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ChIP-chip of siGFP- or siHOTTIP-treated foreskin fibroblasts with anti-H3K4me3, anti-H3K27me3, anti-H3K4me2, anti-histone, anti-MLL1, and anti-WDR5 antibodies on HOX tiling array

ABSTRACT: Coordinate loss of MLL1 and WDR5 occupancy caused by HOTTIP knockdown were observed in distal HOXA genes. These regions correspondingly lost H3K4me3 and H3K4me2, without changes in pan-histone or H3K27me3. human foreskin fibroblasts (CRL2091), anti-H3K4me3 (Abcam ab8580, lot#1016899), anti-H3K4me2 (Abcam ab32356, lot#947550), anti-H3K27me3 (Abcam ab4729, lot#1021724), anti-histone H3 (Abcam ab1791, lot#1025144), anti-MLL1 (gift of R. Roeder, Rockefeller University), and anti-WDR5 (gift of W. Herr, UNIL)

ORGANISM(S): Homo sapiens

PROVIDER: GSE26540 | GEO | 2011/03/21

SECONDARY ACCESSION(S): PRJNA136667

REPOSITORIES: GEO

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ChIP-chip of siGFP- or siHOTTIP-treated foreskin fibroblasts with anti-H3K4me3, anti-H3K27me3, anti-H3K4me2, anti-histone, anti-MLL1, and anti-WDR5 antibodies on HOX tiling array

Project description:Coordinate loss of MLL1 and WDR5 occupancy caused by HOTTIP knockdown were observed in distal HOXA genes. These regions correspondingly lost H3K4me3 and H3K4me2, without changes in pan-histone or H3K27me3. human foreskin fibroblasts (CRL2091), anti-H3K4me3 (Abcam ab8580, lot#1016899), anti-H3K4me2 (Abcam ab32356, lot#947550), anti-H3K27me3 (Abcam ab4729, lot#1021724), anti-histone H3 (Abcam ab1791, lot#1025144), anti-MLL1 (gift of R. Roeder, Rockefeller University), and anti-WDR5 (gift of W. Herr, UNIL) Comparison of occupancy of MLL1 and WDR5 of siGFP and siHOTTIP foreskin fibroblasts on HOX tiling array. Human foreskin fibroblasts are transfected with siGFP or siHOTTIP for 72 hrs. The cells are harvesed and ChIP performed with H3K4me3, H4K27me3, H3K4me2, MLL1, WDR5, and histone antibodies.

2011-03-21 | E-GEOD-26540 | biostudies-arrayexpress

Chromatin immunoprecipitation of human and chimp cell lines GM06990, HFL1, HeLaS3, MOLT4 and PTR8 with anti Histone H3K4me1, H3K4me2, H3K4me3, H3ac and H4ac antibodies using an ENCODE array

Project description:ENCODE ChIP/chip study using human lymphoblastoid cell line GM06990; human cervix carcinoma cell line HeLaS3; human fetal lung fibroblast cell line HFL1; human T cell line MOLT4; chimpanzee lymphoblastoid cell line PTR8; and anti Histone H3K4me1 (Abcam; ab8895); H3K4me2 (Abcam; ab7766); H3K4me3 (Abcam; ab8580); H3ac (Upstate; 06-599) and H4ac (Upstate; 06-866) antibodies. The experiment was conducted in three biological replicates (1;2;3) with up to two technical duplicates (a;b).

2006-08-30 | E-TABM-138 | biostudies-arrayexpress

MLL1 and MLL fusion proteins play distinct roles in regulating MLLleukemic transcription program [ChIP-Seq]

Project description:This study describes the epigenetic profiling change of 1.) Mll1, WDR5 and H3K4me2 in mouse MAF9 leukemia cells treated with or without MM401; 2.) WDR5 and H3K4me2 epigenetic profiling in MLL1 flox/flox, ER-Cre+/- cells with knocking out MLL1 by 4OHT or not.

2016-05-12 | GSE68821 | GEO

Chromatin immunoprecipitation of human erythroleukemia cell line K-562 with H3K4me2, H3K4me3, H3ac, H4ac, Histone H2B and Histone H3 antibodies using an ENCODE array

Project description:ENCODE ChIP-chip study using human myelogenous leukemia cell line K-562 and anti histone H3K4me2 (Abcam; ab7766); H3K4me3 (Abcam; ab8580); H3ac (Upstate; 06-599); H4ac (Upstate; 06-866); Histone H2B (Abcam: ab1790) and Histone H3 (Abcam: ab1791) antibodies. Each antibody experiment was conducted in three biological replicates, with two technical replicates performed for each biological replicate

2006-09-01 | E-TABM-140 | biostudies-arrayexpress

H3K14ac is linked to methylation of H3K9 by the Tudor domains of SETDB1

Project description:Mononucleosomes were isolated from murine ES cells and precipitated with the recombinant SETDB1 Triple Tudor Domain (3TD), recombinant SETDB1 Triple Tudor domain Y268A mutant, anti-H3K9me2 (Abcam, ab1220), or anti-H3K9me1 (Abcam, ab8896, Lot GR185298-1) antibodies.

2018-07-30 | E-MTAB-4982 | biostudies-arrayexpress

Non-canonical PRC1.1 targets active genes independent of H3K27me3 and is essential for leukemogenesis

Project description:Polycomb proteins are classical regulators of stem cell self-renewal and cell lineage commitment and are frequently deregulated in cancer. Here we find that the non-canonical PRC1.1 complex, as identified by mass spectrometry-based proteomics, is critically important for human leukemic stem cells. Downmodulation of PRC1.1 complex members, like the DNA-binding subunit KDM2B, strongly reduces cell proliferation in vitro and delays or even abrogates leukemogenesis in vivo in humanized xenograft models. PRC1.1 components are significantly overexpressed in primary AML CD34+ cells. Besides a set of genes that is co-targeted by PRC1 and PRC2, ChIP-seq studies show that PRC1.1 also binds a distinct set of genes that are devoid of H3K27me3 suggesting a gene regulatory role independent of PRC2. This set encompasses genes involved in metabolism, which have transcriptionally active chromatin profiles. These data indicate that PRC1.1 controls distinct gene clusters involved in unique cell biological processes required for leukemic cell viability. K562 cells were transduced with lentiviral GFP-fusion vectors encoding GFP-CBX2, PCGF1-GPF, PCGF2-GFP, PCGF4-GFP, GFP-RING1A or GFP-RING1B. K562 cells expressing GFP-fusions at relatively low levels were sorted and expanded and subsequently crosslinked. ChIP reactions were performed using the following antibodies: anti-GFP (ab290, Abcam), anti-H3K27me3 (07-449, Millipore), anti-H3K4me3 (ab8580, Abcam), anti-H2AK119ub (D27C4, Cell Signaling Technology), and anti-KDM2B (ab137547, Abcam). Furthermore, ChIP reactions were performed using primary AML CD34+ and Peripheral Blood (PB) CD34+ cells using anti-H3K27me3 (07-449, Millipore), anti-H3K4me3 (ab8580, Abcam), anti-H2AK119ub (D27C4, Cell Signaling Technology), anti-KDM2B (ab137547, Abcam).

2015-11-24 | E-GEOD-54580 | biostudies-arrayexpress

Targeting EZH2 in MYCN-amplified Neuroblastoma [ChIP-seq]

Project description:Purpose: Identify new targets in MYCN-amplified Neuroblastoma Methods: ChIP-Seq experiments were performed on Kelly and LAN-1 neuroblastoma cells by using the following antibodies: anti-EZH2 (Cell Signaling 5246S); anti-H3K27me3 (Millipore 07-449); anti-H3K4me3 (Abcam ab8580). We evaluated the global EZH2 PRC2-dependence by identifiying direct genome-wide target genes for EZH2, H3K27me3 and H3K4me3. Results: We found that EZH2 serves a PRC2-dependent function in neuroblastoma, repressing neuronal differentiation. Moreover, EZH2-regulated genes were strongly repressed in MYCN-amplified and high-risk primary tumors. Conclusion: Our study supports testing EZH2 inhibitors in patients with MYCN-amplified neuroblastoma.

2017-12-02 | GSE85430 | GEO

Homo sapiens

Project description:ChIP-chip of siGFP- or siHOTTIP-treated foreskin fibroblasts with anti-H3K4me3, anti-H3K27me3, anti-H3K4me2, anti-histone, anti-MLL1, and anti-WDR5 antibodies on HOX tiling array

| PRJNA136667 | ENA

Meiotic time course of the trimethylation of the Lysine 4 of Histone H3 (H3K4me3)

Project description:To study the meiotic dynamic of the methylation of H3K4, in relation with the transcriptomic regulation, we determine the meiotic time-course of H3K4me3 by ChIP-chip. Keywords: ChIP-chip, meiotic time course, histone modification Strain ORD7339 meiotic time-course from 0 to 6h. Immunoprecipitation with rabbit polyclonal anti-triMe H3K4 (Abcam #Ab8580).

2010-05-17 | E-GEOD-10840 | biostudies-arrayexpress

Meiotic time course of the trimethylation of the Lysine 4 of Histone H3 (H3K4me3) in a mutant Spo11F

Project description:To study the meiotic dynamic of the methylation of H3K4, in relation with the transcriptomic regulation, we determine the meiotic time-course of H3K4me3 by ChIP-chip in a mutant deficient for DSB formation. Keywords: ChIP-chip, meiotic time course, histone modification Strain ORD7341 meiotic time-course from 0 to 6h. Immunoprecipitation with rabbit polyclonal anti-triMe H3K4 (Abcam #Ab8580).

2010-05-17 | E-GEOD-10837 | biostudies-arrayexpress

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