EMBO/SourceData huggingface dataset:
Figure legend: "C.) Growth curve of the PfMev CLD-EcDPCK-mCherry-apt Δdpck parasite line containing a disrupted apicoplast grown either in the presence of 0.5μM aTc and the absence 0.5μM Shield1 (permissive condition, blue), or the absence of 0.5μM aTc and the presence of 0.5μM Shield1 (non-permissive condition, red). Pantothenate (50nM) and mevalonate  (50μM) were supplied in both conditions and the cultures were diluted 1:5 on day 4. Treatment under non-permissive conditions resulted in reduced parasite growth beginning at day 2 (two-way ANOVA, followed by Bonferroni's correction; **, P &lt; 0.01). Error bars represent the standard error of the mean from two independent experiments, each conducted in quadruplicate."
NCBI gene IDs:
"mCherry: 
DPCK: 949060
dpck: 811997"
Figure legend: "b, Representative phase images of the morphology of WT and Apc-/- organoids before mRNA isolation."
NCBI gene IDs:
"Apc: 11789"
Figure legend: "c, Heat map illustrating differentially expressed genes (DEGs) encoding heat shock proteins between WT and Apc-/- organoids."
NCBI gene IDs:
"Apc: 11789"
Figure legend: "e, f, Relative gene expression of Hspb1 (***P=0.0004, n=6)(e) and protein expression of HSP25 (f) in unrecombined versus recombined murine organoids."
NCBI gene IDs:
"Hspb1: 15507"
Figure legend: "g, Gene expression of Hspb1 in normal (N) versus adenoma (A) tissue (***P=0.0002, n=4)."
NCBI gene IDs:
"Hspb1: 15507"
Figure legend: "H, RNA-ISH for Hspb1 in murine intestinal adenoma. Scalebar, 100 μm. Zoom panel, 25 μm"
NCBI gene IDs:
"Hspb1: 15507"
Figure legend: "i, Relative gene expression of human HSPB1 in paired sets of normal versus adenoma tissue, (****P&lt;0.0001, paired t-test, n=59 pairs)."
NCBI gene IDs:
"HSPB1: 3315"
Figure legend: "Relative gene expression of AXIN2 (*P=0.0129), P21(*P=0.0103), and HSPB1(*P=0.0236) (b) in Ls174t-dnTCF4 cells the presence or absence of doxycycline."
NCBI gene IDs:
"AXIN2: 8313
P21: 1026
HSPB1: 3315
TCF4: 6925"
Figure legend: "protein expression of HSP27 (c) in Ls174t-dnTCF4 cells the presence or absence of doxycycline."
NCBI gene IDs:
"TCF4: 6925"
Figure legend: "Relative gene expression of Hspb1 in murine WT organoids treated with different concentrations of CHIR-99021 (**P=0.0016, one way ANOVA, n=4) (d)"
NCBI gene IDs:
"Hspb1: 15507"
Figure legend: "protein expression of HSP25 in WT and Apc-/- organoids (e)."
NCBI gene IDs:
"Apc: 11789"
Figure legend: "g, h, Representative images of single cell Hspb1 KO clones passaged after loss of Apc (g), and quantification of their clonogenic potential (*P=0.0147(#1), **P=0.0035(#2), **P=0.0032(#3)) (h)."
NCBI gene IDs:
"Apc: 11789
Hspb1: 15507"
Figure legend: "i, j, Representative images of Apc-/- organoids cultured in the absence or presence of 60 μM BVDU (i), and quantification of their clonogenic potential (**P=0.0039) (j)."
NCBI gene IDs:
"Apc: 11789"
Figure legend: "k, l, Relative gene expression of Wnt target genes Axin2 (**P=0.0080) and Lgr5 (*P=0.0142) in Apc-/- organoids cultured in the absence or presence of 60 μM BVDU."
NCBI gene IDs:
"Apc: 11789
Axin2: 12006
Lgr5: 14160"
Figure legend: "m, RNA-ISH for Lgr5 in control or BVDU-treated Apc-/- organoids. Scale bar, 50 μm, zoom panel 20 μm."
NCBI gene IDs:
"Apc: 11789
Lgr5: 14160"
Figure legend: "e, f, RNA-ISH for Notum reveals Apc-mutant clones in crypt bottoms of control or BVDU-treated mice (e), and quantification of the abundance of mutant crypts (n=2 mice per condition, n=5 technical replicates per mouse) (f)."
NCBI gene IDs:
"Apc: 11789
Notum: 77583"
Figure legend: "g, h, Clone size distributions of Notum+ crypts in control (n=265 crypts) or BVDU-treated (n=260 crypts) mice, the average clone size and number of fixed clones are included in the figure."
NCBI gene IDs:
"Notum: 77583"
Figure legend: "(F) Western-blotting of β-catenin, Axin2 and p-GSK3β(S9) in WT or Shank3-/- primary neurons. mice and 5 batches of cells (F) per group. Mean ratio ± SEM. Two-Tailed unpaired T-test. *P&lt;0.05. **P&lt;0.01. ***P&lt;0.001. WT, wild type. KO, Shank3-/- mice."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "(G) Western-blotting of SFRP1 and p-β-catenin(S33) in the total proteins, and TCF7L1 in the nuclear protein of WT or Shank3-/- ACC. 3 in mice Mean ratio ± SEM. Two-Tailed unpaired T-test. *P&lt;0.05. **P&lt;0.01. ***P&lt;0.001. WT, wild type. KO, Shank3-/- mice."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "(D) Western-blotting of ADH1, ALDH3 and ENO1 in the ACC of WT and Shank3-/- mice. Notice the up-regulation of ADH1, ALDH3 and ENO1 in Shank3-/- ACC. 3-4 mice in (D) P&lt;0.05. **P&lt;0.01. ***P&lt;0.001. WT, wild type. KO, Shank3-/-."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "(F) ECAR assay of primary WT and Shank3-/- neurons. Notice the higher ECAR values of Shank3-/- neurons upon glucose and oligomycin stimulation. 5 batches of cells *P&lt;0.05. **P&lt;0.01. ***P&lt;0.001. WT, wild type. KO, Shank3-/"
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "(C, D) Spine density and spine subtypes in the ACC of control and β-catenin over-expressing mice. Notice the reduction of total spine density, stubby and mushroom-like spines in β-catenin over-expressing mice. 20 μm in (C Two-Tailed unpaired T-test (Spine analysis excepting mushoom analysis in D. Mann-Whitney U test (Mushroom analysis in D."
NCBI gene IDs:
"β-catenin: 12387"
Figure legend: "Patch-clamp recording of mEPSC in the ACC of control and β-catenin over-expressing mice. Both the frequency and average amplitudes of mEPSC were reduced in Wnt over-activated ACC. , 9 neurons from 3 mice in H) Social novelty and social preference scores in , H Amplitude of mEPSC in H."
NCBI gene IDs:
"β-catenin: 12387"
Figure legend: "(I) 3-chamber assay of control and β-catenin over-expressing mice. 9-10 mice (I-K) Social novelty and social preference scores in I, Two-tailed paired T-Test (Time in compartment in I)."
NCBI gene IDs:
"β-catenin: 12387"
Figure legend: "ECAR assay of primary cultured control neurons (GFP+EX3) and β-catenin over-expressing neurons (CaMKII-Cre+EX3). 5 batches of cells ECAR in Max ECAR in M."
NCBI gene IDs:
"GFP: 
CaMKII: 12322
Cre: 2777477
β-catenin: 12387"
Figure legend: "(A) Typical images of Golgi staining and reconstructed neurons in the ACC of Shank3-/- mice treated with 2-DG (KO+2-DG) or vehicle (KO+Veh). Sholl analysis of pyramidal neurons in the ACC of Shank3-/- mice treated with 2-DG or vehicle. Bar = 50 μm in (A) N = 24-28 neurons from 4 mice in KO, Shank3-/-. Veh, vehicle."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "(G) Western-blotting of GluR1, PSD95 and Homer1 in the total proteins of Shank3-/- ACC with or without 2-DG treatment. 3 mice in (G) KO, Shank3-/-. Veh, vehicle."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "resident-intruder assay of Shank3-/- mice treated with 2-DG or vehicle. Notice the improvement of social preference and social interaction by 2-DG treatment. 10-12 mice in KO, Shank3-/-. Veh, vehicle."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "(A) ECAR assay of primary Shank3-/- neurons treated with or without XAV939. Notice the lower levels of glycolysis in XAV939 treated cells. (B) ECAR assay of primary Shank3-/- neurons treated with or without ICG-001. N = 4-5 batches of cells in Two-Tailed unpaired t-test *P&lt;0.05. **P&lt;0.01. KO, Shank3-/-."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "(E) Double-immunostaining of ENO1/Axin2 in WT neurons, Shank3-/- neurons, and XAV939 treated Shank3-/- neurons. Notice the colocalization of Axin2/ENO1-immunoreactivity in Shank3-/- neurons and the membrane localization of Axin2-immunoreactivity in XAV939 treated Shank3-/- neurons. Arrows point to membrane Axin2-immunoreactivity. Bar = 5 μm in E. WT, wild type. KO, Shank3-/-."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "(G) Protein CO-IP of Axin2/ENO1 in WT and Shank3-/- neurons treated with or without XAV939. Notice the strong interaction of Axin2/ENO1 in Shank3-/- neurons and diminished interaction upon XAV939 treatment. per group and 3 samples from 9 mice per group in One-way ANOVA with Tukey's multiple-comparison test WT, wild type. KO, Shank3-/-."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "Spine length, spine density and spine subtypes of Shank3-/- ACC neurons treated with or without XAV939. Notice the increase of total spine density, stubby and mushroom-like spines and the decrease of average spine length in XAV939 treated Shank3-/- mice. 32 spines from 3 mice in Filopodia analysis in F. Spines analysis excepting filopodia analysis in F. KO, Shank3-/-."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "(H) Western-blotting of p-PSD95 and Homer1 in WT and Shank3-/- ACC treated with or without XAV939. 4-6 mice in One-way ANOVA with Tukey's multiple-comparison test WT, wild type. KO, Shank3-/-."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "(I, J) Western-blotting of GluR1 in the total and membrane protein of WT and Shank3-/- neurons treated with or without XAV939. Notice the rescuing effects of XAV939 on the expression of GluR1 in Shank3-/- neurons. 4-6 mice in and 3 samples from 12 mice in (J) per group. One-way ANOVA with Tukey's multiple-comparison test WT, wild type. KO, Shank3-/-."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "Calcium response of WT and Shank3-/- neurons treated with or without XAV939. Notice that XAV939 treatment significantly restored the amplitude, rising and decay time of calcium response in Shank3-/- neurons. Bar = 15 μm in (A) and 30 μm in magnified images of (A). N = 39 neurons from 3 batches of cells in Kruskal-Wallis H test with Dunn's multiple-comparison test KO, Shank3-/-. Veh, vehicle."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "Calcium response of WT and Shank3-/- neurons treated with or without XAV939. Notice that XAV939 treatment significantly restored the amplitude, rising and decay time of calcium response in Shank3-/- neurons. N = 39 neurons from 3 batches of cells in Dunn's multiple-comparison test KO, Shank3-/-. Veh, vehicle."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "(D) Patch-clamp recording of mEPSCs in Shank3-/- ACC treated with or without XAV939. Both the frequency and amplitude of Shank3-/- neurons were increased by XAV939. , 7-8 neurons from 3 mice in (D) KO, Shank3-/-. Veh, vehicle."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "resident-intruder assays of Shank3-/- mice treated with or without XAV939. Notice the improvement of social preference, social novelty and social interaction of Shank3-/- mice by XAV939 treatment. 8-10 mice KO, Shank3-/-. Veh, vehicle."
NCBI gene IDs:
"Shank3: 58234"
Figure legend: "(B) Western-blotting of β-catenin, p-β-catenin(S33), GSK-3β, p-GSK-3β(S9) and TCF7L1 in neurons derived from WT or Shank3 mutant human ESCs. Notice the similar change of Wnt signaling components as in Shank3-/- mice. N = 3-4 batches of cells in Mean ratio ± SEM. Two-tailed unpaired t-test (Wnt components expression excepting TCF7L1 and GSK3β in Mann-Whitney U test (TCF7L1 expression in B). Welch's t-test (GSK3β expression in B). WT, wild type. KO, Shank3-"
NCBI gene IDs:
"Shank3: 85358
Shank3: 58234"
Figure legend: "(C) Protein CO-IP assay of Axin2/ENO1 in WT and Shank3 mutant human NPCs. (D) Protein CO-IP assay of Axin2/ENO1 in WT and Shank3 mutant human neurons. Notice the strong interaction of Axin2/ENO1 Shank3 mutant human neurons. N = 3-4 batches of cells in WT, wild type. KO, Shank3-/ NPC, neural progenitor cell.  "
NCBI gene IDs:
"Shank3: 85358"
Figure legend: "Luciferase activity was quantified in lysates of RAW 264.7 cells transfected with pGL3 basic vector harboring wild-type (wt) or mutated (mut1 or 2) IL-23p19 promoter. Transfected cells were pre-treated with JNKi (SP600125, 25 µM, 1h) and stimulated with IMQ (6h). Results are shown as fold change to pGL-3-wt transfected, LAL (Limulus amebocyte lysate) treated RAW264.7 cells. (n = 4; 2 independent experiments)."
NCBI gene IDs:
"IL-23: 83430
JNK: 26414///104771///26420"
Figure legend: "DC subsets (cDC1, cDC2), Macrophages (MP) and Langerhans cells (LC) were sorted from IMQ treated back skin (5h). c-Jun, Ccl2 and Il23p19 mRNA was analyzed by qRT-PCR. Sort strategy is shown in (B). (10 mice were pooled per condition, 1 experiment)."
NCBI gene IDs:
"Ccl2: 20296
Il23: 83430
c-Jun: 16476"
Figure legend: "A) Assessment of the detection limit of synthetic SARS-CoV-2 by the CRISPR-based assay, inferred from fluorescence values after 30 min. Background subtracted fluorescence represents sample minus control fluorescence without target."
NCBI gene IDs:
"CRISPR: "
Figure legend: "Detection of synthetic SARS-CoV-2 RNA using commercially available paper strips (lateral-flow) in buffer (B)"
NCBI gene IDs:
"SARS-CoV-2: "
Figure legend: "Detection of synthetic SARS-CoV-2 RNA using commercially available paper strips (lateral-flow) in saliva (C)."
NCBI gene IDs:
"SARS-CoV-2: "
Figure legend: "(a) Genomic deletion of Atg7 in H-2Db-gp33+ T cells and in total activated (CD44hiCD62Llo) CD8+ T cells from Atg7fl/fl mice (Cre −) and Atg7fl/flGzmb-Cremice (Cre +) at day 8 after infection with LCMV Armstrong strain; results are presented relative to those of Atg7fl/fl mice, set as 100%. Each symbol represents an individual mouse; small horizontal lines indicate the mean (±s.e.m.)."
NCBI gene IDs:
"Cre: 
Atg7: 74244
Gzmb: 14939"
Figure legend: "(b) Immunoblot analysis of Atg7 and the products of its enzymatic activity (left margin) in CD44hiCD62Llo CD8+ T cells isolated at day 8 after infection as in a; β-actin serves as a loading control."
NCBI gene IDs:
"Atg7: 74244"
Figure legend: "(a) Flow cytometry of circulating LCMV-specific CD8+ T cells among peripheral blood mononuclear cells from Atg5fl/fl and Atg5fl/flGzmb-Cremice on days 8, 15 and 50 after infection with LCMV Armstrong strain. Numbers adjacent to outlined areas indicate percent H-2Db-gp33+ T cells, gated on CD8+ T cells. (b) Longitudinal kinetics of the appearance of H-2Db-gp33+ T cells in the peripheral blood of mice as in a (left), and percent H-2Db-gp33+ CD8+ T cells remaining on day 15 (right) (all presented as in Fig. 4h)."
NCBI gene IDs:
"Cre: 
Atg5: 11793
Gzmb: 14939"
Figure legend: "(a,b) Flow cytometry of CD8+ T cell obtained from chimeras generated (as in Supplementary Fig. 5a) by reconstitution of wild-type mice with a mixture of bone marrow cells from Atg7fl/fl C57BL/6 and wild-type C57BL/6C57BL/6 (Atg7fl/fl vs C57BL/6) or from Atg7fl/flGzmb-Cremice and wild-type C57BL/6mice and (Atg7fl/flGzmb-Cre vs C57BL/6), gated (far left) as populations specific for H-2Db-gp33 (a) or H-2Db-NP396 (b) and then assessed, on days 8, 15 and 30 after infection of recipients with LCMV Armstrong infection, as CD45.2+ (Atg7fl/fl or Atg7fl/flGzmb-Cre) donor cells or CD45.1+ (C57BL/6) donor cells (middle). Far right, appearance of tetramer-positive T cells (key, donor source) in the peripheral blood of chimeras from day 8 to day 30 after infection, presented relative to that at day 8 after infection, set as 100%."
NCBI gene IDs:
"Cre: 
Atg7: 74244
Gzmb: 14939"
Figure legend: "(a) Kinetics of the appearance of H-2Db-gp276+ T cells in the peripheral blood of Atg7fl/fl and Atg7fl/flGzmb-Cre mice at various times (horizontal axis) after infection with LCMV clone 13."
NCBI gene IDs:
"Cre: 
Atg7: 74244
Gzmb: 14939"
Figure legend: "(A) Representative image of a typical young WT cortico-hippocampal slice (350 µm) from co-culture (14 DIV) stained with DAPI (gray) to visualize nuclei (left). Dentate gyrus (DG), cornus ammonis 1 (CA1) and cortical (CTX) regions are indicated. An example of the co-culture dish is shown on the right. Co-culture includes 2 young WT (*, young co-culture) and 2 old APPPS1 (+, old co-culture) brain slices."
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "(B) Immunofluorescence analysis of young WT and old APPPS1 slices cultured alone (young alone, old alone) or in co-culture (young co-culture, old co-culture) at 7 days in vitro (DIV) stained with propidium iodide (PI, red) reveals reduced cell viability in old brain slices compared to young.(C) Quantitative analysis of PI positive cells in young WT and old APPPS1 slices cultured alone (white and black bars, respectively) or in co-culture (grey and white squared bars, respectively) at 7 and 14 DIV. The values are expressed as percentages of PI positive cells from the total number of DAPI positive cells. The values represent mean ± SEM from 3 independent experiments, each experiment including 2 independent slice culture dishes (n.s.= not significant; ***P &lt; 0.001)."
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "(D-F) Immunofluorescence analysis of young WT and old APPPS1 slices cultured alone or in co-culture at 7 DIV and immunostained using neuronal (NeuN), astrocytic (GFAP) and microglial (CD68) markers (green) reveals reduced NeuN and GFAP and increased CD68 immunosignal. Scale bar: 75 µm"
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "(A) Immunofluorescence analysis of the old APPPS1 slice in co-culture using antibody 6E10 to detect amyloid plaques (green) and Thiazine Red (TR, red) to visualize fibrillar amyloid cores. At 7 DIV, the majority of amyloid plaques contain 6E10 and TR positive dense core surrounded by 6E10 positive halo of diffuse Aβ. In contrast, at 14 DIV, the majority of amyloid plaques are core-only plaques co-stained with 6E10 and TR without detectable 6E10 positive halo. Lower panels are higher magnification images of boxed regions. Scale bars: 50 µm."
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "(B) Quantitative analysis of core-only plaques in old APPPS1 slices cultured alone (white bars) or in co-culture (gray bars) at 7 and 14 DIV reveals an increased number of core-only plaques upon co-culturing of old APPPS1 brain slices together with young WT slices. The values are expressed as percentages of core-only plaques from the total number of amyloid plaques. The values represent mean ± SEM from 3 independent experiments, each experiment including 3 independent slice culture dishes (***P &lt; 0.001)."
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "(C) Western blot analysis of Aβ levels (triplicates) in the old APPPS1 tissue cultured alone or in co-culture with the young WT (14 DIV) using 2D8 antibody.(D) Quantification of Western blot signals reveals decreased levels of Aβ upon co-culturing compared to old tissue cultured alone. The values are normalized to the levels of Aβ in the old tissue cultured alone and represent mean ± SEM from 2 independent experiments, each experiment was performed in triplicates (**P &lt; 0.01)."
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "(A, B) Immunofluorescence analysis of the old APPPS1 slice in co-culture (14 DIV) using antibodies 6E10 (green) and CD68 (red). Nuclei were counterstained using DAPI (blue). Image of boxed region in A is depicted at higher magnification in B and reveals clustering of several CD68 positive cells around amyloid plaques. Scale bars: 100 µm (A) and 10 µm (B).(C) Quantitative analysis of plaque-associated CD68 positive cells in co-culture samples at 7 and 14 DIV reveals a trend towards increased number of CD68 positive cells. The values represent mean ± SEM from at least 3 independent experiments, including total of at least 6 independent slice culture dishes (n.s.= not significant).(D) Quantitative analysis of co-culture samples at 7 and 14 DIV reveals a decrease in plaque size. The values represent mean ± SEM from at least 3 independent experiments, including total of at least 6 replicates (***P &lt; 0.001).(E) Quantitative analysis of plaques surrounded by CD68 positive cells (clustered plaques) in co-culture samples at 7 and 14 DIV reveals an increase in the number of clustered plaques. The values are expressed as percentages of clustered plaques from the total number of amyloid plaques. The values represent mean ± SEM from at least 3 independent experiments, including total of at least 6 independent slice culture dishes (***P &lt; 0.001)."
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "(F) Immunofluorescence analysis of the old APPPS1 slice in co-culture (14 DIV) treated with cytochalasin D (CytoD) and vehicle control (Ctr) and immunostained with M3.2 (green) and CD68 (red). Inhibition of phagocytosis by CytoD blocks amyloid plaque clearance. Scale bar: 50 µm.(G) Quantitative analysis of core-only plaques in the old APPPS1 slice in co-culture (14 DIV) treated with CytoD and Ctr reveals a decreased number of core-only plaques upon CytoD treatment. The values are expressed as percentages of core-only plaques from the total number of amyloid plaques. The values represent mean ± SEM from 3 independent experiments, including total of 6 independent slice culture dishes (***P &lt; 0.001)."
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "Either young WT (A, B) or old APPPS1 (C-E) tissue was treated with clodronate (Clo) to remove CD68 positive cells or vehicle Ctr from 1 until 7 DIV. Treatment was stopped and subsequently old (A, B) or young (C-E) tissue was added to the culture as schematically indicated in A and C. and analyzed 14 days after. Removal of CD68 positive cells in either young WT or old APPPS1 tissue prevents amyloid plaque clearance in the co-culture model.(A) Immunofluorescence analysis of the old APPPS1 slice co-cultured with the young WT slice pre-treated with Clo and Ctr and immunostained with CD68 (red) and M3.2 (green). Scale bar: 50 µm.(B) Quantitative analysis of core-only plaques in the old APPPS1 tissue co-cultured with the young WT tissue pre-treated with Clo and Ctr as indicated in A reveals a decreased number of core-only plaques upon Clo treatment. The values are expressed as percentages of core-only plaques from the total number of amyloid plaques and represent mean ± SEM from 3 independent experiments, including total of 6 independent slice culture dishes (***P &lt; 0.001).(C) Immunofluorescence analysis of the old APPPS1 slice treated with Clo and Ctr and subsequently co-cultured with the young WT slice and immunostained with CD68 (red) and M3.2 (green). Scale bar: 50 µm.(D) Area of CD68 positive cells (CD68 coverage) in the old APPPS1 tissue treated with Clo and Ctr and subsequently co-cultured with the young WT tissue as indicated in C. CD68 coverage is reduced upon Clo treatment. The values are normalized to CD68 coverage of the Ctr and represent mean ± SEM from 3 independent experiments, including total of 6 independent slice culture dishes (***P &lt; 0.001).(E) Quantitative analysis of core-only plaques in the old APPPS1 tissue treated with Clo and Ctr and subsequently co-cultured with the young WT tissue as indicated in C reveals a decreased number of core-only plaques upon Clo treatment. The values are expressed as percentages of core-only plaques from the total number of amyloid plaques and represent mean ± SEM from 3 independent experiments, including total of 6 independent slice culture dishes (**P &lt; 0.01)."
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "(A) Immunofluorescence analysis of the old APPPS1 slice in co-culture with the young CX3CR1+/GFP slice (14 DIV) and immunostained using GFP (green), CD68 (red) and M3.2 (blue) reveals no co-localization of young, GFP positive microglial cells with CD68 positive cells surrounding amyloid plaques. A GFP antibody was used to amplify the signal of GFP-expressing young microglial cells.(B) Immunofluorescence analysis of the old APPPS1/CX3CR1+/GFP slice in co-culture with the young WT slice (14 DIV) and immunostained using GFP (green), CD68 (red) and M3.2 (blue) reveals co-localization of old, GFP positive microglial cells with CD68 positive cells surrounding amyloid plaques. A GFP antibody was used to amplify the signal of GFP-expressing old microglial cells. Scale bar: 10 µm (A and B)."
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "(C) 3D reconstruction of the old APPPS1/CX3CR1+/GFP slice in co-culture with the young WT slice (10 DIV) and immunostained using GFP (green) and M3.2 (red). GFP positive old microglial cells surrounding amyloid plaques exhibit intracellular M3.2 positive immunoreactivity indicative of Aβ uptake. Overview at low magnification is shown in the left panel. Scale bar: 15 µm. A detailed plaque is shown at higher magnification in the right panels. Scale bar: 10 µm."
NCBI gene IDs:
"APP: 351
PS1: 5663"