imr90 human primary lung embryo fibroblasts  (ATCC)

Journal: PLoS Genetics

Article Title: Dynamic Distribution of Linker Histone H1.5 in Cellular Differentiation

doi: 10.1371/journal.pgen.1002879

Figure Lengend Snippet: (A) Venn diagram of significant peaks of H1.5 binding in H1 hESCs and IMR90 fibroblasts by ChIP-seq. (B) Pie chart of distribution of H1.5 relative to gene structure in H1 hESCs and IMR90 fibroblasts. (C) Venn diagram of number of H1.5 target genes in H1 hESCs and IMR90 fibroblasts. (D) Enrichment of HGNC gene family members in H1.5 target genes. Height of bars represents percentage of gene family members in all RefSeq genes (left) or H1.5 target genes (right). (E) Enrichment of clustered gene family members in H1.5 target genes. Height of bars represents percentage of clustered gene family members in all RefSeq genes (left) or H1.5 target genes (right). (F) Box plot of H1.5 enrichment levels of non-clustered gene family members (left) and clustered gene family members (right). (G) H1.5 enrichment block at the LCE/SPRR/S100A gene clusters. Each dot represents −Log10 of Poisson p-value of ChIPed DNA versus input DNA in a 100-bp window. Lines represent average values. LCE, SPRR and S100A genes are highlighted in orange, green and pink, respectively. (H) An H1.5 enrichment block in an intergenic region of chromosome 2. (I) Histogram of average significance of H1.5 enrichment (x-axis) in 5 kb windows versus the number of windows (y-axis) in H1 hESCs and IMR90 fibroblasts.

Article Snippet: IMR90 human primary lung embryo fibroblasts (ATCC) were cultured in Dulbecco's modified Eagle's medium (DMEM) plus 10% FBS (Hyclone), 100 U/ml penicillin (Gibco), and 100 µg/ml streptomycin (Gibco) at 37°C in 5% CO 2 .

Techniques: Binding Assay, ChIP-sequencing, Blocking Assay

Journal: PLoS Genetics

Article Title: Dynamic Distribution of Linker Histone H1.5 in Cellular Differentiation

doi: 10.1371/journal.pgen.1002879

Figure Lengend Snippet: Gene ontology of H1.5 target genes in IMR90 fibroblasts.

Article Snippet: IMR90 human primary lung embryo fibroblasts (ATCC) were cultured in Dulbecco's modified Eagle's medium (DMEM) plus 10% FBS (Hyclone), 100 U/ml penicillin (Gibco), and 100 µg/ml streptomycin (Gibco) at 37°C in 5% CO 2 .

Techniques: Cell Surface Receptor Assay, Transduction

Journal: PLoS Genetics

Article Title: Dynamic Distribution of Linker Histone H1.5 in Cellular Differentiation

doi: 10.1371/journal.pgen.1002879

Figure Lengend Snippet: Heat maps show the genome wide promoter distribution of H1.5 in (A) H1 hESCs and IMR90 fibroblasts, (B) HSF1 hESCs, neural progenitor cells (NPC), neural cells (Neu), and (C) primary keratinocytes (HK Ca−), calcium-treated keratinocytes (HK Ca+), and (D) primary human hepatocytes (Hepa). Each row represents the promoter of a gene in 500-bp intervals from −5.5 to +2.5 kb of the transcription start sites (TSS) which is indicated by the arrows. The gene promoters for all heat maps are ordered based on the highest to lowest level of H1.5 enrichment in fibroblasts. (E) Average H1.5 enrichment and expression of the epidermal (LCE, SPRR) and KRT gene clusters in HK Ca+ and IMR90 fibroblasts are shown as line charts and bar graphs, respectively. The relative position of genes in each cluster is illustrated schematically.

Article Snippet: IMR90 human primary lung embryo fibroblasts (ATCC) were cultured in Dulbecco's modified Eagle's medium (DMEM) plus 10% FBS (Hyclone), 100 U/ml penicillin (Gibco), and 100 µg/ml streptomycin (Gibco) at 37°C in 5% CO 2 .

Techniques: Genome Wide, Expressing

Journal: PLoS Genetics

Article Title: Dynamic Distribution of Linker Histone H1.5 in Cellular Differentiation

doi: 10.1371/journal.pgen.1002879

Figure Lengend Snippet: (A) Boxplots of expression levels (Affymetrix array) of randomly selected genes (left) and H1.5 target genes (right) in IMR90 fibroblasts. (B–C) Line charts show gene expression levels (mRNA-seq) as a function of H1.5 binding at (B) genic regions or (C) intergenic regions in control knockdown IMR90 fibroblasts. All RefSeq genes were sorted by H1.5 binding levels; each data point represents the average expression value of 2000 genes. Genes located upstream or downstream of an intergenic region were denoted as 5′ gene (red line) and 3′ gene (blue line), respectively. (D) Average expression level of genes bound by H1.5 at either genic (left), intergenic (middle), or both (right) regions in IMR90 fibroblasts. Wilcoxon rank sum test p-values are indicated. (E) Average expression level of genes that belong (‘family’) or do not belong (‘non-family’) to HGNC gene families that were bound (purple bars) or not bound (yellow bars) by H1.5 in IMR90 fibroblasts. (F) Genome-wide promoter binding of Pol II, H1.5, SIRT1 and H3K9me2 in IMR90 fibroblasts. (G) Distributions of H3K4me1, H3K4me2, H3K4me3, DNase I sensitive sites, H3K9me3, H3K27me3, and H1.5 peaks at LCE/SPRR/S100A gene cluster (left panel) and an intergenic region in chromosome 2 (right panel). The scale of DNase I hypersensitive sites represent z-score of counts in each 100-bp window. Scales of H1.5 and other histone modifications represent the Poisson p-values of enrichment at each 100-bp window.

Article Snippet: IMR90 human primary lung embryo fibroblasts (ATCC) were cultured in Dulbecco's modified Eagle's medium (DMEM) plus 10% FBS (Hyclone), 100 U/ml penicillin (Gibco), and 100 µg/ml streptomycin (Gibco) at 37°C in 5% CO 2 .

Techniques: Expressing, Binding Assay, Genome Wide

Journal: PLoS Genetics

Article Title: Dynamic Distribution of Linker Histone H1.5 in Cellular Differentiation

doi: 10.1371/journal.pgen.1002879

Figure Lengend Snippet: (A) Western blotting of H1.5, SIRT1, H3K9me2, and β-Actin in control KD , H1.5 KD , and SIRT1 KD IMR90 cells. (B–D) Genome wide promoter binding of the indicated factors and experimental conditions is shown as heat maps. The genes are ordered as in . (E) Percentage of up-regulated genes with the indicated H1.5 binding pattern. The binomial p-values are indicated. (F) Stacked bar chart of percentage of family (yellow) and non-family (purple) genes in all H1.5 targets (left bar) and up-regulated H1.5 targets (right bar). The binomial p-value is indicated. (G) Stacked bar chart of percentage of clustered (orange) and non-clustered (burlywood) in all H1.5 targets (left bar) and up-regulated H1.5 targets (right bar). The binomial p-value is indicated. (H) Expression levels (mRNA-seq) of clustered and non-clustered H1.5 target genes in control KD and H1.5 KD cells are shown as a bar chart.

Article Snippet: IMR90 human primary lung embryo fibroblasts (ATCC) were cultured in Dulbecco's modified Eagle's medium (DMEM) plus 10% FBS (Hyclone), 100 U/ml penicillin (Gibco), and 100 µg/ml streptomycin (Gibco) at 37°C in 5% CO 2 .

Techniques: Western Blot, Genome Wide, Binding Assay, Expressing