chip-seq data for histone modifications (h3k27ac, h3k27me3, h3k36me3, h3k4me1, h3k4me3, and h3k9me3)  (Epigenomics ag)

Journal: Leukemia

Article Title: The landscape of RNA-chromatin interaction reveals small non-coding RNAs as essential mediators of leukemia maintenance

doi: 10.1038/s41375-024-02322-7

Figure Lengend Snippet: A Clustering of snoRNA binding sites by enrichment of diverse histone modifications. B H3K27ac signals at snoRNA interaction C1 region in MV4-11 cells with FBL knockdown versus control. C Fibrillarin-bound genes revealed by ChIP-seq in MV4-11 cells. D Enrichment of Fibrillarin occupancy, H3K27ac, and H3K9me3 at exemplar loci (a rDNA region) in multiple AML cell lines with or without FBL silencing.

Article Snippet: ChIP was performed with one million or five million cells per IP condition, using an iDeal ChIP- seq kit for Histones (for H3K27ac, H3K9me3) or for Transcription Factors (for FBL) (Diagenode) following the manufacturer’s recommendations.

Techniques: Binding Assay, Knockdown, Control, ChIP-sequencing

Journal: bioRxiv

Article Title: ISWI chromatin remodeling complexes recruit NSD2 and H3K36me2 in pericentromeric heterochromatin

doi: 10.1101/2023.10.20.563387

Figure Lengend Snippet: (A-C) Localization of H3K36me2 by Immunofluorescence. Pmi28 cells (A) and iMEFs (B) were fixed and stained with anti-H3K36me2 (green), anti-H3K9me3 (red), and Hoechst 33342 (blue). (A and B) Single optical sections of confocal microscope images are shown. Insets show magnified views of indicated areas. Line plots indicate intensity profiles of H3K36me2, H3K9me3, and DNA along the yellow line in the merged images. (C) Quantification of the intensity ratio of H3K36me2 in PCH to that in the nucleoplasm in various mouse cell lines. Two box plots display data from two biological replicates with dots representing individual cells (round for the first experiment and triangular for the second). Center lines represent medians; box limits indicate the 25th and 75th percentiles; whiskers extend 1.5 times the interquartile range from these percentiles. The numbers of total cells analyzed (n) and p-value comparing ESCs (H3K36me2 in PCH) to MC12 cells (H3K36me2 in euchromatin), calculated using the Mann-Whitney U test, are indicated. (D) Genome-wide correlation heatmap of H3K36me2 and H3K9me3 in mouse ESCs, B cells, and pancreatic cancer cells. Spearman’s correlation coefficients are indicated inside cells. Scale bars, 10 μm.

Article Snippet: ChIP-seq dataset of H3K36me2 and H3K9me3 were obtained from the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) for ESCs (PRJNA720715), B cells (PRJNA324130), and pancreatic cancer cells (PRJNA565773).

Techniques: Immunofluorescence, Staining, Microscopy, MANN-WHITNEY, Genome Wide

Journal: bioRxiv

Article Title: ISWI chromatin remodeling complexes recruit NSD2 and H3K36me2 in pericentromeric heterochromatin

doi: 10.1101/2023.10.20.563387

Figure Lengend Snippet: (A-E) Immunofluorescence. Cells were fixed and stained with antibodies directed against histone modifications and Hoechst 33342. Single optical sections of confocal microscope images are shown. (A) H3K36me2 (green) and Hoechst33342 (red) in various mouse cell lines. (B) Pmi28 cells and iMEFs stained with another H3K36me2-specific antibody (green; rabbit monoclonal) with H3K9me3 (red) and Hoechst33342 (blue). (C-E) Localization of various modifications (blue), such as H3K27me3 (C), H3K9me2 (D), and H3K36me3 (E), respect to H3K36me2 (green) and H3K9me3 (red) in iMEFs. Insets show magnified views of the indicated PCH areas. (F and G) ChIP-seq signal enrichments of H3K36me2 and H3K9me3 on repeat elements in ESCs and B cells from the transcription start site (TSS) to the transcription end site (TES) (F) and around TSS (G). Scale bars, 10 μm.

Article Snippet: ChIP-seq dataset of H3K36me2 and H3K9me3 were obtained from the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) for ESCs (PRJNA720715), B cells (PRJNA324130), and pancreatic cancer cells (PRJNA565773).

Techniques: Immunofluorescence, Staining, Microscopy, ChIP-sequencing

Journal: bioRxiv

Article Title: ISWI chromatin remodeling complexes recruit NSD2 and H3K36me2 in pericentromeric heterochromatin

doi: 10.1101/2023.10.20.563387

Figure Lengend Snippet: (A and B) Immunofluorescence of tissue sections (A) and 13.5-day embryo sections (B) stained with antibodies against H3K36me2 (red), H3K9me3 (green), and Hoechst 33342 (blue). Single optical sections of confocal microscope images are shown. (A) Low-power views of merged images are shown on the left (Scale bars, 50 μm). Individual and merged images of the indicated area are shown on the right (Scale bars, 10 μm). (B) A tiled image covering the whole embryo is shown on the left (Scale bar, 500 μm). Single images for the brain (pons area; #1), cartilage primordium (#2), and stomach (#3) (Scale bars, 50 μm) and magnified views of the indicated areas are shown from the middle to the right (Scale bars, 10 μm). (C) Different localization of H3K36me2 in maternal PN in zygotes and the 2-cell nucleus in preimplantation embryos analyzed by line plots. Intensity profiles of H3K36me2 and DNA along the yellow lines are shown. Scale bar, 10 μm.

Article Snippet: ChIP-seq dataset of H3K36me2 and H3K9me3 were obtained from the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) for ESCs (PRJNA720715), B cells (PRJNA324130), and pancreatic cancer cells (PRJNA565773).

Techniques: Immunofluorescence, Staining, Microscopy

Journal: bioRxiv

Article Title: ISWI chromatin remodeling complexes recruit NSD2 and H3K36me2 in pericentromeric heterochromatin

doi: 10.1101/2023.10.20.563387

Figure Lengend Snippet: Localization of H3K36me2 in mouse preimplantation embryos at various stages. Embryos were fixed and stained with anti-H3K36me2 (red), anti-H3K9me3 (green), and Hoechst 33342 (blue). (A) Images of single optical sections. Low-power views of merged images are shown on the left. Magnified views of indicated nuclei are shown on the right. PN, pronucleus; TE, trophectoderm; and ICM, inner cell mass. (B) Pearson correlation coefficients of DNA and H3K36me2 (top) or H3K9me3 (bottom). The number of nuclei (n) and p-values, calculated using the Mann-Whitney U test and Hommel correction to the 4-cell stage, are shown. See legend for the details of box plots. Scale bars, 10 μm

Article Snippet: ChIP-seq dataset of H3K36me2 and H3K9me3 were obtained from the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) for ESCs (PRJNA720715), B cells (PRJNA324130), and pancreatic cancer cells (PRJNA565773).

Techniques: Staining, MANN-WHITNEY