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9 protocols using ikaros

1

Western Blot Analysis of Protein Complexes

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Western blot was performed according to the manufacturer’s protocol. Equal amounts of protein were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS–PAGE) gels followed by transfer to PVDF membranes. Membranes were probed with primary antibodies overnight and then washed and incubated with horseradish peroxidase (HRP)-conjugated-secondary antibodies. Detection was performed by the enhanced chemical luminescence (ECL) method. The primary antibodies of NCOR2 (ab24551; 1:1000) was purchased from Abcam. CRBN (NBP1-91810; 1:1,000) antibody was purchased from Novus Biologicals. c-Myc (#5605; 1:1,000), IKAROS (#9034; 1:1,000), MTA1 (#5647; 1:1,000), MBD3 (#14540; 1:1,000), HDAC1 (#5356; 1:1,000), and HDAC2 (#5113; 1:1,000), antibodies were purchased from Cell Signaling Technology, Inc.
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2

Signaling Pathway Protein Analysis

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AA (ab120916), thapsigargin (ab120286), ORAI3 Ab (ab115558), and NUR77 Ab (ab109180) were purchased from Abcam. Abs recognizing p-CAMKII (Thr286, #12716), p-ERK (Thr202/Tyr204, #4377s), CAMKII (#4436), ERK (#4695), Myb (#12319), AP-2a (#3208), and IKAROS (#9034s) were from Cell Signaling. Abs to β-actin (#A5441) were obtained from Sigma, to p-CD3ζ (Y142) from BD Biosciences (558402) and to CD3ζ from BioLegend (644102). Abs for flow cytometry were purchased from BD Biosciences [CD4-V450 (560345), CD8-PE-Cy7 (557746), CD45RA-AF700 (560673), CD69-Percp-Cy5.5 (560738), p-ERK (Thr202/Try204)-AF670 (561992), and p-SLP76 (Y128)-AF647 (558438)] or BioLegend [CD62L-PE (304806), IKAROS-AF647 (368404), and CD3-AF488 (30045)]. The LIVE/DEADTM Fixable Aqua Dead Cell Stain Kit from Molecular Probes, Thermo Fisher Scientific was used to gate out dead cells; Fluo-8 (21080) and Fura RedTM (F3021) for staining cytoplasmic Ca2+ was from AAT Bioquest, Inc., and Thermo Fisher Scientific, respectively.
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3

Protein Expression Analysis by Western Blotting

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Western blotting (WB) was performed as described previously [22 (link)]. Briefly, total protein was extracted from the cells. Aliquots of total protein (10 μg) were electrophoresed on sodium dodecyl sulfate–polyacrylamide and 12% Tris–HCL gels (Bio-Rad Laboratories, CA, USA). The separated proteins were transferred onto polyvinylidene difluoride membranes (Bio-Rad Laboratories) and incubated with primary antibodies overnight at 4 °C. The membranes were probed with the following antibodies: cyclin D1, p27 Kip1, CDK2, p18 INK 4C, CDK6, cyclin D3, p21 Waf1/Cip1, CDK4, pIκBα, IκBα, pro caspase 3, Ikaros, CK2α, c-Myc (1:1000 dilution; Cell Signaling Technology, Inc., MA, USA), and anti-β actin (1:3000 dilution; Sigma, Tokyo, Japan). Bound primary antibodies were detected using secondary antibodies (Cell Signaling Technology, Inc.) in a 1:10,000 dilution for anti-β actin and 1:2000 dilution for the other antibodies.
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4

Immunoblotting Analysis of Thymus Proteins

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Ten milligrams of tissue from thymus or thymic lymphomas was homogenized in 500 μL of 2× Laemmli buffer (0.125M Tris-HCl at pH 6.8, 10% β-mercaptoethanol, 4% sodium dodecyl sulphate, 20% glycerol, 0.05% bromophenol blue). Ten microliters of protein extract was subjected to SDS-PAGE and transferred to an Immobilon-P membrane (EMD Millipore). Western blot was carried out using antibodies to Pten (#9188), Cdk6 (#3136), Cyclin D1 (#2978), Cyclin D2 (#3741), Cyclin D3 (#2936), phospho-Rb (S780) (#9307), Rb (#9313), Ikaros (#5443), and Hes1 (#11988) (Cell Signaling) and Gapdh (#25778) (Santa Cruz Biotechnology, Inc.).
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5

Apoptosis Induction Pathway Dissection

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LCL-161,
AZD5582, birinapant,
and BV6 were obtained from MedChemExpress. Human TNF-α was obtained
from Miltenyi Biotec. MG132, MLN4924, and MLN7243 were purchased from
SelleckChem.
Primary antibodies used for immunoblotting include
BIRC2 (BioRad; VMA00532; clone AB01/3B4), cIAP2 (Cell Signaling; 3130S;
clone 58C7), XIAP (Cell Signaling; 14334S; clone D2Z8W), VHL (Cell
Signaling; 68547S), CRBN (Sigma-Aldrich; SAB2106014), Ikaros (Cell
Signaling; 14859S; clone D6N9Y), Aiolos (Cell Signaling; 15103S; clone
D1C1E), HIF-1α (BD BioSciences, 610958; clone 54), α-tubulin
(Sigma-Aldrich; T5168; clone B512), and beta-actin (Sigma-Aldrich;
A1978). Secondary antibodies include anti-rabbit IgG HRP-linked antibody
(Cell Signaling; 7074) and anti-mouse IgG HRP-linked antibody (Cell
Signaling; 7076).
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6

Western Blot Protein Analysis Protocol

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For Western blot assays, cells were lysed in Laemmli buffer (1 mM PMSF, 150 mM NaCl, 50 mM Tris HCl pH 6.8, 10% glycerol, 2% sodium dodecyl sulfate, 0.1% bromophenol blue, 2.5% β-mercaptoethanol), then sonicated, boiled for 10 minutes, migrated on SDS-polyacrylamide gel and transferred to nitrocellulose membrane (Bio-Rad). IKAROS (Cell signaling #D6N9Y), P21WAF1/CIP1 (BD Biosciences #556431), TP53 (Santa Cruz #393031), GAPDH (MilliporeSigma) or ACTIN (NeoMarkers) and horseradish peroxidase (HRP)-conjugated antibody (Jackson) were used for immunoblotting. Proteins were detected with Clarity Western enhanced chemiluminescence substrate (ECL; Bio-Rad) with a Fujifilm LAS-4000 luminescent image analyzer (GE Healthcare).
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7

MINO MCL Xenograft Model and Drug Efficacy

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The MINO MCL xenograft model was generated by inoculating subcutaneously 6- to 7-week-old nude mice (Shanghai Ling Chang Experimental Animal Co., Ltd.) with 5 × 106 MINO cells. When tumor volume reached 100 to 200 mm3, animals were randomized into five groups of 8 to10 mice each, and were dosed orally with TG-1701 (25, 50, or 100 mg/kg, orally, twice a day), ibrutinib (100 mg/kg, orally, twice a day), or vehicle for 21 days. The tumor volume (V) was calculated as: V = 1/2 × a × b2, where a and b represent the length and width, respectively. In REC-1 and UPN-IbruR xenografts, CB17-SCID mice (Janvier labs) were inoculated subcutaneously with 107 REC-1GFP+Luc+ cells or UPN-IbruR cells and monitored for tumor growth, bioluminescence signal, and vital parameters as described previously (21 (link)), in compliance with the Animal Ethics Committee of the autonomous University of Barcelona (registry number 38/18). Tumor-bearing mice received either TG-1701 (25 mg/kg, every day) or ibrutinib (25 mg/kg, every day) for 17 days. Tumor samples were snap-frozen in OCT medium (Sakura Tissue Tek) or formalin-fixed and paraffin-embedded prior to immunohistochemical (IHC) staining with primary antibodies against Ikaros (Cell Signaling Technology) and CD20 (Beckman Coulter). Preparations were evaluated using an Olympus microscope and MicroManager software.
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8

Immunoblot Analysis of Protein Expression

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Protein expression was measured by immunoblot analysis as previously described (14 (link)). The antibody to BZLF-1 was from Santa Cruz Biotechnologies (Santa Cruz, CA), while the anti-AKT, phospho (p)-GSK3α/βSer21/9, p-AKTSer473, FoxO1 and Ikaros antibodies were from Cell Signaling Technology (Danvers, MA). Antibody to BMRF1 was obtained from Millipore (Billerica, MA), anti-β-actin from Sigma-Aldrich, and anti-VCA p18 antibodies were from Thermo-Scientific (Waltham, MA). Total AKT and pAKTSER473 levels were also measured using sandwich ELISA kit as recommended by the manufacturer Cell Signaling Technology.
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9

Characterization of Immune Cell Lines

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HEK and Ramos cell lines were obtained from ATCC,12 (link) TMD8 was a kind gift of dr. Hernandez-Ilizariturry- it´s origin was authenticated in our laboratory by mutational analysis showing the presence of the specific mutation of CD79B gene (Y196H). The cell lines were grown in IMDM media supplemented with 10% FCS, antibiotics (penicillin, streptomycin) and were mycoplasma negative. Human blood was obtained from volunteers under approval of local ethical committee, samples were processed by Ficoll gradient centrifugation and isolated leukocytes were further used for lentiviral infections. Following fluorochrome labeled antibodies were used: Alexa 647 goat anti-mouse (Jackson Immuno), pacific Blue anti-CD4+, PerCP anti-CD8+, APC anti-CD69, PE anti-CD19 and PE anti-CD20 (all Exbio), for stimulation and western blotting were used unlabeled antibodies specific for: CD3, CD28 (Miltenyi Biotec), TCRzeta (Santa Cruz), Aiolos, Ikaros, pERK, total ERK (all Cell Signaling).
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