Journal: Cell reports methods

Article Title: A fast, aqueous, reversible three-day tissue clearing method for adult and embryonic mouse brain and whole body

doi: 10.1016/j.crmeth.2021.100090

Figure Lengend Snippet: (A–H) Confocal images showing a dorsal view of the hippocampus of (A and B) Thy1-GFP-M, (C and D) GCaMP3-CaMK2-Cre, and (E and F) VGAT-Cre-tdTomato mice, and (G and H) cFos-Cre ERT2 -tdTomato mice after fear conditioning and tamoxifen administration. (I–P) Fluorescence images of whole adult brains scanned at the same plane displaying the hippocampal formation (top) and the DG and Ent (bottom), from wild-type (WT) animals injected with (I and J) Fast Blue, (K and L) AAV1 GCaMP6-CaMK2, (M and N) rAAV2 Arch-tdTomato, or (O and P) rAAV2 IRF670. (Q–X) Shown in (Q)–(T) are the dorsal hippocampus and Ent/Prh labeled with GFP and tdTomato after injection of AAV1 GCaMP6 and tdTomato-Cre virus into WT mice. (Q) Hippocampal formation, (R) entorhinal cortex and dentate gyrus. (S) 10X magnification of dentate gyrus and (T) perirhinal/entorhinal cortex. Shown in (U-X) is the injection of tdTomato-Cre virus into GCaMP3 mice. (U) Hippocampal formation, (V) entorhinal cortex and dentate gyrus. (W) 10X magnification of dentate gyrus and (T) perirhinal/entorhinal cortex. Scale bars, 200 μm for 4× and 80 μm for 10× magnification.

Article Snippet: Msx1-Cre ERT2 , Dr. Carol Mason , (Lallemand et al., 2013).

Techniques: Fluorescence, Injection, Labeling, Virus

Journal: Cell reports methods

Article Title: A fast, aqueous, reversible three-day tissue clearing method for adult and embryonic mouse brain and whole body

doi: 10.1016/j.crmeth.2021.100090

Figure Lengend Snippet: (A and B) Light-sheet images from Thy1-GFP animals in (A) hippocampus and (B) cortex. (C) Light-sheet imaging of CaMK2-GCaMP6 injection in the DG. (D and E) CA1 region of (D) Thy1-GFP and (E) GCaMP3-CaMK2 animals. (F–H) 3D visualization of cleared (F) cFos-Cre ERT2 -tdTomato brain, (G) VGAT-Cre-tdTomato, and (H) spinal cord from Msx1-Cre ERT2 -Tdtomato E18.5 mouse embryos. (I) 3D reconstruction of a whole adult mouse brain injected unilaterally with retro-AAV2 IRF670 and imaged with light-sheet microscopy (2× sagittal view). (J) Different brain with retro-AAV2 IRF670 (top view). (K) 12× magnification image from the same brain as in (J). (L) Injection of retro-AAV2 IRF670 into the S1DZ brain regions showing retro-labeled cells. (M) Light-sheet 3D reconstruction from animals injected with tdTomato-Cre (EC/Prh) and GCaMP6 (DG) virus. (N) 3D reconstruction of cortical neuron from Thy1-GFP animal showing dendritic spines. (O) Digital zoom from the same neuron in (N) showing spines. Scale bars, (A) 1,000 μm, (C) 700 μm, (F, G, J, L) 500 μm, (B, E, H, M) 200 μm, (D) 100 μm, (K, N) 20 μm, (O) 10 μm.

Article Snippet: Msx1-Cre ERT2 , Dr. Carol Mason , (Lallemand et al., 2013).

Techniques: Imaging, Injection, Microscopy, Labeling, Virus

Journal: Cell reports methods

Article Title: A fast, aqueous, reversible three-day tissue clearing method for adult and embryonic mouse brain and whole body

doi: 10.1016/j.crmeth.2021.100090

Figure Lengend Snippet: Brain sections after reverse clearing. (A) Sections from cFos-Cre ERT2 -tdTomato animals incubated with only Alexa 488 and 647 secondary antibodies. Only the endogenous tdTomato can be detected. (B–D) Sections from the same animals stained with antibodies against (B) mCherry (488), (C) tdTomato, and (D) doublecortin (DCX) (647). DCX staining is completely absent from the basolateral amygdala (BLA). (E–H) Confocal images from the (E) DG, (F) central gray of the pons (CGPn), (G) cerebellum, and (H) lateral septum (LSI) of Thy1-GFP half-brains stained with GFAP and TH antibodies. (I–K) 3D visualization (light sheet) from Thy1-GFP half-brains stained with GFAP and TH. (L) 3D visualization of cerebellum from Thy1-GFP half-brain stained with GFAP and TH using confocal microscopy. (M–O) Whole adult mouse hippocampus from GCaMP3-CaMK2-Cre animals cleared with Fast 3D Clear. (M) GCaMP3 fluorescence before staining, (N) fluorescence at 500/30 and 650LP nm for GCaMP3 and DCX in dorsal hippocampus, and (O) ventral hippocampus merged channels. Scale bars, (I, K) 500 μm, (J and L) 200 μm, (E, F, G, H, M, N, O) 80 μm, (A, B, D) 20 μm, (C) 5 μm.

Article Snippet: Msx1-Cre ERT2 , Dr. Carol Mason , (Lallemand et al., 2013).

Techniques: Incubation, Staining, Confocal Microscopy, Fluorescence

Journal: Cell reports methods

Article Title: A fast, aqueous, reversible three-day tissue clearing method for adult and embryonic mouse brain and whole body

doi: 10.1016/j.crmeth.2021.100090

Figure Lengend Snippet:

Article Snippet: Msx1-Cre ERT2 , Dr. Carol Mason , (Lallemand et al., 2013).

Techniques: Virus, Recombinant, Electron Microscopy, Software

Journal: bioRxiv

Article Title: Tissue-specific tolerance mechanisms and lymph node co-drainage converge to shape T cell immunity in the upper digestive system and regulate pancreatic cancer progression

doi: 10.64898/2025.12.02.691870

Figure Lengend Snippet: A-B. Expression levels of OVA in the liver ( A ) and pancreas ( B ) of mice with indicated genotypes ( n = 3-10 per group, as indicated by symbols). C-D . Hepatic ( C ) and pancreatic ( D ) tissue lysates from mice with indicated OVA form and their CRE-negative controls were immunoblotted using antibodies against FLAG, and β-ACTIN as a loading control. E . Sections of pancreas (top) and liver (bottom) from mice with indicated genotypes stained for FLAG and DAPI (nuclei). Scale bar represents 20μm. F-H. OVA expression levels in the liver, pancreas and duodenum tissue of mice with indicated genotypes, showing tissue-specific expression restricted to the intended sites ( n = 3-10 per group, as indicated by symbols). I. Division index of OT-II cells in the indicated LNs 6 days after transfer into Ins1 sOVA , Ins1 cOVA and Ins1 tmOVA mice ( n = 4-7 per group, as indicated by symbols). J . Hepatic tissue lysates from Alb sOVA mice treated with or without tamoxifen and B6 mice were immunoblotted using antibodies against FLAG and β-ACTIN. K. OVA expression levels in liver tissue of Alb sOVA mice treated with or without tamoxifen and sOVA mice infected with adeno-Cre virus and pancreas of Ptf1a sOVA mice ( n = 3-5 per group, as indicated by symbols). L . Hepatic tissue lysates from Alb sOVA mice without tamoxifen treatment and pancreatic lysates from tamoxifen-treated Ptf1a sOVA mice were immunoblotted using antibodies against FLAG and β-ACTIN. Data are pooled from two independent experiments in A, B, F-I. * p<0.05, ** p<0.01, *** p<0.001 by t-test.

Article Snippet: C57BL/6J, CD45.1 congenic (B6.SJL-Ptprc a Pepc b /BoyJ), Villin CRE-ERT2 (B6.Cg-Tg(Vil1-cre/ERT2)23 Syr/J), Ptf1a CRE-ERT2 (B6.129S6(Cg)-Ptf1a tm2 (cre/ESR1)Cvw/J), Ins1 CRE-ERT2 (B6(Cg)-Ins1 tm2.1(cre/ERT2)Thor /J), OT-I (C57BL/6-Tg(TcraTcrb) 1100Mjb/J), OT-II (B6.Cg-Tg(TcraTcrb)425Cbn/J), Alb Cre (B6.Cg-Speer6-ps1 Tg (Alb-cre)21 Mgn/J), p53 LOXP (B6.129P2- Trp53 tm1Brn /J) and Kras FSF-G12D (B6(Cg)- Kras tm5Tyj /J) were purchased from The Jackson Laboratory.

Techniques: Expressing, Control, Staining, Infection, Virus

Journal: bioRxiv

Article Title: Tissue-specific tolerance mechanisms and lymph node co-drainage converge to shape T cell immunity in the upper digestive system and regulate pancreatic cancer progression

doi: 10.64898/2025.12.02.691870

Figure Lengend Snippet: A-B . CFSE dilution flow plots ( A ) and division index ( B ) of OT-II cells in the indicated LNs 96 h after transfer into Alb sOVA , Alb cOVA or Alb tmOVA mice ( n = 3-7 per group, as indicated by symbols). C-D . CFSE dilution flow plots ( C ) and division index ( D ) of OT-II cells in the indicated LNs 96 h after transfer into Ptf1a sOVA , Ptf1a cOVA or Ptf1a tmOVA mice ( n = 4-8 per group, as indicated by symbols). E . Division index of OT-II cells in the indicated LNs 96 h after transfer into Alb cOVA mice treated with con A ( n = 3 per group). F . Division index of OT-II cells in the indicated LNs 96 h after transfer into Ptf1a cOVA mice treated with cerulein ( n = 3 per group). G. Frequencies of OT-II among total CD4 + T cells in the indicated LNs and spleen 96 h after transfer into OVA-naïve, tamoxifen-induced and non-induced Alb sOVA mice ( n = 7-11 per group, as indicated by symbols). H-I. CFSE dilution flow plots ( H ) and frequencies of OT-II among total CD4 + T cells ( I ) in the indicated LNs of adeno-infected Alb sOVA and adeno-infected sOVA mice ( n = 5 per group). J. Flow plots of OT-II cells in livLN of Alb sOVA mice treated with CCl 4 . K . Frequencies of FOXP3 + among total OT-II cells in the indicated LNs 96 h after transfer into Alb tmOVA , Ptf1a sOVA , Ptf1a tmOVA and Ins1 sOVA mice ( n = 3-8 per group, as indicated by symbols). L . Frequencies of FOXP3 + OT-II cells in the indicated LNs 96 h after transfer into Ptf1a sOVA mice treated with cerulein ( n = 5-7 per group, as indicated by symbols). Data are representative of two independent experiments in B, D, E-G, K, L. * p<0.05, ** p<0.01, *** p<0.001 by one-way ANOVA and t-test.

Article Snippet: C57BL/6J, CD45.1 congenic (B6.SJL-Ptprc a Pepc b /BoyJ), Villin CRE-ERT2 (B6.Cg-Tg(Vil1-cre/ERT2)23 Syr/J), Ptf1a CRE-ERT2 (B6.129S6(Cg)-Ptf1a tm2 (cre/ESR1)Cvw/J), Ins1 CRE-ERT2 (B6(Cg)-Ins1 tm2.1(cre/ERT2)Thor /J), OT-I (C57BL/6-Tg(TcraTcrb) 1100Mjb/J), OT-II (B6.Cg-Tg(TcraTcrb)425Cbn/J), Alb Cre (B6.Cg-Speer6-ps1 Tg (Alb-cre)21 Mgn/J), p53 LOXP (B6.129P2- Trp53 tm1Brn /J) and Kras FSF-G12D (B6(Cg)- Kras tm5Tyj /J) were purchased from The Jackson Laboratory.

Techniques: Infection

Journal: bioRxiv

Article Title: Tissue-specific tolerance mechanisms and lymph node co-drainage converge to shape T cell immunity in the upper digestive system and regulate pancreatic cancer progression

doi: 10.64898/2025.12.02.691870

Figure Lengend Snippet: A. Gating strategy for OT-II proliferation and cell fate of both OT-I and OT-II cells. B. Frequencies of T-BET + among total OT-II cells in the indicated LNs 96 h after transfer into Alb tmOVA , Ptf1a sOVA , Ptf1a tmOVA and Ins1 sOVA mice ( n = 3-8 per group, as indicated by symbols). C-F. Frequencies of GATA3 + ( C, E ) or FOXP3 + ( D, F ) among total OT-II cells 72 h after transfer into Ins1 sOVA ( C-D ) or Ptf1a sOVA ( E-F ) mice that were S. venezuelensis - or mock-infected ( n = 8-10 per group, as indicated by symbols). G-H. Frequencies of FOXP3 + ( G ) or T-BET + ( H ) among total OT-II cells in indicated LNs 72 h after transfer into T1L- or mock-infected Ins1 sOVA mice ( n = 5 per group). Data are pooled from two independent experiments in B-H. * p<0.05, ** p<0.01, *** p<0.001 by t-test.

Article Snippet: C57BL/6J, CD45.1 congenic (B6.SJL-Ptprc a Pepc b /BoyJ), Villin CRE-ERT2 (B6.Cg-Tg(Vil1-cre/ERT2)23 Syr/J), Ptf1a CRE-ERT2 (B6.129S6(Cg)-Ptf1a tm2 (cre/ESR1)Cvw/J), Ins1 CRE-ERT2 (B6(Cg)-Ins1 tm2.1(cre/ERT2)Thor /J), OT-I (C57BL/6-Tg(TcraTcrb) 1100Mjb/J), OT-II (B6.Cg-Tg(TcraTcrb)425Cbn/J), Alb Cre (B6.Cg-Speer6-ps1 Tg (Alb-cre)21 Mgn/J), p53 LOXP (B6.129P2- Trp53 tm1Brn /J) and Kras FSF-G12D (B6(Cg)- Kras tm5Tyj /J) were purchased from The Jackson Laboratory.

Techniques: Infection