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7 protocols using pa1 014 a

1

Cellular Stress Response Assay Protocol

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Dulbecco’s Modified Eagle medium (DMEM), fetal bovine serum (FBS), antibiotic mixture, and trypsin-ethylenediaminetetraacetic acid (trypsin-EDTA) solution were obtained from WELGENE Inc. (Daegu, Korea). 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), N-acetylcysteine (NAC), and salubrinal were purchased from Sigma Aldrich (St. Louis, MO, USA). 2ʹ,7ʹ-Dichlorodihydrofluorescein diacetate (DCFDA) was purchased from Molecular Probes (Eugene, OR, USA). Antibodies against caspase-3 (sc-65497), poly(adenosine diphosphate ribose) polymerase (PARP) (sc-365315), β-actin (sc-69879), CHOP (sc-575), and peroxidase-labeled anti-mouse immunoglobulins (sc-16102) were observed from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Antibodies against GRP78 (PA1-014A), ATF4 (PA5-19521), eIF2α (PA5-27366), and p-eIF2α (MA5-15133) were purchased from Thermo Fisher Scientific (Waltham, MA, USA). MitoTracker Green, MitoSOX Red, and MitoTEMPO were also obtained from Thermo Fisher Scientific. Peroxidase-labeled anti-rabbit immunoglobulins (KO211708) was obtained from Koma Biotechnology (Seoul, Korea). All other chemicals were purchased from Sigma-Aldrich.
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2

Western Blot Analysis of Cellular Proteins

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Mouse kidney tissues or BMDM were lysed on ice using radioimmunoprecipitation assay (RIPA) lysis buffer, and the supernatant was collected by centrifugation. The protein concentration was examined using the bicinchoninic acid (BCA) method. The protein samples were heated in a water bath, and gel electrophoresis was performed using sodium dodecyl sulfate–polyacrylamide gel electrophoresis (PAGE), followed by transferring the proteins to polyvinylidene difluoride membranes. After blocking with skimmed milk powder for 2 h, the membranes were incubated with primary antibodies at 4 °C overnight. The blots were incubated with the HRP-coupled goat anti-rabbit secondary antibody (1:2000, ab6721, Abcam) for 1 h at room temperature. The signals were visualized using the ECL Western Blotting Substrate (PE0010, Solarbio) and analyzed using Image Pro-Plus 6.0. The primary antibodies were as follows: HK2 (1:1000, 2867, Cell Signaling Technologies), LDHA (1:1000, ab52488, Abcam), BZW1 (1:1000, GTX120426, GeneTex, Inc., Alton Pkwy Irvine, CA, USA), eIF2α (1:1000, 5324, Cell Signaling Technologies), p-eIF2α (1:1000, 3398, Cell Signaling Technologies), CHOP (1:1000, PA5-104528, Thermo Fisher), GRP78 (1:500, PA1-014A, Thermo Fisher), and β-actin (1:200, ab115777, Abcam).
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3

GRP78 Surface Staining of CSCs

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Prior to the IF staining, CSCs were adhered to plates overnight using laminin (Gibco, USA). For surface staining of GRP78, cells were washed with PBS for 5 min and incubated with GRP78 primary antibodies (PA1-014 A, Invitrogen, USA) at 1:200 dilution for 1 h at room temperature. Cells were washed with PBS for 5 min, fixed by 4% paraformaldehyde for 15 min, and blocked by 10% goat serum in 0.1% BSA, 0.1% Tween-20 and PBS for 1 h. Cells were then incubated with Cy3-conjuncted goat anti-rabbit secondary antibody (A10520, Invitrogen) at 1:1000 dilution for 1 h at room temperature in the dark. Cells were washed three times with PBS for 5 min and stained with 5 µg/mL DAPI for 10 min. Finally, coverslip were extracted, mounted in mounting medium (Polysciences, USA), covered with a slide and stored at 4 ℃ for imaging. Specificity of staining was confirmed by the inclusion of negative controls that were stained with secondary antibodies alone.
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4

EV Uptake and GRP78 Expression

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For vesicle transfer, 3 x 105 BHY or FaDu cells were seeded in 6-well plates. After 24 h, the wells were washed with PBS and 2 ml fresh medium containing 10% EdFBS was added, supplemented by the EVs isolated from 6 ml conditioned medium from 0 or 6 Gy-irradiated cells. 24 h later, cells were detached with a cell scraper and analyzed via Western Blot.
To confirm EV-uptake into recipient cells, the isolated EVs were stained with green fluorescent dye PKH67 (MINI67, Sigma-Aldrich) as previously described (19 (link)). 40,000 BHY cells were seeded in 12-well silicone grids (Ibidi) on glass slides, after 24 h the wells were washed with PBS and 250 µl new EdFBS-supplemented medium was added, containing PKH67-stained EVs isolated from 750 µl conditioned medium of BHY cells. After 24 h, cells were fixed in 4% paraformaldehyde and nuclei were stained with Hoechst 33342.
For visualization of surface GRP78 after irradiation, cells were seeded on glass slides and after 24 h irradiated with 0 and 6 Gy. Further 24 h later, cells were fixed with 4% paraformaldehyde and labelled with an anti-GRP78 antibody dilution of 1:100 (PA1-014A, Invitrogen) followed by a secondary Alexa Fluor 488-coupled antibody (anti-rabbit: A-11008, Thermo Fisher). Cells were not permeabilized for appropriate labelling of surface GRP78.
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5

Protein Expression Analysis of Borax-Treated Cells

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Western blot analysis was performed to assess the protein levels of HSPA5, NRF2 and GPx4 in borax‐treated cells. Initially, protein samples (20 μg) were prepared and separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS‐PAGE). The separated proteins were then transferred from the gel to a polyvinylidene fluoride (PVDF) membrane. To prevent non‐specific binding, the PVDF membranes were blocked using 2% bovine serum albumin (BSA). Subsequently, the membranes were incubated overnight at 4°C with primary antibodies specific to HSPA5 (dilution 1 μg/mL; PA1‐014A; Invitrogen), NRF2 (dilution 1:2000; PA5‐88084; Invitrogen), GPx4 (dilution 1:1000; PA5‐102521; Invitrogen) and cleaved caspase‐3 (dilution 1:1000; Cat No. 9661; Cell Signaling). Following the primary antibody incubation, the membranes were washed to remove any unbound antibodies. Next, the membranes were incubated with secondary antibodies. To visualize the protein bands, a chemiluminescence ECL (enhanced chemiluminescence) kit (34579, Thermo Scientific) was used. The emitted light was captured using an imaging system, and the resulting images were analysed using software such as ImageJ.
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6

Comprehensive Histological Analysis of CAR-T Cell Therapy

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Tumors, hearts, livers, spleens, lungs, kidneys and brains from the mock-BBZ CAR and Pep42-BBZ CAR groups were embedded in paraffin, and then sliced into sections with a thickness of 4 μm. Sections were deparaffinized, rehydrated, and processed for antigen retrieval. H&E staining was performed on heart, liver, spleen, lung, kidney, and brain tissue sections to observe their structure. The tumor, liver and lung tissue sections were blocked with 10% goat serum and incubated with the indicated primary antibodies at 4 ℃ overnight. Cy3-conjuncted goat anti-rabbit secondary antibody (A10520, Invitrogen), FITC-conjuncted goat anti-rabbit secondary antibody (F-2765, Invitrogen), and Cy3-conjuncted goat anti-mouse secondary antibody were used (A10521, Invitrogen). The primary antibodies used were as follows: anti-GRP78 antibody (PA1-014 A, Invitrogen), anti-CD3ζ antibody (ET1607-20, Huabio), anti-NESTIN antibody (sc23927, Santa Cruz), anti-CD4 antibody (ET1606-31, HUABIO), and anti-CD8 antibody (ET1609-52, HUABIO).
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7

Immunofluorescence Assay for Hepatic Progenitors

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On the day of base editing, hepatic progenitors were replated in chamber slides (Thermo Fisher Scientific, 177380PK). Upon completion of the differentiation, cells were fixed with 4% paraformaldehyde for 10 min at room temperature. Cells were permeabilized with 0.3% Triton, then blocked with 5% normal donkey serum, before incubation with primary antibodies overnight at 4°C. Antibodies used were HNF4A (Abcam, ab201460), 2C1 (a kind gift from David Lomas and Elena Miranda), and BiP (Invitrogen, PA1-014A). Following incubation, cells were washed and incubated with appropriate secondary antibodies (Invitrogen, A21202, A21247, and A10042). Finally, nuclei were stained with Hoechst 33342 (Invitrogen, H3570). Cells were imaged using a Leica SP5 confocal microscope, and images were processed in ImageJ and Fiji.
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