white bars), and colony formation after 2 weeks (grey bars). Data represent mean±s.e.m.from three independent experiments; *P0.03, **P0.004, ***P0.001. (e) Representative wells for data in d. The insets show higher magnifications."
NCBI gene IDs:
"Bcl2: 596
E7: 1489445"
Figure legend: "(f) Quantification of MCF10A E7+Bcl2 colony formation with Atg5 knockdown with two separate siRNAs. Data represent mean±s.e.m.from three independent experiments; *P0.001. (g) Representative wells for data in f. The insets show higher magnifications. See also Supplementary Movie S6."
NCBI gene IDs:
"Atg5: 9474
Bcl2: 596
E7: 1489445"
Figure legend: "(a) Time-lapse images of MCF10A cell-in-cell structures with an internalized cell that undergoes apoptosis. The arrows mark the recruitment of LC3 around apoptotic fragments (see Supplementary Movie S7). Scale bar, 10 μm. (b) Quantification of LC3 recruitment to apoptotic internalized cells in the presence of ATG5 or FIP200 siRNA; n, number of cells analysed; ***P0.0001, chi-squared test."
NCBI gene IDs:
"ATG5: 9474
FIP200: 9821"
Figure legend: "(c) Apoptotic U937 cells expressing H2B-mCherry phagocytized by J774 macrophages expressing GFP-LC3. Confocal images show LC3 recruitment to an engulfed corpse (arrow; see Supplementary Movie S8). Scale bar, 15 μm. (d) Quantification of LC3 recruitment to apoptotic phagosomes in control and Atg5-shRNA-expressing cells; ***P0.0001, chi-squared test."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "(f) Representative images of apoptotic cell phagocytosis and degradation in control (n=21) and Atg5 shRNA (n=21) J774 GFP-LC3 cells; ***P0.0001, chi-squared test. Scale bar, 10 μm. See also Supplementary Fig. S3."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "(a) Representative images of a J774 macrophage expressing GFP-LC3 incubated in media containing red dextran. The arrow marks LC3 recruitment to a dextran-containing macropinosome. Scale bar, 2 μm. (b) Quantification of LC3 recruitment to macropinosomes in control and Atg5 shRNA J774 macrophages; n, number of macropinosomes analysed; ***P0.0001, chi-squared test. See Supplementary Movie S9."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "(c) Representative image of LC3 recruitment to macropinosomes (arrows) in MCF10A cells expressing GFP-LC3 incubated with red dextran. Scale bar, 2 μm. (d) Quantification of LC3 recruitment to macropinosomes in MCF10A cells treated with siRNA against FIP200 or ATG5; n, number of macropinosomes analysed; ***P0.0001, chi-squared test."
NCBI gene IDs:
"ATG5: 9474
FIP200: 9821"
Figure legend: "(c) Representative images of apoptotic phagosomes in embryos from control-RNAi- or bec-1-RNAi-fed worms. The insets show higher magnifications of the areas outlined in the main panels. (d) Quantification of GFP::LGG-1- and mCherry::RAB-5-positive phagosomes in control- or bec-1-RNAi embryos determined by time-lapse imaging. Control, 21 embryos, 52 phagosomes; bec-1, 9 embryos, 25 phagosomes; ***P0.0001, chi-squared test."
NCBI gene IDs:
"bec-1: 177345"