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5 protocols using western blocking buffer

1

Protein Analysis of Mature Brown Adipocytes

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Cells were differentiated into mature brown adipocytes according to a standard adipogenic differentiation protocol. After that, cells were scraped from tissue-culture plates into RIPA buffer (Boston BioProducts Inc., Ashland, MA, USA) supplemented with protease and proteinase inhibitors cocktails (Sigma-Aldrich, Dallas, TX, USA) and further homogenized for protein detection. Protein concentrations were determined using a Pierce BCA kit (Life Technologies, Carlsbad, CA, USA), according to the manufacturer’s instructions. For immunoblots, lysates were diluted into Laemmli buffer and boiled for loading onto 10% Tris gels for SDS–PAGE. After complete separation of the proteins, they were transferred onto a PVDF membrane (Amersham Biosciences, Amersham, UK), blocked in western blocking buffer (Roche, Basel, Switzerland), and primary antibodies were applied in blocking buffer overnight at 4 °C. After washing 4× for 15 min with TBS-T, secondary antibodies were applied for 1 h in blocking buffer. Membranes were washed again 3× times for 15 min in TBS-T and developed using chemiluminescence (Thermo Fisher, Waltham, MA, USA).
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2

Mitotic Cell Identification in Planarians

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Immunostaining was performed after FISH development by reblocking planarians in Blocking Solution (5% heat inactivated horse serum, 5% Roche Western Blocking Buffer in TNTx) for 2 hours at room temperature, labeling mitotic cells with anti-phospho-Histone H3 (Ser10) (1:2,000) in Blocking Solution overnight at 12°C, washing 6X in PBSTx (30 minutes each), reblocking for 2 hours at room temperature, and incubating with HRP-conjugated goat anti-mouse (1:500) in blocking solution overnight at 12°C. Planarians were washed 6X in PBSTx (30 minutes each) and TSA was performed for 30 minutes.
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3

Dual-color in situ hybridization in Drosophila embryos

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Embryos were dechorionated and fixed in fixation buffer (0.5x PBS, 25 mM EGTA, 4% formaldehyde and 50% Heptane) for 20 min at room temperature. Antisense RNA probes labeled with digoxigenin (DIG RNA Labeling Mix 10 × conc, Roche) and biotin (Biotin RNA Labeling Mix 10 × conc, Roche) were used to detect lacZ and snail RNAs, respectively. Hybridization was performed at 55 °C overnight in hybridization buffer (50% formamide, 5x SSC, 50 μg/ml Heparin, 100 μg/ml salmon sperm DNA, 0.1% Tween-20). Subsequently, embryos were washed with hybridization buffer at 55 °C and incubated with Western Blocking Buffer (Roche) at room temperature for one hour. Then, embryos were incubated with sheep anti-digoxigenin (Roche) and mouse anti-biotin primary antibodies (Invitrogen) at 4 °C for overnight, followed by incubation with Alexa Fluor 488 donkey anti-sheep (Invitrogen) and Alexa Flour 555 goat anti-mouse (Invitrogen) fluorescent secondary antibodies at room temperature for two hours. DNA was stained with Hoechst 33342 (Thermo Fisher Scientific), and embryos were mounted in ProLong Gold Antifade Mountant (Thermo Fisher Scientific). Imaging was performed on a Zeiss LSM 880 confocal microscope. Plan-Apochromat 20x / 0.8 N.A. objective was used. Images were captured in 16 bit.
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4

Optimized FISH Protocol for Planarian

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FISH protocols were performed as previously described [58 (link),59 (link)] with the following modifications. Asexual and sexual hatchling/sexual adult planarians were killed in 7.5% N-acetyl-L-cysteine in 1X PBS for 5/10 minutes; fixed in 4% formaldehyde in PBSTx (1X PBS + 0.1% Triton X-100) for 15/30 minutes; bleached in Bleaching Solution (1X SSC solution containing 5% deionized formamide and 1.2% hydrogen peroxide) for 2/4 hours; incubated in PBSTx containing 10 μg/ml Proteinase K and 0.1% SDS for 10/20 minutes; and refixed in 4% formaldehyde in PBSTx for 10/15 minutes. Planarians were blocked in Blocking Solution (5% heat inactivated horse serum, 5% Roche Western Blocking Buffer in TNTx [0.1 M Tris pH 7.5, 0.15 M NaCl, 0.3% Triton X-100]) for 2 hours at room temperature, and incubated in Blocking Solution containing anti-Digoxigenin-POD (1:2,000), anti-Fluorescein-POD (1:2,000), or anti- Dinitrophenyl-HRP (1:2,000) for 8 hours at 12°C. For fluorescent development of riboprobes, TSA reactions were performed for 30 minutes.
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5

Immunofluorescence Staining Protocol

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All IF steps were conducted at room temperature. Blocking buffer (Western blocking buffer, Roche) was added to each well, incubated for 30–60 min, then removed. Cells were then incubated with fresh blocking buffer containing the appropriate primary antibodies at designated concentrations (Supplementary file 5) for 60 min followed by four, 5 min, washes with blocking buffer. Blocking buffer containing appropriate concentrations of the secondary antibodies and DAPI stain (Supplementary file 5) were then incubated with the cells for 40 min followed by four, 5 min, washes with PBS. Finally, the cells were fixed with 3.7% formaldehyde for 10 min followed by three washes with PBS.
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