EMBO/SourceData huggingface dataset:
Figure legend: "(A-B) Representative confocal images of Gb3   accumulation, revealed by STX staining, in  brain sections from CLN7Δex2 mice at 3 and 7.5 months of age compared with CLN7 WT mice. Scale bars: 80 µm."
NCBI gene IDs:
"CLN7: 72175"
Figure legend: "(E)  Lipidomic analysis of neurons isolated from CLN7 WT and  CLN7Δex2 mouse forebrain. Data are presented as mean ± SD, **: P ≤ 0.001, ***: P ≤ 0.0001, as determined by ANOVA (n= 3 biological replicas)"
NCBI gene IDs:
"CLN7: 72175"
Figure legend: "(A) Representative  confocal images and quantification of SCMAS staining within the lysosome of ARPE-19  WT and  CLN3 KO upon depletion of Gb3S  (siGb3S), LacCer (siLCS), and  GM3s (siGM3S). (*** vs WT, °°° vs CLN3 KO siSCR). Data are presented as mean ± SD, °°°/***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm."
NCBI gene IDs:
"Gb3S: 53947
LacCer: 9331///9334
LCS: 9331///9334
CLN3: 1201
GM3s: 8869
GM3S: 8869"
Figure legend: "(D) Representative  confocal images and quantification of  STX staining within the  lysosome of ARPE-19 WT and  CLN7  KO in DMSO or treated 48h with Tamoxifen. (*** vs WT, °°° vs CLN3  KO  DMSO). Data are presented as mean ± SD, °°°/***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm."
NCBI gene IDs:
"CLN3: 1201
CLN7: 256471"
Figure legend: "(E) Representative confocal images and quantification of  STX staining within the  lysosome  of NPCs WT and derived from CLN7Pa474 patient IPSCs in  DMSO or treated with  Tamoxifen for 48h. (*** vs WT, °°° vs CLN7Pa474 DMSO). Data are presented as mean ± SD, °°°/***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm."
NCBI gene IDs:
"CLN7: 256471"
Figure legend: "(A) Representative  confocal images  and Quantification of STX  within the  lysosome  in U2-OS  and HeLa  cells after acute silencing of CLN3 (siCLN3) in  DMSO  or treated 48h with Tamoxifen. (*** vs siSCR DMSO, °°° vs siCLN3 DMSO). Data are presented as mean ± SD, °°°/***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm."
NCBI gene IDs:
"CLN3: 1201"
Figure legend: "(B) Representative  confocal image and quantification of Gb3 in ARPE-19 CLN3 KO cells silenced with siRNA against scramble sequence and TFEB (siTFEB) for 72h and treated for the last 48h with DMSO or  Tamoxifen. Data are presented as mean ± SD, ***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm."
NCBI gene IDs:
"CLN3: 1201
TFEB: 7942"
Figure legend: "(C) Representative confocal image and quantification of TFEB  in U2-OS cells silenced with siRNA against scramble sequence and CLN3  (siCLN3) for 72h and treated for the last 48h with DMSO or Tamoxifen (5 µM and 10 µM). Data are presented as mean ± SD, ***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm."
NCBI gene IDs:
"CLN3: 1201"
Figure legend: "(C) Representative confocal image and quantification of TFEB localization in HeLa TFEB-GFP transfected with RagC for 48h and treated for the last 3h with DMSO, Torin1, Tamoxifen  or Ospemifene. Ratios of nuclear to  cytosolic TFEB localization in RagC non-expressing (RagC-) and RagC-expressing cells (RagC+) are presented as mean ± SD, ***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm."
NCBI gene IDs:
"GFP: 
RagC: 64121
TFEB: 7942"
Figure legend: "D) Representative confocal images and quantification of STX in ARPE-19 CLN3 KO cells transfected with empty vector or HA-RagC for 48h and treated for 48h with DMSO or Tamoxifen. STX average spot area presented as mean ± SD, ***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm."
NCBI gene IDs:
"HA: 
CLN3: 1201
RagC: 64121"
Figure legend: "Representative confocal images of STX  in the  Cortex, Hippocampus, and Cerebellum brain  section derived from 7.5 months-old mouse  WT or CLN7Δex2 injected with vehicle or Tamoxifen (Tamox). Quantification of confocal images, the plot shows the quantification of the STX  average spot area normalized for the number of Hoechst positive cells. (*** vs WT, °°°/°° vs CLN7Δex2 Vehicle). Data are presented as mean ± SD, **/oo: P ≤ 0.001, ***/ooo: P ≤ 0.0001, as determined by ANOVA (N≥3 biological replicas). Scale bars: 60 µm."
NCBI gene IDs:
"CLN7: 72175"
Figure legend: "Representative  confocal images  of SCMAS in the Cortex, Hippocampus, and Cerebellum brain  section derived from mouse  WT or CLN7Δex2 injected with vehicle or Tamoxifen. Quantification of  confocal images, the plot shows the quantification of the SCMAS average spot area normalized for the number of  Hoechst  positive cells. (*** vs WT, °°° vs CLN7Δex2 Vehicle). Data are presented as mean ± SD, ***: P ≤ 0.0001, as determined by ANOVA (N≥3 biological). Scale bars: 60 µm."
NCBI gene IDs:
"CLN7: 72175"
Figure legend: "(A-B) Representative confocal images  and quantification of  IBA-1  in the  Cortex, Hippocampus, and Cerebellum brain  section derived from WT or CLN7Δex2 mice injected with the vehicle or Tamoxifen. (***/**/* vs WT, °°°/°°/° vs CLN7Δex2 Vehicle). Data are presented as mean ± SD, */o: P ≤ 0.01, **/oo: P ≤ 0.001, ***: P ≤ 0.0001, as determined by ANOVA (N≥3 biological replicas). Scale bars: 50 µm."
NCBI gene IDs:
"CLN7: 72175"
Figure legend: "(D) Representative Images of  hindlimb clasping test in mouse WT or CLN7Δex2 injected with vehicle or Tamoxifen."
NCBI gene IDs:
"CLN7: 72175"
Figure legend: "F. Dopaminergic neuronal cultures from control lines and glucocerebrosidase (GBA) N370S PD patients were immunoblotted for the presence of LAG3. No band for LAG3 could be observed in neurons."
NCBI gene IDs:
"GBA: 2629
glucocerebrosidase: 2629"
Figure legend: "G. Using high power, high resolution laser scanning confocal microscopy, no human LAG3 signal could be detected in human neurons (Auto-hLAG3 transduced, DOX OFF) by two different anti-human LAG3 antibodies (17B4 and D2G40; left panel and zoomed-in insets) whereas LAG3 was clearly detected in human neurons induced to express hLAG3 (DOX ON; right panel and zoomed-in insets). Scale bars 25 µm."
NCBI gene IDs:
"LAG3: 3902"
Figure legend: "D. Using high power, high resolution laser scanning confocal microscopy, no mouse LAG3 signal could be detected in murine primary neuronal cultures (Auto-mLAG3 transduced, DOX OFF and non-transduced neurons) using anti-mouse LAG3 antibody (MABF954) whereas LAG3 was clearly detected in primary neurons induced to express mLAG3 (Auto-mLAG3 transduced, DOX ON). Scale bars 20 µm."
NCBI gene IDs:
"LAG3: 16768"
Figure legend: "E. RT-qPCR-derived CT values to measure the cDNA copy number. Mixed neuroglial cultures, glial cultures, and neuron-enriched cultures show transcript levels that are close to indistinguishable to those from LAG3‑/‑ BH. Conversely, around 1600 transcripts/ng of RNA were counted in activated T cells."
NCBI gene IDs:
"LAG3: 3902"
Figure legend: "Human neural cultures transduced by Auto-hLAG3 were treated by α-synuclein PFFs 4 days post LAG3 expression induction by DOX and kept in culture for 2 or 4 weeks. Both transgenic (hLAG3 D2G40-positive in (A) and 17B4-positive in (B)) and non-transduced, wild-type neurons (selected neurons in zoomed-in insets) propagated α-synuclein and developed characteristic pS129-positive (81A-positive in (A) and EP1536Y-positive in (B)) α-synuclein aggregates. Scale bars 25 µm. Trained ilastik algorithms were used to segment pixels of 81A, EP1536Y and MAP2 stainings imaged by high-content wide-field microscope, which were used to quantify the signal of 81A-positive (C) and EP1536Y-positive (D) α-synuclein aggregates expressed as % of MAP2-positive area. Almost the entire wells (182 fields per well) were imaged for every condition and replicate and each datapoint in the plot represents the entire well. Error bars indicate mean ± SD of biological replicates (duplicates). For few conditions, unicates were used, shown as one dot. One-way ANOVA followed by Tukey's multiple comparison test demonstrated that neurons that did not express LAG3 (DOX OFF) showed no difference in α-synuclein propagation when compared to LAG3-expressing neurons (DOX ON) as demonstrated by two different pS129 α-synuclein antibodies (p=0.9998 for 81A at 2 weeks and p=0.2522 at 4 weeks; p=0.9986 for EP1536Y at 2 weeks and p=0.3042 at 4 weeks)."
NCBI gene IDs:
"LAG3: 3902"
Figure legend: "A. Survival curves of A53T α-synuclein TG mice, with LAG3 knockout, heterozygous LAG3 expression, or LAG3 WT. Median survival was shortest for α-synuclein TG LAG3‑/‑ at 239 d, followed by α-synuclein TG LAG3+/- at 260 d and α-synuclein TG LAG3+/+ at 268 d. The survivals of ASYNA53T LAG3‑/‑, LAG3+/- and LAG3+/+ mice were similar (Mantel-Cox log-rank test, p-value = 0.165). Mice were euthanized and dissected in the late-stage symptomatic phase, which would inevitably result in death within a week. None of the control LAG3‑/‑ α-synuclein WT mice died over the course of the experiment."
NCBI gene IDs:
"LAG3: 16768
α-synuclein: 6622
α-synuclein: 20617"
Figure legend: "C. Immunofluorescence staining and quantification of pS129-positive α-synuclein inclusions in hippocampal slice cultures (HSCs) at 5 weeks post-seeding with 350 µM PFF. Scale bars represent 500 µm (overview), and 100 µm (insets). Shown is mean ± SEM and individual values are shown; n = 6 cultures per group; two-way-ANOVA revealed for LAG3 F(1, 20) = 0.0294; p = 0.8656; A53T F(1, 20) = 36.42, p &lt; 0.0001; interaction F(1, 20) = 0.0062, p = 0.9382. Bonferroni's correction for multiple comparisons revealed p = 0.9973 for LAG3 WT vs. KO in A53T TG and p &gt; 0.9808 for LAG3 WT vs. KO in A53T WT."
NCBI gene IDs:
"LAG3: 16768"
Figure legend: " C. STING-KO or sgRNA control (Ctrl) MC38 cells were treated in vitro with the indicated concentrations of 5-FU. Cell viability were determined using the CellTiter-Glo assay after two days, with normalized luminescence levels shown. N=3. "
NCBI gene IDs:
"STING: 72512"
Figure legend: " Mice were injected with Ctrl or STING-KO MC38 cells, and treated with PBS or 5-FU. (D) Pictures of tumors and spleens from a representative experiment. Image panels were cropped from the same picture. "
NCBI gene IDs:
"STING: 72512"
Figure legend: "  Mice were injected with Ctrl or STING-KO MC38 cells, and treated with PBS or 5-FU. (E) Tumor volumes were quantified at the indicated days post cancer cell injection. N=4 to N=5 as shown in (D).  "
NCBI gene IDs:
"STING: 72512"
Figure legend: " Mice were injected with Ctrl or STING-KO MC38 cells, and treated with PBS or 5-FU. (F) Tumor and spleen weights at the endpoint for (E), with each dot representing a mouse. "
NCBI gene IDs:
"STING: 72512"
Figure legend: " WT MC38 cells were injected into STING+/+ or STING-/- mice, and treated with 5-FU or PBS following the schematics in (A). (G) Pictures of tumors and spleens from a representative experiment. Image panels were cropped from the same picture. "
NCBI gene IDs:
"STING: 72512"
Figure legend: "  WT MC38 cells were injected into STING+/+ or STING-/- mice, and treated with 5-FU or PBS following the schematics in (A). (H) Tumor volumes were quantified at the indicated days post cancer cell injection. N=5.  "
NCBI gene IDs:
"STING: 72512"
Figure legend: " WT MC38 cells were injected into STING+/+ or STING-/- mice, and treated with 5-FU or PBS following the schematics in (A). (I) Tumor and spleen weights at the endpoint for (H), with each dot representing a mouse. "
NCBI gene IDs:
"STING: 72512"
Figure legend: " B. Western blot for Ctrl and STING KO YUMM1.7 cells, assayed with STING and Gapdh antibodies. "
NCBI gene IDs:
"STING: 72512"
Figure legend: " C. STING-KO or sgRNA control (Ctrl) YUMM1.7 cells were treated in vitro with the indicated concentrations of DTIC. Cell viability were determined using the CellTiter-Glo assay after two days, with relative cell viability shown. N=3. "
NCBI gene IDs:
"STING: 72512"
Figure legend: " YUMM1.7 Ctrl or STING KO cells were injected into mice. 5-FU and DTIC responses were followed according to the schematics in (A). (E) Representative images of tumors and spleens. Image panels were cropped from the same picture. "
NCBI gene IDs:
"STING: 72512"
Figure legend: " YUMM1.7 Ctrl or STING KO cells were injected into mice. 5-FU and DTIC responses were followed according to the schematics in (A). (F) Mean tumor volumes of Ctrl or STING KO YUMM1.7 with DMSO, DTIC or 5-FU treatment were followed during the experiment. N=3 to N=5, as shown in (E). "
NCBI gene IDs:
"STING: 72512"
Figure legend: " YUMM1.7 Ctrl or STING KO cells were injected into mice. 5-FU and DTIC responses were followed according to the schematics in (A). (G) Tumor (left panel) and spleen (right panel) weights were determined at the endpoint for the experiment followed in (F). Each dot represents data from a mouse. "
NCBI gene IDs:
"STING: 72512"
Figure legend: " A. Control (Ctrl) or STING-KO MC38 cells were treated in vitro with STING agonist cGAMP (left) for 6 hours or 5-FU (right) or relevant vehicle controls for 24 hours. The expression of indicated genes was determined by qRT-PCR. N=3. "
NCBI gene IDs:
"STING: 72512"
Figure legend: " B. Ctrl or STING-KO CT26 cells were treated with 5-FU or vehicle control for 24 hours. The RNA expression levels of indicated genes were determined by qRT-PCR. N=3. "
NCBI gene IDs:
"STING: 72512"
Figure legend: " C. Ctrl or STING-KO YUMM1.7 cells were treated with (left panel) vehicle control (DMSO) or DTIC, or (right panel) PBS or 5-FU for 24 hours. The expression of indicated genes was determined by qRT-PCR. N=3. "
NCBI gene IDs:
"STING: 72512"
Figure legend: " D. Western blot analysis was performed with Ifnα and Gapdh antibodies, for control (Ctrl) and Ifna1-Ifnb1-double-KO (Ifn-DKO) MC38 cells. Two independent KO clones are shown. "
NCBI gene IDs:
"Ifna1: 15962
Ifnb1: 15977"
Figure legend: " A. Western blot for control sgRNA (Ctrl) and cGAS-KO MC38 cells, assayed with cGAS and Gapdh antibodies. "
NCBI gene IDs:
"cGAS: 214763"
Figure legend: " Mice were injected with Ctrl or cGAS-KO MC38 cells and treated with PBS or 5-FU. (B) Pictures of tumors and spleens from a representative experiment. Image panels were cropped from the same picture. "
NCBI gene IDs:
"cGAS: 214763"
Figure legend: " Mice were injected with Ctrl or cGAS-KO MC38 cells and treated with PBS or 5-FU. (C) Tumor volumes were quantified at the indicated days post cancer cell injection. N=4 to N=5, as shown in (B). "
NCBI gene IDs:
"cGAS: 214763"
Figure legend: " Mice were injected with Ctrl or cGAS-KO MC38 cells and treated with PBS or 5-FU. (D) Tumor and spleen weights at the endpoint for (C), with each dot representing a mouse. "
NCBI gene IDs:
"cGAS: 214763"
Figure legend: " A. Western blot for Ctrl and Ifnar1-KO MC38 cells, analyzed with Ifnar1 and Gapdh antibodies. "
NCBI gene IDs:
"Ifnar1: 15975"
Figure legend: " B. Ctrl or Ifnar1-KO MC38 cells were treated with PBS or recombinant Ifnβ for 4 hours. The RNA expression levels of indicated ISGs were analyzed using qRT-PCR. N=3. "
NCBI gene IDs:
"Ifnar1: 15975"
Figure legend: " Mice were injected with control (Ctrl) or Ifnar1-KO MC38 cells, and treated with 5-FU or PBS. (C) Pictures of tumors and spleens from a representative experiment. "
NCBI gene IDs:
"Ifnar1: 15975"
Figure legend: " Mice were injected with control (Ctrl) or Ifnar1-KO MC38 cells, and treated with 5-FU or PBS. (D) Tumor volumes were quantified at the indicated days post cancer cell injection. N=5. "
NCBI gene IDs:
"Ifnar1: 15975"
Figure legend: " Mice were injected with control (Ctrl) or Ifnar1-KO MC38 cells, and treated with 5-FU or PBS. (E) Tumor and spleen weights at the endpoint for (D), with each dot representing a mouse. Ctrl tumor data in (C-E) are the same as those in Figure 4B-4D. "
NCBI gene IDs:
"Ifnar1: 15975"
Figure legend: "  experiment to test the function of Ifnar1 in bone marrow (BM) derived cells. WT C57BL/6 mice were transplanted with either Ifnar1+/+ or Ifnar1-/- BM cells. Recipient mice were allowed to recover followed by the injection of WT MC38 cells, before treatment with 5-FU or PBS. (G) Pictures of tumors and spleens from a representative experiment. Image panels were cropped from the same picture. "
NCBI gene IDs:
"Ifnar1: 15975"
Figure legend: "
 experiment to test the function of Ifnar1 in bone marrow (BM) derived cells. WT C57BL/6 mice were transplanted with either Ifnar1+/+ or Ifnar1-/- BM cells. Recipient mice were allowed to recover followed by the injection of WT MC38 cells, before treatment with 5-FU or PBS. (H) Tumor volumes were quantified at the indicated days post cancer cell injection. N=4 to N=5, as shown in (G). 
"
NCBI gene IDs:
"Ifnar1: 15975"
Figure legend: "
 experiment to test the function of Ifnar1 in bone marrow (BM) derived cells. WT C57BL/6 mice were transplanted with either Ifnar1+/+ or Ifnar1-/- BM cells. Recipient mice were allowed to recover followed by the injection of WT MC38 cells, before treatment with 5-FU or PBS. (I) Tumor and spleen weights at the endpoint for (H), with each dot representing a mouse. 
"
NCBI gene IDs:
"Ifnar1: 15975"
Figure legend: " Mice were injected with control (Ctrl) or STING-KO MC38 cells and treated with PBS or 5-FU. Tumors were harvested 2 weeks after cancer cell injection and intratumoral immune cells were examined by flow cytometry. A. The counts of CD45+ cells per gram of tumor. B. The percentages of CD45+ cells among forward scatter (FSC) and side scatter (SSC) gated live cell population. C. The counts of CD3+, CD3-NK1.1+, CD3-CD19+, CD11b+ and CD11c+CD103+ cells per gram of tumor were quantified. D. The percentages of CD3+, CD3-NK1.1+, CD3-CD19+, CD11b+ and CD11c+CD103+ cells among CD45+ cells were quantified. E. The counts of CD4+ and CD8+ T cells per gram of tumor. F. The percentages of CD4+ and CD8+ cells among CD3+ T cells were quantified. "
NCBI gene IDs:
"STING: 72512"
Figure legend: " Mice were injected with control (Ctrl) or STING-KO MC38 cells, and subjected to treatments, with each dose consisting of 25 mg/kg, 50 mg/kg or 75 mg/kg 5-FU, or PBS. A. Pictures of tumors and spleens from a representative experiment. Image panels were cropped from the same picture. "
NCBI gene IDs:
"STING: 72512"
Figure legend: " Mice were injected with control (Ctrl) or STING-KO MC38 cells, and subjected to treatments, with each dose consisting of 25 mg/kg, 50 mg/kg or 75 mg/kg 5-FU, or PBS. B. Tumor volumes were quantified at the indicated days post cancer cell injection. N=5. "
NCBI gene IDs:
"STING: 72512"
Figure legend: " Mice were injected with control (Ctrl) or STING-KO MC38 cells, and subjected to treatments, with each dose consisting of 25 mg/kg, 50 mg/kg or 75 mg/kg 5-FU, or PBS. C. Tumor and spleen weights at the endpoint for (B), with each dot representing a mouse. "
NCBI gene IDs:
"STING: 72512"
Figure legend: " B. STING RNA expression from the same 58 specimens were partitioned into STING-Low (bottom 15 samples) and STING-Hi (top 43 samples) groups. Kaplan Meier curve is shown with P value indicated. "
NCBI gene IDs:
"STING: 340061"
Figure legend: " C. Stage II and Stage III patients from the TCGA COAD dataset were partitioned into STING-Hi (top 1/3 of samples, N=87) and STING-Low (bottom 1/3 of samples, N=87). Kaplan Meier curve is shown with P value indicated. "
NCBI gene IDs:
"STING: 340061"
Figure legend: "D. From a published colorectal cancer chemotherapy response study, STING RNA expression in responders and non-responders were compared, with each dot representing a tumor."
NCBI gene IDs:
"STING: 340061"
Figure legend: "C Comparison of 3H-serine incorporation in ApoE ACM-treated WT- and Mfn2-KO MEFs (mean±SE; n=3, with 3 replicates/experiment)."
NCBI gene IDs:
"ApoE: 348
Mfn2: 170731"
Figure legend: "D Duramycin sensitivity in ApoE ACM-treated fibroblasts. Note increased sensitivity after 20 min to 5 μM duramycin in ApoE4-treated cells, which was blocked upon the addition of 15 μM exogenous PtdEtn (mean±SD; n=3, with 3 replicates/experiment)."
NCBI gene IDs:
"ApoE: 348"
Figure legend: "B Fractions from the discontinuous gradient were blotted with anti-ApoE (WUE-4) antibody; the doublet is a characteristic feature on ApoE western blots due to ApoE sialylation [16]."
NCBI gene IDs:
"ApoE: 348"
Figure legend: "C An ApoE-containing fraction (fraction 5 [+]), an ApoE-negative fraction (fraction 3 [-]), and recombinant lipid-free ApoE protein were applied to human fibroblasts. Note increase in phospholipid synthesis using an ApoE4-containing lipoprotein fraction, but not with either an ApoE4-negative fraction or with lipoprotein-free recombinant ApoE3 or ApoE4 protein (mean ± SE; n=3, with 3 replicates/experiment)."
NCBI gene IDs:
"ApoE: 348"
Figure legend: "A Cholesteryl ester synthesis, as measured by 3H-oleate incorporation. Note increased CE in ApoE4-treated cells, whereas there was essentially no difference in triglyceride (TAG) production (mean±SE; n=3. with 3 replicates/experiment). †, p=0.06 vs E3."
NCBI gene IDs:
"ApoE: 348"
Figure legend: "B Comparison of 3H-oleate incorporation in ApoE ACM-treated WT- and Mfn2-KO MEFs (mean±SE; n=3, with 5 replicates/experiment)."
NCBI gene IDs:
"ApoE: 348
Mfn2: 170731"
Figure legend: "C ApoE ACM-treated fibroblasts were stained with LipidTox green neutral lipid stain, and lipid droplets were visualized (example at left) and counted (right). Note significantly more lipid droplets in ApoE4-treated cells (mean ± SD, n=3)."
NCBI gene IDs:
"ApoE: 348"
Figure legend: "HeLa cells were transfected with plasmids to visualize ER (in green) and mitochondria (in red), and then were treated with ApoE3- and ApoE4-ACM for 24 hours. Shown is a box-and-whisker plot comparing co-localization in ApoE3 ACM (n = 15 images analyzed [gray circles, average of co-localization in ~5 cells in each image field]) compared to that in ApoE4 ACM (n = 18 images)."
NCBI gene IDs:
"ApoE: 348"
Figure legend: "(A) SDS-PAGE gels stained with coomassie showing the purity of the Chlamydomonas IFT-B2 components, over-expressed in E. coli or insect cells, after the last purification step by SEC. IFT54/20 and IFT57/38 were purified as hetero-dimeric complexes whereas IFT80, IFT172 and an N-terminal IFT172(1-968) (IFT172ΔC) constructs were purified as single components. A cartoon representation of the predicted domain architecture of IFT-B2 components using HHPRED (Söding et al, 2005) is shown at the center."
NCBI gene IDs:
"IFT172: 5717250"
Figure legend: "(B)Pull-down analysis for the hexameric IFT-B2 complex. A mixture of IFT172ΔC, IFT80, and the IFT57/38 complex ('input') shows only weak non-specific binding to GSH-resin ('empty'), but all proteins are pulled down by IFT54/20-GST complex. Note that the IFT20-GST and IFT38 proteins co-migrate on the gel and cannot be properly resolved. However, the presence of the IFT57 protein in the pull-down sample implies that its binding partner IFT38 is also there."
NCBI gene IDs:
"IFT172: 5717250"
Figure legend: "(A-C) SEC elution profiles and corresponding SDS PAGE gels of IFT172ΔC, IFT57/38, IFT80, IFT54/20 as well as mixtures of IFT172ΔC/57/38, IFT80/57/38 and IFT172ΔC/80/57/38 demonstrating that IFT57/38 associates with both IFT80 and IFT172ΔC. Only the central peak fraction from each SEC experiment is shown on the SDS PAGE gel. Note that the presence of both IFT172ΔC and IFT80 in a single peak in (c) (peak 3) is due to the fact that these two proteins elute in the same position, and not because they physically interact (see also Appendix Fig. S2B)."
NCBI gene IDs:
"IFT172: 5717250"
Figure legend: "(D) GSH resin pull-down of a mixture of IFT80 and IFT172ΔC (input, lane 1) with GST-tagged CH-domains of IFT57 or IFT38 (IFT57CH or IFT38CH) or with the GST-tagged coiled-coil (CC) region of IFT57 mixed with His-tagged coiled-coil region of IFT38. The SDS-PAGE gel shows interaction between IFT57CH-IFT172ΔC, IFT38CH-IFT80 and IFT57CC-IFT38CC."
NCBI gene IDs:
"IFT38: 5722691
IFT172: Q5DM57///5717250
IFT57: 5724201"