Magna chip hisens chromatin immunoprecipitation kit

Manufactured by Merck Group

The Magna ChIP HiSens Chromatin Immunoprecipitation kit is a laboratory tool designed for the isolation and purification of protein-bound DNA fragments from cellular samples. It is a key component in the process of chromatin immunoprecipitation, which is used to study protein-DNA interactions.

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Lab products found in correlation

Ab4070, by Abcam (1 mentions) Lightcycler 480, by Roche (1 mentions) 550 sonic dismembrator, by Thermo Fisher Scientific (1 mentions) Lightcycler 480 sybr green 1 master, by Roche (1 mentions) Formaldehyde, by Polysciences (1 mentions) Rabbit anti srebp1 h 160, by Santa Cruz Biotechnology (1 mentions) Ab4729, by Abcam (1 mentions) H3k27me3, by Merck Group (1 mentions) H3k4me3, by Merck Group (1 mentions) Tet1 antibody, by Merck Group (1 mentions) Normal rabbit igg, by Santa Cruz Biotechnology (1 mentions) Qiaquick gel extraction kit, by Qiagen (1 mentions) Perfecta sybr green fastmix low rox, by Quanta Biosciences (1 mentions) Dzup genomic dna isolation reagent, by Sangon (1 mentions) Anti gli1, by Santa Cruz Biotechnology (1 mentions)

Close spelling variants of this product

ChIP kit (270 citations) Magna ChIP Kit (136 citations) Chromatin Immunoprecipitation Kit (96 citations) Magna ChIP HiSens Kit (22 citations) Immunoprecipitation Kit (14 citations) ChIP chromatin immunoprecipitation kit (11 citations) Magna Chip HiSens (6 citations) EZ-Magna ChIP™ HiSens Chromatin Immunoprecipitation Kit (6 citations)

8 protocols using magna chip hisens chromatin immunoprecipitation kit

Chromatin Immunoprecipitation Assay for RRM1 and RRM2 Promoters

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ChIP assay was performed using Magna ChIP HiSens Chromatin Immunoprecipitation Kit (17-10460, Merck Millipore), according to the manufacturer’s instructions. The DNA fragments isolated in the complex with the target protein were identified by qPCR using primers for RRM1 and RRM2 promoters. The antibody used for ChIP was anti-E2F1 (ab4070, Abcam). The sequences of primers used for qPCR were as follows:

RRM1: 5′-GTTCCCGCCGGTTAGGTTTT-3′ and 5′-CTGCTCTCCTGCTACCATGT-3′, and

RRM2: 5′-TTTGGAAGTCGCGCTAACCT-3′ and 5′-GCGCGTTTTGACATCTGCAT-3′.

Zou Y., Li W., Zhou J., Zhang J., Huang Y, & Wang Z. (2019). ERK Inhibitor Enhances Everolimus Efficacy through the Attenuation of dNTP Pools in Renal Cell Carcinoma. Molecular Therapy. Nucleic Acids, 14, 550-561.

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ChIP-qPCR Analysis of HT-144 Cells

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For each ChIP assay, 5 × 10⁷ HT-144 cells were used. HT-144 cells were seeded in 10% FBS medium, and then medium was replaced with 10% FBS or 1% ITS medium and cultured for 24 hours before ChIP-qPCR analyses. Chromatin from HT-144 cells was fixed with 1% formaldehyde (Polysciences) and prepared with Magna ChIP HiSens chromatin immunoprecipitation kit (EMD Millipore). Nuclei were sonicated on a sonic dismembrator 550 (Fisher Scientific) with a microtip (model 419) from Misonix Inc. Lysates were sonicated on ice with 10 pulses of 20 seconds each (magnitude setting of 3.5) and a 40-sec rest interval. The supernatant was used for immunoprecipitation with the following antibodies: rabbit anti-SREBP1 (H-160, Santa Cruz Biotechnology), rabbit anti-CBP (C-22, Santa Cruz Biotechnology), rabbit anti-RNA polymerase II (8WG16, BioLegend) and rabbit anti-histone H3 (acetyl K27) (ab4729, Abcam). qPCR reactions in triplicates were performed on a LightCycler 480 instrument (Roche) using LightCycler 480 SYBR green I master (Roche). The ChIP-qPCR primers were designed with software Primer 3. The primer sequences are listed in Table 2.

Wu S, & Näär A.M. (2019). A lipid-free and insulin-supplemented medium supports De Novo fatty acid synthesis gene activation in melanoma cells. PLoS ONE, 14(4), e0215022.

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Epigenetic Analysis of TNFA Promoter

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Epigenetic modifications at the TNFA promoter were assessed by ChIP. Cryopreserved PBMCs were thawed from 1 viremic and 1 suppressed time point for each patient and enriched for monocytes using an AutoMACS Monocyte Isolation Kit (Miltenyi Biotec). Equal numbers of monocytes from each patient were pooled into viremic and suppressed samples. ChIP was performed using a Magna ChIP HiSens Chromatin Immunoprecipitation Kit (EMD Millipore) with the following Abs: H3K4me3, H3K9me1, H3K27me3, H4Ac, and IgG (EMD Millipore). The Ab clones are listed in Supplemental Table 3. qPCR was performed using primers for 4 regions of the TNFA promoter that have been previously described (60 (link)). Enrichment was calculated by comparison of IP samples with input DNA, and background IP was subtracted out on the basis of enrichment of nonspecific IgG. Fold change in histone occupancy was calculated between viremic and suppressed samples.

Scully E.P., Lockhart A., Garcia-Beltran W., Palmer C.D., Musante C., Rosenberg E., Allen T.M., Chang J.J., Bosch R.J, & Altfeld M. (2016). Innate immune reconstitution with suppression of HIV-1. JCI Insight, 1(3), e85433.

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ChIP-seq Data Analysis and Quantification

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ChIP-seq data were obtained from GSM2104246 and GSM1571714 and were analyzed with WashU EpiGenome Browser (Washington University) to ascertain the binding site and the experimental design of ChIP-PCR^{29 (link),30 (link)}. According to the manufacturer’s protocol of the Magna ChIP HiSens Chromatin Immunoprecipitation kit (Millipore), 2 × 10⁶ cells were harvested in each ChIP reaction. Protein and DNA of each sample were crosslinked by applying 37% formaldehyde solution. SDS lysis buffer with protease/phosphatase inhibitor cocktail (CST, 1:100) was added after cell harvesting. After restriction enzyme digestion, centrifugation, and precipitation with beads, the precipitated DNA samples were quantified with specific primers via real-time PCR^{5 (link)}.

Liu C., Xiong Q., Li Q., Lin W., Jiang S., Zhang D., Wang Y., Duan X., Gong P, & Kang N. (2022). CHD7 regulates bone-fat balance by suppressing PPAR-γ signaling. Nature Communications, 13, 1989.

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TET1 ChIP Assay Protocol

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ChIP was performed with Magna ChIP HiSens chromatin immunoprecipitation kit (Millipore), TET1 antibody (09-872, Millipore), and analyzed using qPCR (Table S2 and S3). 10% of input DNA was used as a control. All data were collected from 3 independent experiments.

Wu B.K, & Brenner C. (2014). Suppression of TET1-Dependent DNA Demethylation is Essential for KRAS-Mediated Transformation. Cell reports, 9(5), 1827-1840.

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Chromatin Immunoprecipitation Enrichment Analysis

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Chip studies were conducted using the Magna ChIP™ HiSens Chromatin Immunoprecipitation Kit (Millipore) with the following modifications. 3 ug of normal rabbit IgG (Santa Cruz Biotechnology) was added to the lysate for 1.5 hr at 4°C and precleared with 40 ul of protein A/G magnetic beads cells at room temperature. The precleared chromatin was split into aliquots. 1.5 ug of E2F3, E2F1, ChIPAb+ Androgen Receptor- ChIP Validated Antibody (Millipore) and normal rabbit IgG (Santa Cruz Biotechnology) were added to separate aliquots. Following cleanup, the DNA was fractionated on a 1% low melt agarose gel and the region between 200 to 500 bp was excised and purified using the QIAquick gel extraction kit (Qiagen, Inc.). Quantification of the recovered DNA products was determined by qPCR using primer sets (Supplementary Materials and Methods) using PerfeCTa SYBR Green FastMix Low ROX according to manufacturer’s recommendations (Quanta Biosciences, Gaithersburg, MD). Recovered products after ChIP were normalized to the respective negative control (IgG) using the formula ΔCt = Ct_{target product or input} – Ct_IgG, and further calculated as percent of input.

Siddiqui S., Libertini S.J., Lucas C.A., Lombard A.P., Baek H.B., Nakagawa R.M., Nishida K.S., Steele T.M., Melgoza F.U., Borowsky A.D., Durbin-Johnson B.P., Qi L., Ghosh P.M, & Mudryj M. (2020). The p14ARF tumor suppressor restrains androgen receptor activity and prevents apoptosis in prostate cancer cells. Cancer letters, 483, 12-21.

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ChIP-seq of SW190 Cell Line

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A total of 1 × 10⁷ SW190 cells were collected for ChIP assay, and ChIP was performed using Magna ChIP HiSens Chromatin Immunoprecipitation Kit (Millipore) according to the manufacturer’s protocol. The precipitated DNA specimens were analyzed using qPCR.

Jiang J., Yu C., Guo X., Zhang H., Tian S., Cai K., He Z, & Sun C. (2020). G Protein-Coupled Receptor GPR87 Promotes the Expansion of PDA Stem Cells through Activating JAK2/STAT3. Molecular Therapy Oncolytics, 17, 384-393.

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ChIP-seq Profiling of Gli1 and SOX2

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ChIP was performed with Magna ChIP® HiSens Chromatin Immunoprecipitation Kit (Millipore) as described previously [44 (link)]. Cells (2 × 10⁸) were fixed with 37% formaldehyde, and the reaction was quenched using 2.5 M glycine. Cells were washed with ice-cold PBS and collected via centrifugation. Cell pellets were lysed using a lysis buffer containing protease inhibitors, and chromatin DNA was sheared into 100–500 base pair (bp) fragments using nucleic acid lyase. Anti-Gli1 (Santa Cruz Biotechnology, Beijing, China, 1:100) and anti-SOX2 (Zen-BioScience, Chengdu, China, 1:100) antibodies were used for immunoprecipitation. The chromatin-antibody complexes were precipitated with magnetic beads and washed with lysis buffer and 1× Tris buffer saline. Crosslinked sections were incubated overnight at 65 °C to reverse the cross-linking. Finally, DNA was extracted using Dzup Genomic DNA Isolation Reagent (Sangon Biotech, Shanghai, China) and analyzed using PCR. The primers used are listed in Supplementary Table S1.

Dong H., Zeng L., Chen W., Zhang Q., Wang F., Wu Y., Cui B., Qi J., Zhang X., Liu C., Deng J., Yu Y., Schmitt C.A, & Du J. (2023). N6-methyladenine-mediated aberrant activation of the lncRNA SOX2OT-GLI1 loop promotes non-small-cell lung cancer stemness. Cell Death Discovery, 9, 149.

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