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Ab1012

Manufactured by Abcam
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Sourced in United Kingdom, United States

Ab1012 is a laboratory equipment product offered by Abcam. It serves as a core tool for scientific research and analysis. The product's primary function is to provide a reliable and consistent platform for performing various experimental procedures. Technical specifications and detailed information about the intended use of Ab1012 are not available.

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Lab products found in correlation

Ab8898, by Abcam (9 mentions) Ab4729, by Abcam (8 mentions) Ab6002, by Abcam (8 mentions) Ab8895, by Abcam (5 mentions) Ab9050, by Abcam (5 mentions) Ab1220, by Abcam (4 mentions) Ab1791, by Abcam (4 mentions) Ab5131, by Abcam (3 mentions) Ab12179, by Abcam (3 mentions) Ab194678, by Abcam (2 mentions) Pcmv ha jmjd3 plasmid, by Addgene (2 mentions) Anti histone h3, by Cell Signaling Technology (2 mentions) Anti ha, by Santa Cruz Biotechnology (2 mentions) Anti h3k27me3, by Merck Group (2 mentions) Real time pcr reactions, by Roche (2 mentions) Chemiluminescence kit, by Bio-Rad (2 mentions) Miracloth, by Merck Group (2 mentions) Sc 2025, by Santa Cruz Biotechnology (2 mentions) Protein coated a g agarose beads, by Santa Cruz Biotechnology (2 mentions) Vibra cell, by Sonics (2 mentions)

Spelling variants of this product

H3K4me3 (ab1012) (4 citations)

32 protocols using ab1012

1

Quantifying Epigenetic Modifications in Cells

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pCMV-HA-JMJD3 plasmid was obtained from Addgene (#24167). Lentiviral shRNAs (Extended Data Table 5) were provided by the Vector Core at the University of Michigan or kindly provided by Dr. Arul Chinnaiyan (University of Michigan). Antibodies including monoclonal anti-EZH2 (1:2000, BD Biosciences, 612667), anti-H3K27me3 (1:1000, Millipore, 07-449), H3K9me2 (1:2000, ab1220, Abcam), H3K9me3 (1:500, ab8898, Abcam), H3K4me1 (ab8895, Abcam), H3K4me2 (ab194678, Abcam), H3K4me3 (ab1012, Abcam), anti-Histone H3 (1:2000, Cell Signaling, 9715), anti-HA (1:200, Santa Cruz Biotechnology, sc-805), anti-DNMT1 (1:250, Abcam, ab13537) were used for Western blotting. Anti-human CXCR3 (1C6) blocking antibody was prepared from mouse hybridoma (ATCC, #HB-12330) by Hybridoma Core at the University of Michigan.
Peng D., Kryczek I., Nagarsheth N., Zhao L., Wei S., Wang W., Sun Y., Zhao E., Vatan L., Szeliga W., Kotarski J., Tarkowski R., Dou Y., Cho K., Hensley-Alford S., Munkarah A., Liu R, & Zou W. (2015). Epigenetic silencing of Th1 type chemokines shapes tumor immunity and immunotherapy. Nature, 527(7577), 249-253.
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2

ChIP-qPCR for Histone Modifications

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ChIP was performed as previously described and followed by qPCR analysis48 (link). The antibodies used for the immunoprecipitation were the following: H3K4me3 (ab1012, Abcam), H3K9me3 (ab8898, Abcam) and H3K27ac (ab4729, Abcam). Real-time PCR reactions (Roche) were performed in triplicates using primers for the correspondent genomic regions. Fold enrichment over 1% input was calculated using the 2DeltaCt method. Primers for ChiP are described in Supplementary Table IV.
Sosa M.S., Parikh F., Maia A.G., Estrada Y., Bosch A., Bragado P., Ekpin E., George A., Zheng Y., Lam H.M., Morrissey C., Chung C.Y., Farias E.F., Bernstein E, & Aguirre-Ghiso J.A. (2015). NR2F1 controls tumor cell dormancy via SOX9 and RARβ driven quiescence programs. Nature communications, 6, 6170.
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3

ChIP-seq Analysis of Histone Modifications

Cited 2 times
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Chromatin for native ChIP of histone modifications was digested with Micrococcal nuclease (MNase) and immunoprecipitated as described69 (link). For SIRT6, 40 × 106cells (L-C-B and SIRT6.2–7) were crosslinked with 0.4% PFA for 10 min at RT. ChIP was performed as described70 (link). Immunoprecipitations were performed with 10 µg of specific antibodies anti-SIRT6 (Abcam, Ab62739), anti-H3K4me1 (Abcam, ab8895), anti-H3K4me3 (Abcam, ab1012), anti-H3K9ac (Abcam, Ab10812), anti-H3K27ac (Abcam, ab4729), and anti-H3K56ac (Abcam, ab76307). Sequencing libraries were generated and barcoded for multiplexing as described69 (link). Libraries were sequenced on NextSeq500 (50–75 bp single-end reads). Reads were trimmed for Illumina adapter sequences using in-house scripts and aligned to the GRCh37/hg19 using Bowtie (version 0.12.7) with parameters -l 65 -n 2 -S -best -k 1 -m 20. SIRT6 significant peaks were identified using MACS2 (version 2.1.1.2) and matching Input control was used to call peaks. Coverage tracks were generated from BAM files using deepTools (version 2.4.1) bamCoverage with parameters -normalizeUsingRPKM -binsize 10. Differential ChIP-seq-binding profiles for the histone marks H3K9ac and H3K56ac between L-C-B and SIRT6.2–7 cells were found by using MACS2 bdgdiff (parameters: -l 100 –g 100 or –l 250 –g 250 for H3K9ac and H3K56ac, respectively).
Strub T., Ghiraldini F.G., Carcamo S., Li M., Wroblewska A., Singh R., Goldberg M.S., Hasson D., Wang Z., Gallagher S.J., Hersey P., Ma’ayan A., Long G.V., Scolyer R.A., Brown B., Zheng B, & Bernstein E. (2018). SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling. Nature Communications, 9, 3440.
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4

ChIP-Seq Profiling of Histone Modifications

Cited 3 times
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ChIP-seq was conducted as previously described [43 (link)-45 (link)]. The following antibodies were used in each experiment: anti-histone H3K4me3 antibody (Abcam, Cambridge, UK, ab1012) ,anti-RNA polymerase II (Abcam ab817), monoclonal anti-H3K27me3 antibody (Abcam, ab6002), polyclonal anti-H3K27Ac antibody (Abcam, ab4729), polyclonal anti-H3K36me3 antibody (Abcam, ab9050) For ChIP-seq, Illumina’s Eland was used to map the 36 bp reads to the reference human genome (hg19). Peaks were called by MACS 1.4.1 [24 (link)] at default settings.
Maekawa S., Imamachi N., Irie T., Tani H., Matsumoto K., Mizutani R., Imamura K., Kakeda M., Yada T., Sugano S., Suzuki Y, & Akimitsu N. (2015). Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance. BMC Genomics, 16(1), 154.
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5

ChIP-qPCR Analysis of H3K4me3

Cited 1 time
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Native ChIP for H3K4me3 (Abcam, ab1012) was performed in MDA-MB-231 cells that were either untreated, treated with 1 μM or 2.5 μM Tat-SID, or transfected with Scr-shRNA or PF1-shRNA as previously described [65 (link)]. Input DNA was used as control for the background. DNA obtained from input or immunoprecipitated DNA was analyzed by real-time PCR using primers mapping to the CD44, ITGA6 and SNAI2 promoter regions. Percent Input method was used for analysis. The following PCR primers were used: CD44-F 5′-TCACATAGCCAGGAGCAGTG-3′; CD44-R 5′-AAATCCTTCCCTCCCTGAAA-3′; ITGA6-F 5′-ACCTCCCAGGAGAAAGAGGA-3′; ITGA6-R 5′-GCGACTAAGCGCCAAAATAC-3′, SNAI2-F 5′-CAGACCCTGGTTGCTTCAA-3′; SNAI2-R 5′-CTTCATGCAAATCCAACAGC-3′; RPL30-F 5′-GCAAAGCGAAATTGGTCATT-3′; RPL30-R 5′-CTGTTTTCACTCCTGCCACA-3′.
Bansal N., Petrie K., Christova R., Chung C.Y., Leibovitch B.A., Howell L., Gil V., Sbirkov Y., Lee E., Wexler J., Ariztia E.V., Sharma R., Zhu J., Bernstein E., Zhou M.M., Zelent A., Farias E, & Waxman S. (2015). Targeting the SIN3A-PF1 interaction inhibits epithelial to mesenchymal transition and maintenance of a stem cell phenotype in triple negative breast cancer. Oncotarget, 6(33), 34087-34105.
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6

ChIP-qPCR for H3K4me3 in IMR90 cells

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Chromatin from IMR90 cells expressing H3.1FL and H3.3cs1 was digested with MNase and used for native ChIP using H3K4me3 antibody (Abcam, ab1012), and immunoprecipitated DNA was used for qPCR essentially as described42 (link). Primers were designed <1kb downstream of the TSS and controls were designed within intergenic regions. Primer sequences can be found in Supplementary Table 2.
Duarte L.F., Young A.R., Wang Z., Wu H.A., Panda T., Kou Y., Kapoor A., Hasson D., Mills N.R., Ma’ayan A., Narita M, & Bernstein E. (2014). Histone H3.3 and its proteolytically processed form drive a cellular senescence program. Nature communications, 5, 5210.
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7

Chromatin Profiling of Cbx8 Knockdown

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Native ChIP-seq for H3K27me3 (Millipore, 07-449), H3K27ac (Abcam, ab4729) and H3K4me3 (Abcam, ab1012) were performed in control (shScramble) and Cbx8 knockdown cells (Cbx8-sh68 for MMTV-Myc cells; CBX8-sh94 for MDA-MB-231-Luc cells) as described (Gaspar-Maia et al., 2013 (link)). Input DNA was used to control for background. High throughput sequencing on all samples was performed using Illumina HiSeq 2500 with 100nt single-end sequencing.
Chung C.Y., Sun Z., Mullokandov G., Bosch A., Qadeer Z.A., Cihan E., Rapp Z., Parsons R., Aguirre-Ghiso J.A., Farias E.F., Brown B.D., Gaspar-Maia A, & Bernstein E. (2016). Cbx8 acts non-canonically with Wdr5 to promote mammary tumorigenesis. Cell reports, 16(2), 472-486.
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8

Comprehensive Protein Detection and Histone Modification Analysis

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To identify histone modifications, acid extraction of histone was performed as previously reported [48 (link)]. To detect other proteins, cells were extracted with lysis buffer (50 mM Tris-HCl, 250 mM NaCl, 5 mM EDTA, 50 mM NaF, 1.5 mM PMSF and protease inhibitors cocktail). Equal amounts of protein were size fractionated on 6.0 to 15.0% SDS-PAGE gel. The antibodies used were anti-COX-2 (sc-19999, Santa Cruz), anti-c-Fos (ab7963, Abcam), anti-c-Jun (sc-44, Santa Cruz), anti-KMT3A (ab31358, Abcam), anti-KMT3B (17-10264, Merck Millipore), anti-KDM2A (ab31739, Abcam), anti-KDM2B (ab108276, Abcam), anti-KDM4A (ab70786, Abcam), anti-KDM4B (ab80473, Abcam), anti-NF-κB (sc-372G, Santa Cruz), anti-p300 (H-272, Santa Cruz), anti-CEBPβ (sc-150, Santa Cruz), anti-H3K4me1/2/3 (ab8895/ab7766/ab1012, Abcam), anti-H3K9me1/2/3 (ab9045/ab1220/ab8898, Abcam), anti-H3K27me1/2/3 (ab113671/ab24684/ab6002, Abcam), anti-H3K36me1/2/3 (ab9048/ab9049/ab9050, Abcam), anti-H3K79me1/2/3 (ab2886/ab3594/ab2621, Abcam), anti-H4K20me1/3 (ab9051/9053, Abcam), anti-histone H3 (ab131711, Abcam) and anti-β-actin (sc-1615, Santa Cruz).
Lu S., Yang Y., Du Y., Cao L.L., Li M., Shen C., Hou T., Zhao Y., Wang H., Deng D., Wang L., He Q, & Zhu W.G. (2015). The transcription factor c-Fos coordinates with histone lysine-specific demethylase 2A to activate the expression of cyclooxygenase-2. Oncotarget, 6(33), 34704-34717.
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9

Antibody Characterization for Protein Study

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The antibodies used in this study were anti-Myc antibody (sc-40, Santa Cruz), anti-HA antibody (sc-57592, Santa Cruz), anti-HBO1 antibody (sc-13284, Santa Cruz), anti-DDB2 antibody (sc-81246, Santa Cruz), anti-XPC antibody (sc-30156, Santa Cruz), anti-TFIIH p89 antibody (sc-293, Santa Cruz), anti-CPD antibody (NMDND001, Cosmo Bio), anti-Orc2 antibody (sc-13238, Santa Cruz), anti-acetyl-Histone H4 antibody (#06-866 Millipore), anti-Histone H4 antibody (ab10158, Abcam), anti-acetyl-Histone H3K14 antibody (A-4023, EPIGENTEK), anti-Histone H3 (tri methyl K4) antibody (ab1012, Abcam), anti-Histone H3 antibody (39763, ACTIVE MOTIF), anti-γH2AX antibody (50-171-736, Upstate), anti-SNF2H antibody (ab3749, Abcam), anti-ACF1 antibody (NB100-61041, Novusbio), anti-CSB antibody (553C5a, BIO MATRIX RESEARCH), anti-UVsS-A antibody (H00057654-B01, Abnova) and anti-β-actin antibody (sc-47778, Santa Cruz). Phospho Ser50 and Ser53 HBO1 rabbit polyclonal antibodies were generated by immunization with a synthetic phosphopeptide (CSARLpSQSpSQD). To perform immunoprecipitation of GFP-SNF2H, anti-GFP mAb-Agarose (D153-8, MBL) was used.
Niida H., Matsunuma R., Horiguchi R., Uchida C., Nakazawa Y., Motegi A., Nishimoto K., Sakai S., Ohhata T., Kitagawa K., Moriwaki S., Nishitani H., Ui A., Ogi T, & Kitagawa M. (2017). Phosphorylated HBO1 at UV irradiated sites is essential for nucleotide excision repair. Nature Communications, 8, 16102.
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10

Chromatin Immunoprecipitation (ChIP) Assay

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Chromatin immunoprecipitation (ChIP) assays were performed according to the Abcam-X-ChIP protocol with modifications as described in (36 (link)). For immunoprecipitation 2–10 μg of the following antibodies were used: H3K4me3 (ab1012 or ab12209, Abcam, Cambridge, UK). H3K9me3 (ab8898, Abcam), H3K27me3 (ab6002, Abcam), RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131, Abcam). As control immunoglobulin G (IgG) was used: IgG mouse (sc-2025, Santa-Cruz, Dallas, TX, USA). Purification of ChIP-DNA was performed using DNA purification columns (ChIP DNA Clean and ConcentratorTM, Zymo Research, Irvine, CA, USA). ChIP-DNA was eluted with 30 μl of buffer and analyzed by SYBR green (Thermo Fisher Scientific, Waltham, MA, USA) based quantitative PCR using 1 μl of chromatin. Primers used are listed in Supplementary Table S1.
Müller-Kuller U., Ackermann M., Kolodziej S., Brendel C., Fritsch J., Lachmann N., Kunkel H., Lausen J., Schambach A., Moritz T, & Grez M. (2015). A minimal ubiquitous chromatin opening element (UCOE) effectively prevents silencing of juxtaposed heterologous promoters by epigenetic remodeling in multipotent and pluripotent stem cells. Nucleic Acids Research, 43(3), 1577-1592.
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