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13 protocols using ab3350

1

Postnatal Pancreas Development Analysis

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P1 pups were intraperitoneally injected with BrdU (100 mg/kg; Sigma-Aldrich). Their pancreata were fixed in 4% PFA in PBS for 12 h at 4 °C followed by dehydration, paraffin embedding, and histologically analyzed as described previously (Lee et al, 2007 (link); Wei et al, 2014 (link)). For β-cell proliferation analysis in P1 pups every other section was labeled with guinea pig anti-insulin (1:200; DAKO A0564) and mouse anti-BrdU (1:500 Sigma B2531) antibodies, followed by fluorochrome-coupled secondary antibodies (Millipore) and DAPI counterstaining (Abcam). β-cell proliferation was quantified by counting the number of BrdU/insulin-positive cells over the total number of insulin-positive cells using ImageJ software. An average of 2000 insulin-positive cells per specimen was counted. Bmal1 and Clock levels were assessed on pancreas sections of P1 pups following co-labeling with rabbit anti-Bmal1 (1:500 Abcam ab3350) or rabbit anti-Clock (1:1000 Abcam ab3517) antibodies and a guinea Pig anti-insulin (1:800 DAKO A0564) antibody while Pck1 levels were assessed using a rabbit anti-PCK1 (1:400 Abcam ab70358) antibody, followed by fluorochrome-coupled secondary antibodies (Invitrogen A21206 and A21450).
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2

Quantitative Western Blot Protein Analysis

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Bicinchoninic acid assay (BCA assay) relative protein quantification was used for normalization of sample loading. Proteins with 6 μg (EGFR, CD81, FGF-2, Flottin-1, Grp94, HSA), 8 μg (securin) or 10 μg (NLGN3) were loaded on per channel. Samples were separated using the assay of vertical slab polyacrylamide gel electrophoresis. After that, proteins were transferred onto polyvinylidene fluoride membranes (PVDF Invitrogen) using wet electrophoretic transfer. The membranes were blocked with 5% (w/v) skim milk and then incubated with primary antibody in 3 mL primary antibody dilution buffer. Next, the membranes were washed three times for 5 min each with 5 mL TBST followed by incubation with secondary IgG and HRP-linked antibody.
Western blot antibodies are listed below: Anti-EGFR, Abcam, ab52894, 1/5000. Anti-CD81, CST, 10037S, 1/1000. Anti-FGF2, Abcam, ab16828, 2 μg/ mL. Anti-Securin, Abcam, ab3350, 1/1000. Anti-HSA, Biorbyt, orb24991, 1/1000. Anti-Grp94, Sino Biological, 106461, 1/1000. Anti-Flotillin 1, Abcam, ab133497, 1/10000. Anti-CD81, CST, sc166029, 1/500. Anti-mouse IgG, HRP-linked Antibody, CST, #7076, 1/1000. Anti-rabbit IgG, HRP-linked Antibody, #7074, 1/1000.
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3

Forskolin and Melatonin Modulate Chondrocyte Signaling

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Forskolin and melatonin were purchased from Sigma-Aldrich. Y-27632 and arachidonic acid (AA) were purchased from Selleck Chemicals. The following antibodies were used in this study: BMAL1 (Abcam ab3350 for immunofluorescence and Santa Cruz Biotechnology sc-365645 for western blot), aggrecan (Millipore Sigma AB1031), MMP13 (Abcam ab39012 for western blot and Proteintech 18165-1-AP for immunofluorescence), and phosphomyosin light chain 2 (Ser19; Cell Signaling Technology 3671). Horseradish peroxidase (HRP)-conjugated β-actin mouse monoclonal antibody, HRP-conjugated AffiniPure goat anti-mouse or goat anti-rabbit IgG (H + L), fluorescein (FITC)-conjugated AffiniPure goat anti-rabbit IgG (H + L), and Cy3-conjugated AffiniPure goat anti-rabbit IgG (H + L) were purchased from Proteintech. Cell culture reagents were purchased from Gibco.
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4

Chromatin Immunoprecipitation of Clock Proteins

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CHiP was performed using SimpleChIP® Enzymatic Chromatin IP Kit (Agarose Beads) (Cell signaling, Tokyo, Japan, #9002). Isolated IECs or cultured cells (HCT116 and Caco-2) were cross-linked in 1% formaldehyde, followed by the CHiP assay according to the manufacturer’s protocol. Rabbit polyclonal antibodies to CLOCK (ab3517) and BMAL1 (ab3350) were from Abcam (Cambridge, UK). DNA was purified and Q-PCR was done using SYBRgreen reagent (QIAGEN, Hilden, Germany). Primers used were as follows: mouse Occludin promoter forward 5′-CTCCCATCCGAGTTTCAGGT-3′ and reverse 5′-GCTGTCGCCTAAGGAAAGAG-3′, mouse Claudin-1 promoter forward 5′-GTTTGCAGAGACCCCATCAC-3′ and reverse 5′-AGAAGCCAGGATGAAACCCA-3′, human Occludin promoter forward 5′-CTCCCATCCGAGTTTCAGGT-3′ and reverse, human Claudin-1 promoter forward 5′-CTCCCCGCCTTAACTTCCTC-3′ and reverse 5′-CAGGAAGGCGAGAATGAAGC-3′, 5′-GGAGTGTAGGTGTGGTGTGT-3′.
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5

Oxidative Stress and Autophagy Protein Expression

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The expression of BMAL1 protein and proteins related to oxidative stress and autophagy was determined by the WB technique as previously described [17 (link)]. Total proteins were extracted by using RIPA lysis buffer supplemented by a protease inhibitor cocktail (Complets, Roche). The equivalent (50 μg) protein was transferred onto the PVDF membrane (IPFL00010; Millipor; USA) after 10% SDS-PAGE electrophoresis. Then, the membranes were blocked with 5% skimmed milk at room temperature and incubated overnight at 4 °C with primary antibodies. The antibody reagents were BMAL1 (ab3350; Abcam; USA,), β-Actin (AP0060; Abcam), Gp91phox (ab129068, Abcam) p67phox (3923, Cell Signaling technology), SOD2 (ab38155, Abcam), HO-1 (ab13243, Abcam), LC3 (12741, CST, USA), P62 (23214, CST), ATG 5,12 (AAM79-1, AbD Serotec, UK), ATG 7(2631, Cell Signaling technology) and Beclin1 (3738, Cell Signaling technology). HRP-conjugated secondary antibodies were then applied to bind and visualize the primary antibodies. Finally, images were obtained by Odyssey Infrared Imaging System (LI-COR Biosciences, USA) to quantify protein expression.
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6

Chromatin Immunoprecipitation of Acetylated Histones

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Hippocampal tissues were treated using the Magna CHIPTM G Tissue kit (Millipore, Darmstadt, Germany) according to the manufacturer's protocol and sonicated using a Biorupter Pico instrument (Diageuode, Japan) for 12.5 min (45 s, on; 30 s, off; 10 cycles). Cell samples were treated using the Zymo-Spin™ ChIP Kit (ZymoResearch, Irvine, CA) according to the manufacturer's protocol and sonicated for 10 min (30 s, on; 30 s, off; 10 cycles). Cross-linked chromatin was immunoprecipitated with antibodies against acetylated chromatin: anti-H3K9 (ab10812; Abcam, Hong Kong, China), anti-H3K27 (ab3350; Abcam), and anti-H3k4 (#ABE223; Millipore); normal rabbit IgG-B (sc-2763; Santa Cruz Biotechnology, Dallas, TX) was used as a negative control antibody. Three pairs of primers specific for the Asct2 promoter region (see Figure 4G) were used to detect the acetylation status of H3K9, H3K4, and H3K27. Real-time PCR was performed in triplicate.
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7

Comprehensive Antibody Validation Protocol

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Antibodies against Necdin (ab18554), SGT1 (ab30931), BMAL1 (ab3350), HSP90 (ab13492), PER1 (ab136451), PER2 (ab180655), CRY1 (ab104736) were purchased from Abcam. Antibody against AVP (sc-390723) were obtained from Santa Cruz. Antibodies against Myc-tag (2276), Flag-tag (14793), HA-tag (3724), VIP (63269) were obtained from Cell Signaling Technology. Antibody against CRY2 were obtained from Invitrogen. Antibody against GRP (20073) were obtained from ImmunoStar. 17-AAG (HY-10211) and Geldanamycin (HY-15230) were purchased from MedChemExpress.
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8

ChIP-Seq Protocol for Clock and Bmal1

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ChIP-Seq was performed as previously described (Kowalczyk et al., 2012 (link)) with minor modifications. Specifically, THP-1 cells were fixed in 2 mM EGS (Thermo Scientific) for 30 or 60 minutes followed by 1% formaldehyde for 30 or 15 minutes at RT, respectively. Chromatin was sonicated to a size less than 500 bp and then incubated overnight with either anti-Clock IgG (ab3517, Abcam) or anti-Bmal1 IgG (ab3350, Abcam). ChIP-Seq libraries were prepared through the process of DNA end-repair (Epicentre), A-base addition, and adaptor ligation using indexed Illumina adaptors followed by enrichment PCR. All enzymatic steps were carried out using enzymes from New England Biolabs. Final libraries were pooled, size selected, and sequenced on HiSeq2500 with 25 paired-end reads.
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9

Isolation and Fractionation of Retinal Proteins

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Isolated retinas were lysed in lysis buffer for protein extraction as previously described19 (link). Isolation of membrane and cytoplasmic fraction was performed as described58 (link). Blots were probed with antibodies against Bmal1 (ab3350; Abcam, Cambridge, MA, USA), Sema6D (AV49583, Sigma), and β-actin (4970 L; Cell Signaling Technology, Danvers, MA, USA), β-tubulin (9F3; Cell Signaling Technology, Danvers, MA, USA). Immunoblots were visualized using IRDye 680RD donkey anti-mouse/rabbit antibody or 800CW donkey anti-mouse/rabbit secondary antibody (925-32213; Li-Cor Biosciences, Lincoln, NE, USA). Membranes were scanned with an Odyssey infrared scanner (Li-Cor Biosciences).
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10

Circadian Rhythm Protein Quantification

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Mice were perfused with 4% paraformaldehyde in phosphate-buffered saline (PBS) at the indicated time of day (TOD), and the isolated brains were postfixed in the same fixative for 24 h. The brains were then cryoprotected in 30% sucrose and sectioned at 20-µm thickness on a cryostat. The SCN-containing brain sections were blocked by incubation with PBS containing 10% horse serum and 0.3% Triton X-100 for 30 min. Primary antibodies against BMAL1 (ab3350, Abcam, Cambridge, UK), PER1 (ab3443, Abcam) and PER2 (PER21-A, Alpha Diagnostic Int’l, San Antonio, TX, USA) were applied for 1 h. After washing six times with PBS, the sections were incubated with a Cy3-labeled anti-rabbit IgG antibody (Jackson ImmunoResearch Laboratory, West Grove, PA, USA) for 0.5 h. Subsequently, the sections were washed six times with PBS, mounted with 4′,6′diamidino-2-phenylindole (DAPI)-containing medium (Sigma-Aldrich, St. Louis, MO, USA) and observed under a confocal microscope (LSM510; Zeiss, Goettingen, Germany). BMAL1-, PER1- and PER2-immunoreactivity (ir) was quantitatively analyzed using the National Institutes of Health (NIH) program ImageJ (available at https://imagej.nih.gov/ij/) and then normalized against the DAPI signal intensity.
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