The largest database of trusted experimental protocols

12 protocols using alkbh5

1

Immunostaining of Mouse Pancreatic Tissue

Check if the same lab product or an alternative is used in the 5 most similar protocols
Mouse pancreas was collected and fixed in 4% formaldehyde at 4°C overnight, followed by paraffin embedding. Five-micron thick slides were cut and subjected to immunostaining. Slides were heated in 10mM sodium citrate, followed by blocking with donkey serum and incubated with various primary antibodies: Ki67 (#550609, BD, USA), Anti-METTL3 (#195352, Abcam, USA), Anti-METTL14 (#HPA038002, Sigma, USA), ALKBH5 (#HPA007196, Sigma, USA), PDX1 (#5679, Cell Signaling, USA), Insulin (#ab7842, abcam, USA), Glucagon (#G2654, Sigma, USA), Somatostatin (#ab64053, abcam, USA). Specific signal was detected by using fluorescence-conjugated secondary antibodies (Jackson Immunoresearch, Alexa 488, Alexa 594, and AMCA) (please see Reporting Summary for details on antibodies used). Images were captured using Zeiss Axio Imager A2 upright fluorescence microscope. The β-cell mass was calculated by generating the ratio of the cross-sectional area of total number of pixels of Insulin positive cells to the cross-sectional area of total number of pixels of the pancreatic tissue, multiplied by the pancreas weight of the mouse. We evaluated β-cell proliferation by co-immunostaining one section of each pancreas sample with Ki67, Insulin and DAPI and counting 1000–2000 cells in a blinded manner by a single observer33 (link),34 (link),37 (link).
+ Open protocol
+ Expand
2

Immunostaining of Mouse Pancreatic Tissue

Check if the same lab product or an alternative is used in the 5 most similar protocols
Mouse pancreas was collected and fixed in 4% formaldehyde at 4°C overnight, followed by paraffin embedding. Five-micron thick slides were cut and subjected to immunostaining. Slides were heated in 10mM sodium citrate, followed by blocking with donkey serum and incubated with various primary antibodies: Ki67 (#550609, BD, USA), Anti-METTL3 (#195352, Abcam, USA), Anti-METTL14 (#HPA038002, Sigma, USA), ALKBH5 (#HPA007196, Sigma, USA), PDX1 (#5679, Cell Signaling, USA), Insulin (#ab7842, abcam, USA), Glucagon (#G2654, Sigma, USA), Somatostatin (#ab64053, abcam, USA). Specific signal was detected by using fluorescence-conjugated secondary antibodies (Jackson Immunoresearch, Alexa 488, Alexa 594, and AMCA) (please see Reporting Summary for details on antibodies used). Images were captured using Zeiss Axio Imager A2 upright fluorescence microscope. The β-cell mass was calculated by generating the ratio of the cross-sectional area of total number of pixels of Insulin positive cells to the cross-sectional area of total number of pixels of the pancreatic tissue, multiplied by the pancreas weight of the mouse. We evaluated β-cell proliferation by co-immunostaining one section of each pancreas sample with Ki67, Insulin and DAPI and counting 1000–2000 cells in a blinded manner by a single observer33 (link),34 (link),37 (link).
+ Open protocol
+ Expand
3

Western Blot Analysis of Protein Targets

Check if the same lab product or an alternative is used in the 5 most similar protocols
Cells were washed twice with ice-cold phosphate-buffered saline (PBS) and ruptured with RIPA buffer (Pierce, Rockford, IL) containing 5 mM EDTA, PMSF, cocktail proteinase inhibitors, and phosphatase inhibitor cocktail. Cell extracts were centrifuged at 12000 × g for 15 min and the supernatants were then collected. Cell lysates were resolved by SDS-PAGE and transferred onto PVDF membranes which were blocked with 5% non-fat milk (Bio-Rad) in Tris-buffered saline containing 0.1% Tween 20 for 1 hour and incubated sequentially with primary and secondary antibodies and detected by immunoblotting with the Pierce ECL Western Blotting Substrate (Thermo Fisher Scientific) or Amersham ECL Prime Western Blotting Detection Reagent (GE Healthcare). Antibodies used for Western blotting were as follows: ALKBH5 (ab195377, abcam), ALKBH5 (HPA007196, Sigma-Aldrich), TACC3 (sc-376883, Santa Cruz Biotechnology), Flag (F3165, Sigma-Aldrich), c-Myc (9402S, Cell Signaling Technology), P21 (2947S, Cell Signaling Technology) GAPDH (sc-47724, Santa Cruz Biotechnology), β-Actin (3700, Cell Signaling Technology), Vinculin (sc-25336, Santa Cruz Biotechnology). GAPDH or β-Actin or Vinculin was used as a loading control.
+ Open protocol
+ Expand
4

Western Blot Analysis of Signaling Proteins

Check if the same lab product or an alternative is used in the 5 most similar protocols
Protein samples were lysed in Laemmli buffer, separated by SDS-PAGE, and transferred to a nitrocellulose membrane (37 (link)). The membrane was blocked with 5% milk and then incubated with primary antibody to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (catalog number 5174S; Cell Signaling Technology [CST]), p38 (catalog number 8690S; CST), p-p38 (catalog number 4511S; CST), ERK (catalog number 4695S; CST), p-ERK (catalog number 4370S; CST), JNK (catalog number 9252S; CST), p-JNK (catalog number 4668S; CST), DUSP1 (catalog number NBP2-67909; Novus), IL-1β (catalog number AB-401-NA; R&D Systems), or ALKBH5 (catalog number HPA007196; Sigma) overnight at 4°C. The membrane was washed with Tris-buffered saline (TBS)–Tween (TBS-T) and probed with a secondary antibody conjugated to horseradish peroxidase (HRP). After further washing with TBS-T, the blot was visualized using SuperSignal West Femto maximum-sensitivity substrate (catalog number 34096; Thermo) and imaged on a ChemiDoc MP imaging system (catalog number 12003154; Bio-Rad).
+ Open protocol
+ Expand
5

Western Blot Analysis of Protein Expression

Check if the same lab product or an alternative is used in the 5 most similar protocols
Cultured cells and mouse brain tissues were homogenized in lysis buffer (RIPA) in the presence of protease inhibitor (PMSF) on ice for 30 min and centrifuged at 10,000 × g for 20 min at 4 °C. Protein samples (30–60 μg) were separated using 10% SDS-PAGE gels and subsequently immunoblotted onto polyvinylidene difluoride (PVDF) membranes (Millipore) in ice-cold buffer (25 mM Tris HCl, 192 mM glycine, and 20% methanol) by electrotransfer for 2 h. The membranes were blocked with 5% nonfat milk powder dissolved in TBST and then incubated with the indicated antibodies at 4 °C overnight (ALKBH5, Sigma: HPA007196, 1:1000; GLT-1 Abcam: Ab205247, 1:1000; GAPDH, Proteintech: 60004, 1:5000). Horseradish peroxidase (HRP)-conjugated goat-anti-rabbit (Abclonal: AS014, 1:5000) and goat-anti-mouse Abclonal: AS003, 1:5000) secondary antibodies were incubated at room temperature for 1 h. Blots were detected using enhanced chemiluminescence (Pierce). Protein abundance was quantified by analyzing the Western blot bands using Image Lab (Bio-Rad) software. Quantified band intensities were normalized to GAPDH levels and averaged from at least three independent experiments.
+ Open protocol
+ Expand
6

Western Blot and Immunohistochemistry Analysis of Proteins

Check if the same lab product or an alternative is used in the 5 most similar protocols
Total protein of cells was extracted by KeyGEN Bio TECH protein extraction kit (KGP1100) and separated on 10% SDS-PAGE and transferred onto nitrocellulose membrane. After blocking, blots were immunostained with primary antibodies and secondary antibodies respectively as previously described. The antibodies were as follows: PLOD2 (1:1,000; Preteintech, United States); ALKBH5 (1:1,000; Sigma, United States); YTHDF1 (1:1,000; Preteintech, United States); ERK (1:1,000; Cell Signaling Technology, United States); p-ERK (1:1,000; Cell Signaling Technology, United States) and GAPDH (1:10,000; Preteintech, United States). Immunohistochemistry staining was performed using a primary antibody of PLOD2 at a 1:300 dilution following a protocol described previously. All photographs were taken randomly and measured using Image Pro Plus (Media Cybernetics, Rockville, MD, United States).
+ Open protocol
+ Expand
7

Ubiquitin-Mediated Protein Regulation Assay

Check if the same lab product or an alternative is used in the 5 most similar protocols
USP9X (Abcam; catalog no.: ab180191), GAPDH (Proteintech; catalog no.: 60004-1-Ig), ALKBH5 (Sigma; catalog no.: HPA007196), Ubiquitin (P4D1) (catalog no.: sc-8017), K48-linkage specific polyubiquitin (CST; catalog no.: 8081), m6A (Abcam; catalog no.: ab151230), FLAG (Sigma; catalog no.: F2922), HA (Sigma; catalog no.: B9183), GFP (Proteintech; catalog no.: 66002-1-Ig), horseradish peroxidase (HRP)-mouse (Proteintech; catalog no.: 00014-1-Ig), HRP-rabbit (CST; catalog no.: 7074), HRP-mouse (light-chain specific) (ROCKLAND; catalog no.: 38282), HRP-rabbit (light-chain specific) (CST; catalog no.: 93702), goat anti-Rabbit IgG antibody (Sigma; catalog no.: AP132). WP1130 (MedChemExpress; catalog no.: HY-13246), CHX (Sigma; catalog no.: 01810), benzonase nuclease (Sigma; catalog no.: E8263), and 3× FLAG peptide (Sigma; catalog no.: F4799).
+ Open protocol
+ Expand
8

Protein Extraction and Immunoblotting

Check if the same lab product or an alternative is used in the 5 most similar protocols
Proteins were extracted from cells or tissue samples as described previously34 . The proteins were quantified using a BCA protein assay kit (Beyotime) and resolved using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) with 10%-12.5% gels. The separated proteins were transferred to a methanol-activated nitrocellulose (NC) filter membrane (PALL). Major antibodies specific for the following proteins were used for immunoblotting: YAP (1:1000 dilution; Santa), ALKBH5 (1:1000; Millipore), and tubulin (1:5000; Affbiotech).
+ Open protocol
+ Expand
9

Protein Analysis by Western Blot

Check if the same lab product or an alternative is used in the 5 most similar protocols
Proteins, separated by SDS-PAGE were analyzed by Western blot using the indicated antibodies: Actin, ALKBH5 (Millipore, Molsheim, France), Rad51, FOXM1, YAP1, CHK1, phospho-CHK1 (Cell Signaling, Ozyme, St Cyr l’ecole, France), and gamma-H2AX (BioLegend, Ozyme, St Cyr l’ecole, France).
+ Open protocol
+ Expand
10

Protein Extraction and Western Blot Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Total proteins were extracted from specimens and cells using radioimmunoprecipitation assay lysis buffer with protease inhibitor on ice and quantified by bicinchoninic acid protein assay kit (Thermo, USA). The western blot was performed according to standard procedures. The following specific antibodies were applied: ALKBH5 (Millipore Corporation, USA), SOX2, Wnt5a, β-catenin, C-myc, CylinD1, LEF1, TCF1/TCF7, Met/pro-Met, Caspase-3, Caspase-7, Caspase-8, Caspase-9, MDR1, BCRP1, MRP1, and β-actin (Cell Signaling Technology, USA). The antibody information is listed in Supplementary Table S4. The membranes were incubated with HRP-labeled goat-anti-rabbit or goat-anti-mouse secondary antibodies (Cell Signaling Technology, USA). The proteins were detected and visualized by chemiluminescence (Biosciences, Foster City, CA, USA). The protein expression was analyzed by the Image J software, and β -actin was used as loading control.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!