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14 protocols using calbindin

1

Immunofluorescence Staining of Signaling Proteins

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Sections were blocked with 2.5% normal horse serum and incubated overnight at 4 °C in primary antibodies as follows: Egr-1 and phosphorylated c-Jun N-terminal kinase (p-JNK) from Cell Signaling, aquaporin-1 (AQP1) from Santa Cruz Biotechnology (Dallas, TX, USA), and Calbindin from Abcam (Cambridge, MA, USA). After washing, the sections were incubated with Alexa Fluor488-conjugated and/or Alexa Fluor594-conjugated secondary antibodies (Vector Laboratories, Burlingame, CA, USA). Fluorescence was visualized using a Fluoview 1000 IX-81 confocal microscope (Olympus). The fluorescence intensity of p-JNK was analyzed using Image J software, Version 1.52a (NIH, Bethesda, MD, USA).
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2

Assessing Neuroinflammation and Neurodegeneration in R6/2 Mice

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Eighty animals (20 R6/2 treated with vehicle, 20 R6/2 treated with Olaparib, 20 vehicle and 20 Olaparib-treated Wild type mice) were transcardially perfused under deep anesthesia with saline solution containing 0.01 mL heparin, brains were removed and cut in half. Tissue sectioning was performed on a sliding frozen microtome at 40 μm thickness. All brain sections were processed for single label EM-48 ubiquitin (1:500, Chemicon, Temecula, CA); NLRP3 (1:200, Abcam, Novus Biologicals, Italy); Calbindin (1:500, Abcam, Novus Biologicals, Italy); Parvalbumin (1:200, Chemicon International, Inc., Temecula, CA, USA); Calretinin (1:200, Chemicon International, Inc., Temecula, CA, USA), and GFAP (1:600 polyclonal anti-GFAP, Millipore, Italy). We used Alexa Fluor 488 and Alexa Fluor 555 (Immunological Sciences, Italy) as secondary antibodies. Brain sections from the same level of the bregma, were mounted on gelatin-coated slices and cover slipped with Gel-Mount. Samples were examined with the support of confocal laser scanner microscopy (Zeiss LSM 800); images were acquired and subsequently analyzed to quantify the immunofluorescence intensity of Calbindin, NLRP3, Parvalbumin, Calretinin, and GFAP-positive cells. To evaluate pyroptosis, peroxidase-antiperoxidase diaminobenzidine tetrahydrochloride single-label immunohistochemistry for caspase-1 was performed [23 (link)].
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3

Immunostaining of Mouse Retinal Cells

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Transduced mouse retinas were dissected and fixed in 4% paraformaldehyde for 30 min at room temperature. The retinas were incubated in PBS with 1% Triton X-100, 0.5% Tween 20 for 1 h at room temperature and in 10% normal goat serum for 1 h at room temperature and then incubated overnight at 4 °C with primary antibody: Brn3a (1:100; Santa Cruz Biotechnology, Santa Cruz, CA, USA), rhodopsin (1:500; Abcam, Cambridge, UK), PKCα (1:500; Abcam), calbindin (1:500; Abcam) and glutamine synthetase (GS) (1:500; Abcam) in blocking buffer. Secondary anti-rabbit IgG and anti-mouse IgG conjugated with Alexa TM594 and Alexa TM555, respectively (1:1,000; Molecular Probes), were applied for 1 h at room temperature. The retinas then were flat-mounted and the sections mounted on slide glass.
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4

Immunostaining of Retinal Sections

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After hydration and 3 × 5 min washes in 0.01M PBS, retinal sections were blocked for 1 hour at room temperature in PBS + 0.1% Triton X-100 + 10% donkey serum. After 3 × 5 min washes, the sections were incubated at 4°C overnight with the primary antibody (PKCalpha 1:1000, Epitomics (1510-1); Calbindin 1:1000 Abcam (ab11426); Brn-3a 1:250, Santa Cruz (sc-31984)) and subsequently for 2 hours at room temperature with secondary antibody (Alexa Fluor 555 donkey anti-rabbit IgG) both in PBS + 0.1% Triton X-100 + 1% serum. After each step, sections were rinsed for 2 × 5 min in PBS + 0.05% Tween20, followed by 1 × 5 min in PBS alone. All sections were counter-stained with Hoechst 33342 (Invitrogen) 1:5000 and mounted with an antifade reagent (Prolong Gold; Invitrogen).
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5

Antibody Sources for Neuroscience Research

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Primary antibodies were purchased from Abcam (Cambridge, UK) (calbindin, cat. no. ab82812: IHC: 1:200; MAP2, cat. no. EPR19691: ICC: 1:500), Covance (Princeton, NJ, USA) (βIII-tubulin, cat. no. PRB-435P: WB 1:5000), OriGene (Herford, Germany) (ZIP4, cat. no. TA333766: ICC 1:500, WB 1:500), Sigma-Aldrich (Arklow, Ireland) (β-actin, cat. no. A2228: WB 1:10000), Synaptic systems (BASSOON, cat. no. 141004: ICC 1:500; HOMER1b/c, cat. no. 160022: ICC 1:500, IHC: 1:200) and Thermo Fisher Scientific (ZIP4, cat. no. PA5-101971: ICC 1:150, IHC 1:200, WB 1:1000). SHANK3 antibodies (ICC 1:500, WB 1:500) have been described previously [32 (link)]. Secondary Alexa-coupled antibodies were purchased from Invitrogen and HRP-coupled from Dianova and Dako. Secondary-HRP conjugated antibodies were purchased from Thermo Fisher (Thermo Fisher Scientific, Waltham, MA, USA). Unless otherwise indicated, all other chemicals were obtained from Sigma-Aldrich (Merck, Ireland).
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6

Fluorescent Labeling and Immunostaining Protocol

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As shown in Figures 7, 10, 11, 17, and 18, we performed fluorescent mRNA labeling and protein immunostaining of the same sections using a modification of previously described methods (Watakabe et al., 2010). Hybridization with DIG‐labeled probes and washing were performed as described above. Subsequently, the sections were incubated in 1% blocking buffer (11096176001, Roche) for 1 hr. Primary antibodies for PV (1:400; Abcam), calbindin (1:400; Abcam), or calretinin (1:400; Millipore) and an anti‐DIG antibody conjugated with alkaline phosphatase (1:500; Roche) were included in the incubation mixture. The sections were washed three times with TNT and incubated with an Alexa Fluor 488‐conjugated secondary antibody (1:400; Jackson ImmunoResearch Labs) for 2 hr. After three washes with TNT and one wash with TS 8.0, alkaline phosphatase activity was detected using the HNPP fluorescence detection set (11758888001, Roche) according to the manufacturer's instructions. The sections were incubated with the substrate three times for 30 min, and the reaction was stopped by washing with PBS. The sections were then counterstained with DAPI diluted in PBS (2 μg/ml) for 5 min. After washing with PBS, the sections were mounted in PermaFluor (Thermo Fisher Scientific).
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7

Comprehensive Antibody Validation for Research

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Primary antibodies used in this study are as follows: antibodies against RBM4 (1:2000 for immunoblotting, 1:150 for IHC; ProteinTech, 11614-1-AP), Pax6 (1:150; Millipore, AB2237), BrdU (1:50; ABclonal, A1482), Ki67 (1:300; Abcam, ab15580), calbindin (1:200; Abcam, ab108404), NeuN (1:1000; Abcam, ab177487), cleaved caspase-3 (1:100; 5A1E, Cell Signaling Technology, 9664), BDNF (Abcam, ab108319), TrkB (1:1000; Cell Signaling Technology, 4603), phospho-TrkB Tyr816 (1:200; Millipore, ABN1381), phospho-TrkB Tyr817 (1:1500; Invitrogen, MA5-32207), FLAG® (1:2500; Sigma-Aldrich, F1804), GAPDH (1:3000; ProteinTech, 60004-1-Ig), β-actin (1:5000; ProteinTech, 66009-1-Ig) and α-Tubulin (1:3000; Millipore, 05-829). These antibodies were quality-checked by previous publications.
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8

Neuronal Activation Mapping in Mouse Brain

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Mice were sacrificed 90 min after the last trial of the behavioural tasks by a lethal dose of sodium pentobarbital. The brains were removed after transcardial perfusion, and then post-fixed overnight using 4% paraformaldehyde (PFA), after which they were put into 25–30% sucrose solution for 3 days in PBS and then sliced in 30 µm thick coronal sections. For immunofluorescence, sections were washed in PBS-T (PBS consists of 0.1% Triton X-100) and subsequently incubated using Calbindin (1:500; Cat no. Ab108404, Abcam), Calbindin D-28k (1:500; Code No:300, Swant) and/or c-Fos (1:300; Cat no. 226003, Synaptic Systems) for 17–20 h. Followed by 1 h incubation with the secondary antibody using Alexa Fluor 488 donkey to rabbit IgG(H+L), 1:300, Invitrogen A21206; using Alexa Fluor 488 donkey to mouse IgG(H+L), 1:300; Invitrogen A21202 or Alexa Fluor 546 Donkey Anti-Rabbit IgG, 1:300, Invitrogen A10040 at 37 °C, the sections were washed with PBS-T (10 min, three times). Finally, the slices were counterstained with DAPI. Fluorescence images were analyzed by Image J 64. Information of antibodies for immunostaining was listed in Supplementary Table 2.
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9

Immunohistochemical Analysis of Transgenic Brains

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The animals were terminally anesthetized with Mebunat (Orion, Finland) and perfused intracardially with 4% paraformaldehyde in PBS or sacrificed with CO2. Brains were removed, post-fixed with 4% paraformaldehyde in PBS followed by embedding in paraffin. All histological and immunoassays were carried out on 7–10 μm sagittal sections. Immunohistochemical and immunofluorescence stainings were described previously40 (link) and performed on a minimum of n = 3 of each genotype. COX/SDH activity analysis is described elsewhere38 (link). Images were acquired with either Zeiss AxioImager epifluorescent microscope or Zeiss LSM 780 confocal microscope. Primary antibodies were rabbit Calbindin (Abcam), GFAP (Millipore), ALDH1L1 (Abcam), cleaved Caspase 3 (Cell Signaling Technology), IBA1 (Wako), Olig2 (Merck Millipore), KI67 (Merck Millipore); mouse Nestin (Merck Millipore), SDHA (CII) (Abcam), NeuN (Chemion), GAD67 (Merck Millipore); Neurofilament Marker pan axonal cocktail (BioLegend); chicken MAP2 (Thermo Scientific); rat MBP (Nordic BioSite). Golgi staining was processed using the FD Rapid GolgiStain Kit (FD Neuro Technologies). Fluoro-Jade C was from Millipore. Morphometrical analysis of coronal 80-μm-thick sections was described in ref. 41 (link). For cell counting, images from mid-sagittal sections were taken from three to six mice per genotype.
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10

Kidney Organoid Development and Characterization

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Sox9 (Sigma, #SAB4502834 and #WH0006662M2), Pax8 (Abcam, #ab13611), Ki67 (Sigma, # SAB4501880), LTL (Vector Labs, #FL-1321), DBA (Vector Labs, #FL-1031), PNA (Vector Labs, #FL-1071), E-cadherin (Cell Signaling, #31955), N-cadherin (Cell Signaling, #4061), aquaporin I (Abcam, #ab11025), aquaporin II (Abcam, #ab62628), calbindin (Abcam #ab11426), FBS (Atlanta Biologicals), EGF, Wnt4, Activin A, BMP7 TGFβ3 (Peprotech), hydrocortisone and dexamethasone (Sigma), RPMI 1640, Penicillin Streptomycin and ITS (Cellgro), collagenase I (Worthington Biochemical Product), 100 μm mesh (Fisherbrand), doxycycline-containing chow (Bioserv S3888).
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