EMBO/SourceData huggingface dataset:
Figure legend: "B) Characterization of the Doxycycline-inducible cell lines expressing siRNA resistant wild type (WT) or mutant (TMA or TMD) FLAG/HA-tagged PALB2. The cell lines were transfected with UNC (Negative Control) or PALB2 siRNA for 24 hours prior to induction with Doxycycline. Immunoblots were performed with indicated antibodies."
NCBI gene IDs:
"PALB2: 79728"
Figure legend: "A) PALB2 cell lines transfected with PALB2 siRNA followed by inducible expression of siRNA resistant PALB2 versions were exposed to 15 Gy of IR and fixed for IF 2 hours later. Z-stack images were acquired with a 60X oil objective (Deltavision). Z stack max intensity projection, background subtraction, and foci count was done using ImageJ/Fiji. (* p&lt;0.0001, unpaired Student's t-test). Scale bar = 5μm."
NCBI gene IDs:
"PALB2: 79728"
Figure legend: "B) PALB2 cell lines were transfected and the exogenous PALB2 induced as in Figure 3A before they were pulsed with 10 μM EdU for 20 minutes prior to addition of 2 mM HU. 24 hours later the cells were fixed and processed for IF as in Figure 3A. Cells in S-phase (EdU+) at the time of HU treatment were Click-IT labeled with an Alexa Fluor 647 azide and RAD51 foci in EdU positive cells were enumerated using ImageJ/Fiji. (* p&lt;0.0001, unpaired Student's t-test). Scale bar=5μm."
NCBI gene IDs:
"PALB2: 79728"
Figure legend: "C) HeLa DR-GFP cell line was used to analyze homologous recombination activity. Cells were transfected with PALB2 siRNA followed by transfection of I-SceI together with empty vector (EV), WT-, TMA-, or TMD-PALB2 the next day. 72 hours later cells were fixed and analyzed by FACS. The percentage of cells with GFP signal from the empty vector sample was set to one (dotted line). The graph shows a representative image from three biological repeats (error bars=SEM)."
NCBI gene IDs:
"PALB2: 79728"
Figure legend: "D) Phosphorylation of PALB2 supports RAD51 foci. Cells were transfected with siPALB2 overnight followed by forward transfection of siFBH1/siBLM for 6 hours then induced for expression of PALB2 (WT and TMA). 24 hours following induction cells were pulsed with EdU and exposed to HU as in Figure 3B. Cells in S-phase (EdU+) at the time of HU treatment were Click-IT labeled with an Alexa Fluor 647 azide and RAD51 foci in EdU positive cells were enumerated using ImageJ/Fiji (* p&lt;0.0001, unpaired Student's t-test). Representative images of displaying RAD51 (green) and HA-PALB2 (red) localization in HU treated EdU positive (not shown) cells. Scale bar=5μm."
NCBI gene IDs:
"BLM: 641
FBH1: 84893
PALB2: 79728"
Figure legend: "A) U2OS and PALB2 cell lines were transfected with UNC (Negative Control) or PALB2 siRNA and 24 hours later Doxycycline was added to the PALB2 cell lines. Left panel, cells were treated the following day with IR (5 Gy) and 2 hours later Nocodazole was added for 6 hours, or treated with only Nocodazole for 6 hours. Right panel, cells were treated with IR (5 Gy) and left to recover for 16 hours. Cells were fixed and stained with the pMPM2 antibody to detect the mitotic cells by flow cytometry. The percentages of mitotic cells in the IR+Nocodazole samples were normalized to the Nocodazole samples (left panel, n=3, error bars=SEM). For the samples with the 16 hour recovery after IR the percentage of mitotic cells in the WT-PALB2 expressing cells was set to one (right panel). (n=3, **p&lt;0.005, *p&lt;0.05, unpaired Student's t-test, error bars=SEM)."
NCBI gene IDs:
"PALB2: 79728"
Figure legend: "B) The relative intensity of phosphorylated H2AX (pS139) was examined in the total population of WT- and TMA-PALB2 expressing cell lines 18 hours post exposure to IR (5 Gy). Cell lines were prepared as in above, fixed at the indicated time point, and stained for pH2AX. Cells were imaged with a 20X air objective on a Scan^R workstation (Olympus), mean relative pH2AX intensity was calculated from background subtracted images using the Scan^R analysis software. (* p&lt;0.0001, unpaired Student's t-test)."
NCBI gene IDs:
"PALB2: 79728"
Figure legend: "C) Number of 53BP1 nuclear in TMA-PALB2 expressing G1 daughter cells. Cell lines were prepared as above and left untreated (NT) or exposed to IR (3 Gy), and 16 hours later Cytochalasin B was added for 8 hours to block cytokinesis. The irradiated bi-nucleated cells were scored for 53BP1 nuclear bodies. Scale bar = 10μm."
NCBI gene IDs:
"PALB2: 79728"
Figure legend: "Display of differentially expressed genes in NeuNT tumors (WT, TNCKO) as volcano plot representing all associated genes in WT tumors. N = 3 tumors per genotype. (A) Log2 Fold Change (X-axis) and the negative log10 (P.Value) (Y-axis) is displayed, the blue line indicating p = 0.05 (Y-axis), points above the line, p &lt; 0.05. The dashed red lines indicate the log 2 Fold Change cutoff of -0.25 and 0.25, respectively (X-axis). Green dots represent genes that display both statistical significance (p &lt; 0.05) and fold changes -0.25 and 0.25, respectively. Selected genes regulated by TNC are marked in red (type I interferon response) or pink (Cxcl12) dot."
NCBI gene IDs:
"Cxcl12: 20315
type I interferon: 15975
TNC: 21923"
Figure legend: "(A) Representative staining images (N = 5) of tissue from TNC  high (WT/shC) and TNC low (KO/shTNC) tumors (N = 5 per condition) with the indicated antibodies. Arrows point at the respective immune subtype. Scale bar, 50 µm."
NCBI gene IDs:
"TNC: 21923"
Figure legend: "(D, E)  Apoptosis measurement upon tumor staining for  cl. casp3 (D) and signal quantification per field (E) in TNC high and TNC low tumors (N = 7 per condition), 2 sections per tumor, 5 random fields. *** p = 0.0006, Mann-Whitney test, Mean ± SEM. Scale bar, 50 µm."
NCBI gene IDs:
"TNC: 21923"
Figure legend: "(I, J) Detection (I) and quantification (J) of CD8 TIL in lung metastasis of NeuNT WT and TNCKO mice (N = 3 mice, n = 7 and 12 lung metastases, respectively). Scale bar, 100 µm. ** p = 0.0097, Mann Whitney test. Mean ± SEM."
NCBI gene IDs:
"TNC: 21923"
Figure legend: "(E) Analysis of Cxcl12  (qRT-PCR) in tumor cells upon pretreatment with the indicated inhibitors for 45 minutes (GW, BOP, DMSO and PBS as control respectively) or 60 minutes (Sunitinib) and 6 hours (Cli95) (6 hours DMSO as control) before incubation with TNC for 24 hours. N = 6 independent experiments, ** p = 0.0022, Mann Whitney test. Mean ± SEM."
NCBI gene IDs:
"Cxcl12: 20315
TNC: 21923"
Figure legend: "(I-L) qRT-PCR assessment of Neu (I), Cd8a (J), Ifnγ (K) and Gzmb (L) by qRT-PCR. PBS (N = 16) and AMD (N = 19) treated mice, *, p = 0.0364, Mann whitney test (I), **, p = 0.0086 unpaired t-test (J), **, p = 0.0055, unpaired t-test (K), ***, p = 0.0003 unpaired t-test (L), respectively. The central band represents the median, the ends of the box the first and the third quartiles, and the whiskers reach from each quartile to the minimum or maximum."
NCBI gene IDs:
"Cd8a: 12525
Neu: 13866
Gzmb: 14939
Ifnγ: 15978"
Figure legend: "(D-G)  Kaplan Meier  analysis to address correlation of TNC expression (D), total  numbers of CD8 TIL (E), combined high (above median) CD8 TIL and high or low (above/below median) TNC (F) and stromal CD8  cells (G) with metastasis-free survival (MFS) of breast cancer patients. Stromal CD8- or CD8+ is defined as below or above median  stromal CD8 TIL per area. Log-rank test."
NCBI gene IDs:
"TNC: 3371"
Figure legend: "(H, I) Correlation of TNC  and CD8a levels with overall survival  (OS) using survival analysis on breast cancer patient cohort GSE 19783-GPL6580. Hazard ratio (HR) and p values are indicated in Appendix Fig. S5N. Log-rank test."
NCBI gene IDs:
"CD8a: 925
TNC: 3371"
Figure legend: "(D) Kaplan Meier survival analysis of breast cancer patients upon stratification into tumors with a CXCL12 Hscore below or above the median, p = 0.002. Mann-Whitney test. (E) Survival analysis of  breast cancer patients in the GSE 19783-GPL6580 cohort upon stratification into tumors with high or low expression of TNC and CXCL12. Log-rank test. HR and p values are indicated, "
NCBI gene IDs:
"CXCL12: 6387
TNC: 3371"
Figure legend: "K qPCR analysis of human β2-microglobulin (B2M), human specific mitochondrial (Mito) and mouse specific (β-actin) gene expression levels in UC-MSCs, mouse derived spleen cells or FACS sorted CD45+ mouse cells after 24 hrs co-culture with UC-MSCs (n=3 biological replicates). n/d = not detected."
NCBI gene IDs:
"Mito: 
β-actin: 11461
B2M: 567
β2-microglobulin: 567"
Figure legend: "(K) Representative immunofluorescence staining  of ∆FosB (green) in cultured MSNs  extracted from mutant mice  lacking ALK4  in GABAergic neurons  (Gad67Cre;Alk4fl/fl) and control mice  (Alk4fl/fl) after exposure to consecutive stimulation (same treatment in both treatment days) with activin A (Act), SKF81297  (SKF) or their combination as indicated. Counterstaining  with MAP2  and DAPI  is shown in the second and fourth rows. Scale bar, 25μM. (L) Quantification of  ∆FosB+ nuclei  in cultured MSNs  from mutant and control mice  after the indicated treatments (same treatment in both treatment days). Results are expressed as average ± SEM of % of MAP2+ cells displaying  ∆FosB in the nucleus. N=6. Data information: *, p&lt;0.05; **, p&lt;0.01;***, p&lt;0.001; one-way ANOVA followed with Tukey's multiple comparisons test. N denotes biological replicates."
NCBI gene IDs:
"ALK4: 11479
Alk4: 11479
Cre: 2777477
Gad67: 14415"
Figure legend: "(I) RT-qPCR analysis of PCBP1  mRNA in cultured MSNs  exposed to consecutive stimulation as indicated (same treatment in both treatment days). Results are expressed as average ± SEM of fold change over vehicle. No significant differences were found by one-way ANOVA followed with Tukey's multiple comparisons test (p≥0.05; N=4). Data information: *, p&lt;0.05; **, p&lt;0.01;***, p&lt;0.001; one-way ANOVA followed with Tukey's multiple comparisons test. N denotes biological replicates."
NCBI gene IDs:
"PCBP1: 23983"
Figure legend: "(D) Representative images of RNA-PLA  (green) between PCBP1  (left) or Smad3  (right) and sequences in exon 4 (pE4) of FosB  mRNA, respectively, in HeLa  cells exposed to consecutive stimulation (same treatment in both treatment days) as indicated. Counterstaining  with phalloidin and DAPI  is shown in the second and fourth columns. Scale bars, 20μM. (E, F) Quantification of RNA-PLA between PCBP1  (E) or Smad3  (F) and pE4 in HeLa  cells after the indicated treatments. Results are expressed as average ± SEM of number of  RNA-PLA  dots per cell. Only nuclear  dots were quantified in this analysis. N=4. Data information: *, p&lt;0.05; **, p&lt;0.01;***, p&lt;0.001; one-way ANOVA followed with Tukey's multiple comparisons test. N denotes biological replicates."
NCBI gene IDs:
"FosB: 2354"
Figure legend: "(G) Representative images of RNA-PLA  (green) between PCBP1  (left) or Smad3  (right) and sequences in exon 4 (pE4) of FosB  mRNA, respectively, in cultured MSNs  exposed to consecutive stimulation as indicated. Counterstaining  with phalloidin  and DAPI  is shown in the second and fourth columns. Scale bars, 20μM. (H, I) Quantification of RNA-PLA   between PCBP1  (E) or Smad3  (F) and pE4 in cultured MSNs  after the indicated treatments. Results are expressed as average ± SEM of number of RNA-PLA  dots per cell. Only nuclear  dots were quantified in this analysis. N=4. Data information: *, p&lt;0.05; **, p&lt;0.01;***, p&lt;0.001; one-way ANOVA followed with Tukey's multiple comparisons test. N denotes biological replicates."
NCBI gene IDs:
"FosB: 14282"
Figure legend: "(D) Representative immunofluorescence staining  of ∆FosB (red) in cultured MSNs  treated with scrambled and shPCBP1 lentiviruses  and exposed to consecutive stimulation (same treatment in both treatment days) with activin A  (Act), SKF81297  (SKF) or their combination as indicated. Counterstaining  with green fluorescent protein (GFP, expressed by the lentiviruses) and DAPI  is shown in the second and fourth rows. Scale bar, 25μM. (E) Quantification of ∆FosB+ nuclei  in cultured MSNs  treated with scrambled and shPCBP1 lentiviruses  followed by the indicated treatments. Results are expressed as average ± SEM of % of GFP+ cells displaying ∆FosB in the nucleus. N=4. Data information: *, p&lt;0.05; **, p&lt;0.01;***, p&lt;0.001; two-way ANOVA followed with Tukey's multiple comparisons test in E). N denotes biological replicates."
NCBI gene IDs:
"PCBP1: 23983"
Figure legend: "(A-F) RT-qPCR analysis of FosB  (A, D), c-Fos (B, E) and  ∆FosB  (C, F) mRNAs in NAc  of Gad67Cre;Alk4fl/fl (A-C) mutant mice  1 hour (A-C) or 24 hour (D-F) after the second saline  (Sal) or cocaine  (Coc) injection of TIPS. Results are expressed as average ± SEM of fold increase over the saline  group (Sal/Sal) of  Gad67Cre mice. N=5. Data information: *, p&lt;0.05; **, p&lt;0.01;***, p&lt;0.001; one-way ANOVA followed with Tukey's multiple comparisons test. N denotes biological replicates."
NCBI gene IDs:
"Alk4: 11479
Cre: 2777477
c-Fos: 14281
∆FosB: 14282
FosB: 14282
Gad67: 14415"
Figure legend: "(G) Representative immunofluorescence staining  of ∆FosB in Nac  of control (Gad67Cre) and mutant (Gad67Cre;Alk4fl/fl) mice, 24 hours after the second injection of the TIPS protocol. Scale bars 20 μm. (H) Quantification of ∆FosB positive cells 24 hours after the second injection of TIPS protocol in the Nac  of Gad67Cre and Gad67Cre;Alk4fl/fl mice. Results are expressed as average ± SEM of the number of  ∆FosB+ cells per mm2. At least 10 images from both left and right hemispheres were analyzed per mouse  and condition. N=5. Data information: *, p&lt;0.05; **, p&lt;0.01;***, p&lt;0.001; one-way ANOVA followed with Tukey's multiple comparisons test. N denotes biological replicates."
NCBI gene IDs:
"Alk4: 11479
Cre: 2777477
Gad67: 14415"
Figure legend: "(I)  Western blot  analysis of FosB  and  ∆FosB in in NAc  of Gad67Cre and Gad67Cre;Alk4fl/fl mice 24 hour after the second injection of TIPS. Blots  were probed with an antibody that recognizes both FosB  (upper band, 48kDa) and ∆FosB (lower band, 38 kDa). Lower blot  shows reprobing with anti-β-actin. (J, K) Quantification of FosB  (J) and ∆FosB (K) levels in NAc  of Gad67Cre and Gad67Cre;Alk4fl/fl mice  24 hour after the second injection of TIPS. Results are expressed as average ± SEM of fold increase of FosB  and ∆FosB  over the saline group (Sal/Sal) of  Gad67Cre mice  normalized to  β-actin levels. N=4s. Data information: *, p&lt;0.05; **, p&lt;0.01;***, p&lt;0.001; one-way ANOVA followed with Tukey's multiple comparisons test. N denotes biological replicates."
NCBI gene IDs:
"Alk4: 11479
Cre: 2777477
Gad67: 14415"
Figure legend: "(A) Fluorescence micrograph images of representative cells stained for NONO and NEAT1_2 after transfection with plasmids expressing YFP fused NONO_WT and NONO_∆RRM1 protein. DAPI (blue) stain indicates cell nuclei, YFP fused NONO (green) and NEAT1_2 RNA FISH (red). (B) The enrichment of mean NONO fluorescence detected within RNA FISH foci is quantitatively determined as a ratio relative to mean nuclear NONO fluorescence in (A). Bars are SD. The numbers of biological replicates are indicated in (A)."
NCBI gene IDs:
"YFP: 
NEAT1: 283131
NONO: 4841"
Figure legend: "Sphericity per NONO segment, NONO foci number per nucleus and NONO foci size between YFP fused NONO_WT and NONO_∆RRM1 plasmids. Bars are SD. Biological replicates n=60 in (C) and n=50 in (D)"
NCBI gene IDs:
"YFP: 
NONO: 4841"
Figure legend: "(A) Relative NONO mRNA and protein levels in KELLY cells treated with control or NONO KD siRNAs. Representative Western blot image for NONO protein."
NCBI gene IDs:
"NONO: 4841"
Figure legend: "(B) Western blot quantitation analysis of GATA2 and HAND2 protein levels between control and NONO KD siRNAs. (C) Representative Western blot images for GATA2 and HAND2 proteins in (B)."
NCBI gene IDs:
"NONO: 4841"
Figure legend: "Effect of TFL457 on MEF2-promoter activity. Cultures transfected with pMEF2 (two minimal wild type MEF2 elements) or pMEF2mut (mutant) were preincubated with CPPs (25 μM, 30 min) and treated with NMDA (100 µM, 2 h). Means ± SEM of luciferase activities obtained in excitotoxicity, relative to values found in cells treated with same peptide and no NMDA, are presented."
NCBI gene IDs:
"luciferase: 
MEF2: 74490"
Figure legend: "Effect on CRE-promoter activity. pCRE contains two minimal CREs. Peptide preincubation was as above with or without KG-501 (10 µM). Mean ± SEM luciferase activities are given relative to values in cells treated with the same peptide but no NMDA or KG-501."
NCBI gene IDs:
"CRE: 
luciferase: "
Figure legend: "Effect on NMDAR-subunit promoters. Cells transfected with pGluN1 or pGluN2A were treated and analyzed as in panel A (pGluN1, *p = 0.016; pGluN2A, *p = 0.029; n = 14)."
NCBI gene IDs:
"NMDAR: 
GluN1: 24408
GluN2A: 14811"
Figure legend: "Effects on BDNF promoter III or TrkB promoter. Cells transfected with pIIIBDNF (n = 9), pTrkB (n = 7) or pCRE (n = 5), as a control, were processed as above but using 20 µM NMDA for 4 h. Data are presented and analyzed as in panel A (pCRE, **p = 0.0098; pIIIBDNF, *p = 0.029; pTrkB, *p = 0.033)."
NCBI gene IDs:
"BDNF promoter III: 24225
IIIBDNF: 24225
CRE: 2777477
TrkB: 18212"
Figure legend: "Effects of TFL457 on mRNA levels of CREB/MEF2-regulated genes. Total RNA was extracted from cultures preincubated with CPPs (25 μM, 30 min) and treated or not with NMDA (100 µM, 4 h). Levels of mRNA were normalized to NSE (genes expressed in neurons, left panel) or GAPDH (neuronal and glial expression, right panel). Means ± SEM of levels obtained in excitotoxicity relative to values found in cells treated with same peptide and no NMDA are presented. Differences found in excitotoxicity were analyzed by ANOVA test followed by post-hoc Tukey HSD test (GluN1, ***p = 0.00096; GluN2A, p = 0.98; TrkB-FL, ***p = 0.00037; BDNF, *p = 0.045; n = 8)."
NCBI gene IDs:
"GAPDH: 
NSE: 
BDNF: 12064
CREB: 78284///208677///208647///26427///231991///12913///11911///12912
GluN1: 24408
GluN2A: 14811
MEF2: 74490
TrkB: 18212"
Figure legend: "(C) Micrographs of starved HEK GFP-LC3 cells treated with nontargeting or siSNX18-3 siRNA. (left and middle) 3 × 3 fields of cells. (right) Close-up of a few cells from the respective population. The images in the right panels are shown again in Fig. S1 B alongside cells treated with other SNX18-targeting siRNAs. Bars, 10 µm. See also Table S1 and Table S2."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(A) HEK GFP-LC3 cells transfected with control (siCtrl) or two different SNX18 siRNA oligos (siSNX18-3 and siSNX18-5) were starved or not starved for 2 h in the presence or absence of BafA1. GFP-LC3 lipidation and SNX18 protein knockdown were monitored by immunoblotting. The graph shows the average GFP-LC3-II relative to actin normalized to siCtrl-1 fed ± SEM (error bars), n = 4."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(B) The degradation of long-lived proteins in HeLa cells transfected with control or SNX18 siRNA was quantified after 4 h of starvation in the absence or presence of 3-MA and normalized to the degradation in fed cells (mean ± SEM [error bars], n = 3)."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(C) HEK GFP-LC3 cells were transfected with control or SNX18 siRNA and then with a myc control or siRNA-resistant myc-SNX18 plasmid. The number of GFP-LC3 spots per cell was quantified (graph shows mean ± SEM [error bars], n = 3)."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(D) HEK GFP-LC3 cells were transfected with myc-SNX18 or a myc control plasmid and treated as in A. The graph shows the average LC3-II levels relative to actin normalized to myc-transfected fed cells, ±SEM (error bars). n = 3."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(E) HEK GFP-LC3 cells were transfected with control or Atg7 siRNA and then with myc-SNX18 or a myc control plasmid, followed by quantification of the number of GFP-LC3 spots per cell (graphs show mean ± SEM [error bars], n = 3). Representative images are shown. Bars, 5 µm."
NCBI gene IDs:
"Atg7: 10533
SNX18: 112574"
Figure legend: "(F) The degradation of long-lived protein in HeLa cells transfected with myc-SNX18 or a myc control plasmid was quantified as in B (graph shows mean ± SEM [error bars], n = 4). *, P &lt; 0.05; **, P &lt; 0.01. See also Figs. S1 and S2."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(F) HeLa cells were transfected with control or SNX18 siRNA, starved for 2 h, and immunostained against SNX18 and Atg16L1."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(G) HEK GFP-DFCP1 cells were transfected with control or SNX18 siRNA, starved for 50 min, and immunostained for Atg16L1. All images are from confocal microscopy. Inset panels show enlarged views of the boxed regions. Bars, 5 µm. See also Fig. S3."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(D) HeLa cells were transfected with the indicated myc-SNX18 plasmids for 6 h and starved for an additional 2 h before harvest. Equal parts of cytosol (C) and membrane (M) fractions were analyzed by Western blotting. The graph shows the average membrane-bound myc-SNX18 ± SEM (error bars), n = 3."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(E and F) HEK GFP-LC3 cells were transfected with the indicated mCherry-SNX18 (E) or mycSNX18 (F) constructs for 16 h. The number of GFP-LC3 spots per transfected cell (E; graph shows mean ± SEM [error bars], n = 5) or ratio of LC3-II to actin determined by Western blotting (F) was quantified."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(G and H) HEK GFP-LC3 cells transfected with myc-SNX18 or a myc control plasmid alone (G) or together with CFP-FRB and mRFP-FKBP or mRFP-FKBP 5pase (H) for 6 h were treated or not treated with 5 µM ionomycin (G) or 2.5 µM A/C heterodimerizer (rapalog; H) for the last 3 h before analysis of the total intensity of GFP-LC3 spots per transfected cell (graph shows mean ± SEM [error bars], n = 3)."
NCBI gene IDs:
"FKBP: 2280
FRB: 2475
SNX18: 112574"
Figure legend: "(I) MEFs were transfected with myc, myc-SNX18 WT, or KR for 16 h, starved or not starved for 2 h, and immunostained for endogenous Atg16L1. Insets show enlarged views of the boxed regions. Bars, 5 µm."
NCBI gene IDs:
"SNX18: 170625"
Figure legend: "(A) HeLa GFP-SNX18 cells were starved for the indicated time, followed by incubation in full medium (Refeed) where indicated. Cell lysates were analyzed for LC3 by immunoblotting, or immunoprecipitated with GFP-Trap before immunoblotting against SNX18(pS233) and GFP. The ratio of pS233 to GFP, and the ratio of LC3-II to LC3-I, was quantified, and normalized to 1 for the zero-time sample in both cases (graph shows mean ± SEM [error bars], n = 4; *, P &lt; 0.05)."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(B) The indicated myc-SNX18 PX-BAR constructs were transfected into HeLa cells, and their tubulation efficiency was measured by scoring the percentage of cells displaying more than three elongated structures longer than 5 µm (n = 300). The graph shows the mean of two independent experiments ± range (error bars). Bars, 10 µm."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(C) The indicated myc-tagged SNX18 constructs were transfected into HEK GFP-LC3 cells, and the number of GFP-LC3 spots per cell was quantified. The graph shows mean ± SEM (error bars), n = 5."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(D) HeLa GFP-LC3 cells were transfected with the indicated myc-tagged SNX18 constructs for 16 h, starved for 2 h, and analyzed by confocal imaging. Bars, 10 µm."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(E) HEK GFP-LC3 cells were transfected with myc-SNX18 WT or myc-SNX18 PX-BAR constructs, and the number of GFP-LC3 spots per cell was quantified. The graph shows mean ± SEM (error bars), n = 3."
NCBI gene IDs:
"SNX18: 112574"
Figure legend: "(F) HeLa GFP-LC3 cells were transfected with siRNA against Atg16L1 and later with myc-SNX18 constructs before immunostaining and confocal imaging. Bar, 5 µm."
NCBI gene IDs:
"Atg16L1: 55054
SNX18: 112574"
Figure legend: "(A) GFP, GFP-LC3, or GFP-LC3 G120A were immunoprecipitated from transfected HeLa cells. The immunoprecipitates and 2% of the lysate were analyzed by immunoblotting against SNX18. The GFP proteins were detected by Ponceau staining."
NCBI gene IDs:
"LC3: 440738///81631///84557"