The largest database of trusted experimental protocols

16 protocols using ab12169

1

ChIP Assay with Antibodies for Transcription and Epigenetics

Check if the same lab product or an alternative is used in the 5 most similar protocols
The antibodies used for the ChIP assays were directed against RNA Pol II (Santa Cruz [sc-899 X]), HDAC2 (Abcam [ab12169]), AcH3 (Abcam [ab47915]), PAX5 (Santa Cruz [sc-13146 X]), and H3K27me3 (Millipore [07–449]. Antibodies against PAX5 (Santa Cruz [sc-13146 X]) and Flag (Sigma [F3165]) were used in the immunoprecipitation (IP) and PAX5 (Santa Cruz [sc-1974]) and HDAC2 (Abcam [ab12169]) were used in the immunoblot assays.
+ Open protocol
+ Expand
2

Hippocampal and Cortical Protein Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Tissue from the hippocampus and whole cortex of the left hemisphere of the brain was homogenized in radioimmunoprecipitation assay (RIPA) buffer. Protein samples were run on 4%–20% TGX Gels (Bio-Rad), transferred to polyvinylidene fluoride (PVDF) membranes (Millipore), and blotted using standard protocols. Primary antibodies were the following: HDAC2 (Abcam; ab12169) ACTIN (Abcam; ab3280), and BDNF (Abcam; ab108319). Bands shown in western blot images for these proteins were at the expected sizes of 55, 42, and 15 kDa, respectively. Secondary antibodies were goat anti-mouse infrared (IR) 680 (LI-COR Biosciences; #926-68020), goat anti-mouse IR 800 (LI-COR Biosciences; #926-32210), and goat anti-rabbit IR 800 (LI-COR Biosciences; #925-32211). Membranes were imaged on the LI-COR Biosciences Odyssey fluorescence imaging system.
+ Open protocol
+ Expand
3

ChIP Assays for Transcription Factors

Check if the same lab product or an alternative is used in the 5 most similar protocols
ChIP assays were performed using anti-Gata3 (D-16, Santa Cruz Biotechnology, Inc.), anti-p300 (N-15, Santa Cruz Biotechnology, Inc.) and Hdac2 (ab12169, Abcam) antibodies as described previously33 (link). Quantitative-PCR analyses were performed on an ABI prism 7500 real-time PCR machine with probes from the Roche Universal Probe Library System. The specific primers and TaqMan probes used in this report were described previously4 (link).
+ Open protocol
+ Expand
4

Romidepsin and Lipopolysaccharide Interactions

Check if the same lab product or an alternative is used in the 5 most similar protocols
Romidepsin (FK228) (S3020), was purchased from Shanghai Selleck Chemicals Co., Ltd. (Shanghai, China). Lipopolysaccharide (LPS) derived from Escherichia coli 055: B5 (L2637) was purchased from Sigma-Aldrich (St Louis, MO, USA). Antibodies to acetyl-histone H3 (4499) were purchased from Cell Signaling Technology, Inc. (Danvers, MA, USA). Anti-KIM-1 (AF1817) was purchased from R&D Systems (Chengdu, China). Antibodies to CYP2E1 (ab28146), HDAC1 (ab7028), HDAC2 (ab12169), HDAC3 (ab7030), hepatocyte nuclear factor-1 alpha (HNF-1α) (ab96777) and Nrf2 (ab62352) were purchased from Abcam (Cambridge, UK). Anti-GAPDH (TA-08) was purchased from ZSGB Biotechnology (Beijing, China).
+ Open protocol
+ Expand
5

Western Blot Analysis of HDACs

Check if the same lab product or an alternative is used in the 5 most similar protocols
Samples containing 30 µg protein were diluted with 4x LDS sample buffer containing DTT (Invitrogen), boiled for 5 minutes and separated by gel electrophoresis at 100 volts. Gels were transferred to nitrocellulose membranes with iBlot2 transfer system (P3 for 7 minutes) and visualized with Odyssey Sa imager at 800 nm. Membranes were then blocked with Odyssey blocking buffer for 2 hours at rt or overnight at 4 °C. The blots were incubated with desired antibodies (anti-HDAC1 (Abcam ab7028), anti-HDAC2 (Abcam, ab12169), anti-HDAC3 (Abcam, ab7030), anti-HDAC8 (Abcam, ab187139) and anti-HDAC4,5,9 (Abcam, ab131524)) at the recommended dilutions for each in Odyssey blocking buffer (LI-COR) overnight at 4 °C. The blots were then washed 3 × 5 minutes with PBST, incubated with relevant species of IRDye® 680RD secondary antibody (LI-COR) for 1 hour and visualized with Odyssey Sa imager at both 700 nm and 800 nm. If additional antibody probing was necessary, membranes were stripped with 0.2 N NaOH for 10 minutes and re-blockedwith Odyssey blocking buffer.
+ Open protocol
+ Expand
6

Piceatannol Inhibits Fibrosis Markers

Check if the same lab product or an alternative is used in the 5 most similar protocols
Piceatannol was purchased from Future Chem (Seoul, Korea). Anti-alpha smooth muscle actin (α-SMA; 1:1000, sc-130617), anti-CTGF (1:1000, sc-14939), anti-HDAC3 (1:1000, sc-11417), anti-HDAC4 (1:1000, sc-11418), anti-HDAC5 (1:1000, sc-133225), anti-TGF-β1 (1:1000, sc-146), anti-JNK (1:1000, sc-7345), anti-ERK1 (1:1000, sc-271269), and anti-GAPDH (1:1000, sc-32233) antibodies were purchased from Santa Cruz Biotechnology (Dallas, TX, USA). Primary antibodies against collagen type I (1:1000, ab34710), HDAC2 (1:1000, ab12169), HDAC8 (1:1000, ab137474), and HDAC10 (1:1000, ab53096) were purchased from Abcam (Cambridge, MA, USA). Anti-fibronectin antibody (1:1000, MA5-11981) was purchased from Thermo Fisher Scientific (Waltham, MA, USA). Anti-HDAC1 antibody (1:1000, 06–720) was purchased from Merck Millipore (Darmstadt, Germany). Anti-HDAC6 (1:1000, 7612), anti-Smad3 (1:1000, 9523), anti-Smad2 (1:1000, 3103), anti-Smad4 (1:1000, 9515), anti-p-Smad3 (1:1000, 9520), anti-p-JNK (1:1000, 9251), anti-p-p38 (1:1000, 4511), anti-p-ERK1/2 (1:1000, 4370), and anti-p38 (1:1000, 8690) antibodies were purchased from Cell Signaling Technology (Danvers, MA, USA).
+ Open protocol
+ Expand
7

ChIP-qPCR Analysis of p16 Regulation

Check if the same lab product or an alternative is used in the 5 most similar protocols
ChIPs were performed for human ESCC cell lines (EC109 and TE-1) and were analyzed essentially according to the instructions of One-Day Chromatin Immunoprecipitation Kit (Millipore). The DNA precipitated by the target antibodies (DNMT1, Abcam, ab13537; HDAC2, Abcam, ab12169) was detected with qRT-PCR. The primer sequences of the ChIP-qPCR reaction were as follows: p16-1, 5′-CTG CTC TTA TAC CAG GCA ATG TA-3′ (sense) and 5′-CCT GTA CGA CTA GAA AGT GTC CC-3′ (antisense); p16-2, 5′-TTT CCC TAT GAC ACC AAA CAC C-3′ (sense) and 5′-CCG CGA TAC AAC CTT CCT AAC-3′ (antisense); p16-3, 5′-CCT CCT TGC GCT TGT TAT ACT CT-3′ (sense) and 5′-CCC TCC ACC ACC CTC ACT TA-3′ (antisense). Control PCRs for each antibody immunoprecipitation were performed using primers for GAPDH and IGFBP3 (DNMT1) or CD4 and von Willebrand factor (HDAC2) as negative and positive controls dependent on the antibody used. All PCR product sizes were confirmed by electrophoresis. Each ChIP experiment was done in triplicate and repeated at least three times.
+ Open protocol
+ Expand
8

Protein Extraction and Western Blot Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
AGS and MKN45 cells were lysed with pierce RIPA buffer (Thermo Fisher Scientific) to
obtain the protein samples. The cells were blown into a mixture with a pipette gun and
then left at 4°C for 45 min. After ultrasonic lysis, the cells were centrifuged at 15,000
g for 10 min, the supernatant was taken, and the precipitate was
discarded. The protein concentration was then measured using a BCA kit (Thermo Fisher
Scientific). Then, electrophoresis and transmembrane operation were applied to the protein
samples. Afterward, the membranes were trimmed according to molecular weight and then
blocked with 5% BSA and incubated with anti-HDAC2 antibody (1:8000, ab12169; Abcam),
anti-E-cadherin antibody (1:5000, ab40772; Abcam), or anti-GAPDH antibody (1:1000, ab8245;
Abcam) at 4°C. After 16 h, the membranes were washed with PBS, followed by incubation with
the secondary antibody for 2 h. The blots were visualized using enhanced chemiluminescence
(ECL) reagents (Thermo Fisher Scientific) [20] (link).
+ Open protocol
+ Expand
9

Protein Interactome Analysis of Bcl11b in Scid.adh.2c2 Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols
Protein extracts from Myc-Flag-tagged Bcl11b-infected Scid.adh.2c2 cells were subjected to immunoprecipitation as described previously43 (link). Nuclear extracts were prepared using NE-PER Nuclear and Cytoplasmic Extraction Reagents (Thermo Scientific). The antibodies used for the immunoblot analyses were anti-Chd4 (A301–081A, Bethyl), anti-Mta2 (sc-9447, Santa Cruz Biotechnology, Inc.), anti-HDAC2 (ab12169, Abcam), anti-Rest (12C11–1B11, Caltech Protein Expression Center), anti-Ring1b (A302–869A, Bethyl), anti-LSD1 (ab17721, Abcam), anti-Runx1 (ab23980, Abcam), anti-Bcl11b (ab18465, Abcam), anti-Lamin B (sc-6217, Santa Cruz Biotechnology, Inc.), and anti-Myc (My3, MBL).
+ Open protocol
+ Expand
10

Quantitative Analysis of Histone Deacetylases

Check if the same lab product or an alternative is used in the 5 most similar protocols
For western blot analysis, heart tissues were homogenized with a RIPA lysis buffer, as described previously.16) (link) Proteins were subjected to 8% or 10% SDS-PAGE and transferred to a PVDF membrane. The membranes were incubated in a 5% skim milk blocking solution for 1 h and then with the following primary antibodies: anti-HDAC1 (06-720, Millipore), anti-HDAC2 (ab12169, Abcam), anti-HDAC3 (sc-11417, Santa Cruz), anti-HDAC4 (sc-11418, Santa Cruz), anti-HDAC5 (sc-133225, Santa Cruz), anti-HDAC6 (#7612, Cell Signaling), anti-HDAC7 (3607-100, BioVision), anti-HDAC8 (ab137474, Abcam), anti-HDAC9 (3609-100, BioVision), anti-HDAC10 (ab53096, Abcam), and anti-GAPDH (sc-32233, Santa Cruz). The blots were incubated with anti-rabbit or anti-mouse horseradish-peroxidase-conjugated secondary antibodies for 1 h. The blots were developed using Immobilon™ Western Detection Reagents (Millipore, Billerica, MA, USA).
+ 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!