The largest database of trusted experimental protocols
Sourced in United States, United Kingdom, China

H3K4me3 is an antibody that specifically recognizes the trimethylated form of histone H3 at lysine 4. Histone modifications, such as methylation, play a crucial role in regulating gene expression and chromatin structure. H3K4me3 is associated with active transcription and is commonly used as a marker for actively transcribed regions of the genome.

Automatically generated - may contain errors

106 protocols using h3k4me3

1

TROP2 Expression in Colorectal Tumors

Check if the same lab product or an alternative is used in the 5 most similar protocols
FFPE colorectal tumor samples were obtained from excision biopsies as described previously14 (link). Tissue blocks were assembled. Slices (2 µM thick) were stained with HE, TROP2 (1:2000, rabbit IgG, ab214488, Abcam, Cambridge, UK), and H3K4me3 (1:1000, rabbit IgG, #9751, Cell Signaling, Danvers, USA). The samples were scored for TROP2 expression by a pathologist (KEW). The total immunostaining score (0–300) consists of the intensity (0–3) and the percentage of positive cells (0–100%). Using the median of 90, the tumor samples were categorized into a TROP2 high-expressing group (> 90) and a TROP2 low-expressing group (< 90).
+ Open protocol
+ Expand
2

Examining EPB41L4A-AS1 RNA Interactions

Check if the same lab product or an alternative is used in the 5 most similar protocols
Different fractions of EPB41L4A-AS1 were constructed with the pcDNA3.1 plasmid containing the T7 promoter. The RNA pulldown assay was performed following the protocol of the Pierce Magnetic RNA-Protein Pull-Down Kit (Thermo Fisher Scientific, USA). Antibodies, including SET1A and H3K4me3, were purchased from Cell Signaling Technology.
+ Open protocol
+ Expand
3

Western Blot Analysis of Stress Responses

Check if the same lab product or an alternative is used in the 5 most similar protocols
Protein lysates were prepared using RIPA lysis buffer and separated on 4–12% NuPAGE gels (Invitrogen), transferred onto a nitrocellulose membrane (Millipore) and incubated with the following antibodies: ACTIN (ab6276) and NRF2 (EP1808Y) mAb (both Abcam), NQO1 (HPA007308) and PHGDH (HPA021241) (both Sigma), PSAT1 (PA5-22124, Pierce), and ATF4 (11815, Cell Signaling). Alternatively, nuclear extracts were prepared as described31 . Histone extracts were prepared with the Histone Extraction Kit according to the manufacturer’s instructions (Abcam, ab113476). Histone extracts were probed with the following antibodies: H3K4me3 (9727, Cell Signaling), H3K27me3 (07-449, Millipore), total H3 (4499, Cell Signaling).
+ Open protocol
+ Expand
4

Antibody and Inhibitor Reagents for Assays

Check if the same lab product or an alternative is used in the 5 most similar protocols
Rat anti-mouse F4/80 antibody was purchased from Serotec; Rat anti-mouse CD31 was purchased from Dianova (Hamburg, Germany). Anti-actin and anti-smooth muscle actin (SMA) monoclonal antibodies were purchased from Sigma (St. Louis, MO). Antibodies directed against phopsho-AMPK alpha, phospho-p38 and phospho-JNK, histone H3 and H3K4-di (H3K4me2) and -tri (H3K4Me3) methylation, H3K27 tri-methylation and acetylated H2BK5 were purchased from Cell Signaling Technology (Beverly, MA). Anti-WDR5, anti-BiP, and anti-Ly6g antibodies were purchased from Abcam (Cambridge, UK). The selective inhibitors of LSD1 (GSK-2879552), WDR5 (OICR-9429), MKL1 (CCG-203971), CXCR2 (SB 225002), p38 (SB208530), and JNK (sp600125) were purchased from ApexBio (Boston, MA) and were dissolved in DMSO as stock solutions. DMSO (Sigma D2438) was added to the cell culture medium as control. The heparanase inhibitors H1001 and PG545 were kindly provided by HepaRx Ltd (Ness-Ziona, Israel) and Zucero Therapeutics (Darra, Queensland, Australia), respectively. Mouse CXCL2/MIP-2 Quantikine ELISA kit was purchased from R&D Systems (Minneapolis, MN). The MyD88 peptide inhibitory set was purchased from Novus Biologicals (Centennial, CO). Latent heparanase was purified from medium conditioned by CHO cells overexpressing heparanase essentially as described (25 ) and was added to cell cultures at 1 μg/ml.
+ Open protocol
+ Expand
5

Chromatin Immunoprecipitation Profiling of Epigenetic Factors

Check if the same lab product or an alternative is used in the 5 most similar protocols
Chromatin immunoprecipitation was performed as previously described 7 using antibodies against HIF‐1 (PM14), HIF‐2 (PM9) 42, 43, HIF‐1 (Novus NB‐100‐110), H3K4me1 (Millipore, #07‐436), H3K4me3 (#9751, Cell Signaling Technology), H3K27ac (#ab4729, Abcam), CTCF (#07‐729, Millipore), and RNApol2 (#sc‐899, Santa Cruz Biotechnology). Each ChIP was performed in duplicate. Libraries were prepared using PrepX Complete ILMN DNA library kit (#400076, Wafergen).
+ Open protocol
+ Expand
6

Western Blot Analysis of Cell Cycle Regulators

Check if the same lab product or an alternative is used in the 5 most similar protocols
Western blots were conducted as previously described [25 (link)]. Primary antibodies specific to CDK1, CCNB1, CCNE2, BIRC5, AURKA, FOXM1, WDR5, H3K4me3 (1:1000, Cell Signalling Technology, Danvers, MA, USA), histone H3 (1:2000, Cell Signalling Technology, Danvers, MA, USA), XRCC2, MCM2, PLK1, and GAPDH (1:1000, Abcam) were used. The PVDF films were then incubated with secondary antibodies (anti-mouse or anti-rabbit, Promega, USA) and visualized using Immobilon enhanced chemiluminescence (Millipore). The full images of all Western blots are shown in Supplementary Fig. 9.
+ Open protocol
+ Expand
7

Western Blot Analysis of Mitochondrial and Epigenetic Proteins

Check if the same lab product or an alternative is used in the 5 most similar protocols
Western blot was performed as described2 (link) using the following antibodies: TFAM (7495S, Cell Signaling Technology; sc-23588, Santa Cruz Technology), PHB2 (14085S, Cell Signaling Technology), ATP5A1 (sc-136178, Santa Cruz Technology), ATP5B (sc-16690, Santa Cruz Technology), ATP5D (ab97491, Abcam), ATP5O (ab110276, Abcam, clone 4C11C10D12), 4EBP1 (9644S, Cell Signaling Technology), phos-4EBP1 (Thr37/46) (2855S, Cell Signaling Technology), p70S6K (2708S, Cell Signaling Technology), phos-S6K (Ser235/236) (2211S, Cell Signaling Technology), GATA1 (ab47490, Abcam), GATA2 (ab22849, Abcam), TSC1 (6935, Cell Signaling Technology), TSC2 (4308, Cell Signaling Technology), H3K9ac (9649, Cell Signaling Technology), H3K27ac (8173, Cell Signaling Technology), H3K56ac (4243, Cell Signaling Technology), H4K5ac (ab51997, Abcam), H3K4me3 (9571, Cell Signaling Technology), H3K9me3 (13969, Cell Signaling Technology), H3K27me3 (9733, Cell Signaling Technology), H3K36me3 (4909, Cell Signaling Technology), H3 (4499, Cell Signaling Technology), ACTB (MAB1501, Millipore, clone C4), and GAPDH (sc-26778, Santa Cruz Biotechnology). Densitometry quantification was performed using ImageJ software. All antibodies were used at 1:1,000 dilutions except phos-4EBP1 (1:500), phos-S6K (1:500) and ACTB (1:2,500).
+ Open protocol
+ Expand
8

Chromatin Profiling of H2Bub1 and H3K4me3

Check if the same lab product or an alternative is used in the 5 most similar protocols
Chromatin immunoprecipitation was performed as described previously35 (link) 72 h after transfection with control or RNF40 siRNAs using antibodies against H2Bub1 (Cat. No. 5546 S, Cell Signaling Technology) and H3K4me3 (Cat. No. C15410003-50, Diagenode). Next-generation sequencing libraries were prepared using the Microplex Library Preparation kit v2 (Diagenode, Cat.No. C05010011) according to manufacturer’s instructions and samples were sequenced (single-end 50 bp) on a HiSeq4000 (Illumina) at the NGS Integrative Genomics Core Unit (NIG) at the University Medical Center Göttingen (ArrayExpress accession E-MTAB-9234). Processing of sequencing data was performed in the Galaxy environment (galaxy.gwdg.de). Briefly, ChIP-seq reads were mapped to the hg19 reference genome assembly using Bowtie2 (version 2.3.2.2). PCR duplicates were removed using the RmDup tool (version 2.0.1). The deeptools suite (version 3.2.0.0.1) was utilized to generate normalized coverage files (bamCoverage), call peak changes (bigwigCompare), and to generate aggregate plots and heatmaps (computeMatrix and plotHeatmap). Occupancy profiles were visualized using the Integrative Genomics Viewer (IGV 2.4.8). A detailed analysis workflow is available in Supplementary Data.
+ Open protocol
+ Expand
9

Comprehensive Antibody Panel for Chromatin Studies

Check if the same lab product or an alternative is used in the 5 most similar protocols
BAP1 (1/500 dilution; C-4; sc-28383), FOXK1 (1/500 dilution; G-4; sc-373810), YY1 (1/500 dilution; sc-7341) and RAR-alpha (1/500 dilution; sc-551 × ) antibodies were purchased from Santa-Cruz; FLAG (1/1000 dilution; M2; F1804) was purchased from Sigma; HCFC1 (1/1000 dilution; A301-400A) and RNF2 (1/1000 dilution; A302-869A) antibodies were purchased from Bethyl Laboratories; Lamin B1 (1/3000 dilution; ab16048); RING1A (1/1000 dilution; 2820S), RING1B (1/1000 dilution; D22F2; 5694S) H2AK119ub1 (1/3000 dilution; D27C4; 8240S), H3K27me3 (1/3000 dilution; C36B11, 9733S), H3K4me3 (1/3000 dilution; C42D8, 9751) and H4 (1/3000 dilution; 2935S) antibodies, were purchased from Cell Signaling Technology; H2A.Z (1/1000 dilution; 39113), H2B (1/1000 dilution; 5HH2-2A8; 61037); H2BK120ub (1/1000 dilution; C56; 39623), H3 (1/3000 dilution; C-terminal; 39163), and KDM1B (1/1000 dilution; 61457) antibodies were purchased from Active Motif; H3K4me2 (1/3000 dilution; MCA-MAB10003-100-Ex) antibody was purchased from Cosmo Bio; alpha-Tubulin (1/3000 dilution; 1F4E3; A01410) was purchased from Genscript.
+ Open protocol
+ Expand
10

Comprehensive Immunohistochemistry Profiling

Check if the same lab product or an alternative is used in the 5 most similar protocols
The antibodies used were: ASCL1 (Abcam, #ab211327), INSM1 (Abcam, #ab170876), E2F7 (Abcam, ab245655), RB1 (Abcam, ab181616), SYP (Santa Cruz, #sc-17750), RCOR1 (Santa Cruz, #sc-376567), CCN1 (Santa Cruz, #sc-374129), CCN2 (Santa Cruz, #sc-365970), YAP/TAZ (Santa Cruz, #sc-101199), P53 (Santa Cruz, #sc-126), E2F1 (Santa Cruz, #sc-251), GAPDH (Santa Cruz, #sc-47724), LATS1 (Cell signaling, #3477), LATS2 (Cell signaling, #5888), p-LATS (Cell signaling, #8654), H3 (Cell signaling, #4499), H3K27ac (Cell signaling, #8173), H3K4me3 (Cell signaling, #9751), VIN (Cell signaling, #13901), Flag (Sigma, #1804),
+ 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!