Journal: BMC Genomics

Article Title: Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7

doi: 10.1186/1471-2164-15-537

Figure Lengend Snippet: Distribution of segmental duplications (SDs) and bundled long distance interactions in relation to acetylation of H4K8, transcriptional activity and lamina associated domains on human chromosome 7 (derived from IMR90 unless indicated otherwise). A) H4K8 acetylation profile, dark yellow: hyperacetylation of H4K8; blue: hypoacetylation of H4K8. B) the red and blue curve represent RNA-seq read counts/100 kb bin for coding and non-coding RNA, respectively (IMR91L). C) grey areas underlying the two histograms mark lamina associated domains (LADs, Tig3 cells). D) idiogram of chromosome 7, the Williams-Beuren syndrome region is highlighted in yellow beside the idiogram (at 72-74 Mb, hg18). E) transparent blue shading of the idiogram illustrates the inversion-affected segments of chromosome 7 depicted in Figure A-C. Bundled long distance interactions (F) and segmental duplications (G) are depicted in the inner circle; green ribbons: long distance interactions between genomic regions; grey: SDs with sequence similarity <98%; yellow: SDs with sequence similarity 98-99%; orange: SDs with sequence similarity >99%.

Article Snippet: Human fetal lung fibroblast cell lines IMR91L (male) and IMR90 (female) were obtained from the Coriell Institute for Medical Research.

Techniques: Activity Assay, Derivative Assay, RNA Sequencing, Sequencing

Journal: BMC Genomics

Article Title: Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7

doi: 10.1186/1471-2164-15-537

Figure Lengend Snippet: Higher order chromatin organisation and SD localisation around the Williams-Beuren syndrome region. All data are referring to genome release hg19 and are derived from IMR90 unless indicated otherwise. The proximal, central and distal SD clusters (P, C, D) of the 7q11 segment encompassing 4.8 Mb are highlighted in green within the chromosome banding track. A-C) localisation of SDs; colouring according to sequence similarity; grey: <98%, yellow: 98%-99%; orange: >99%; D) genomic interval commonly deleted in WBS and the distal 7q11.23 deletion syndrome; E) topological domains as defined by Dixon et al. ; F) topological domains identified in the corresponding region in mouse after conversion to human hg19. Note that the murine topological domain homologous to sequences deleted in the distal 7q11.23 syndrome is not fully represented due to a break of synteny within this genomic interval. See Figure for details; G-H) heatmap and arc view of CTCF binding sites as detected by ChIA-PET in MCF7; I) number of G4 motifs/100 kb bins; J) average GC-content within 100 kb bins; K) number of Alu repeats/100 kb bin; L) number of structural variants as annotated by Database of Genomic Variance (DGV) , *maximum of 1080 CNVs not shown; M) log2 ratio scores of the LaminB1 DamID Map (Tig3 cells) as reported by Guelen et al. ; N) log2 ratio scores of DNA regions prone to early apoptotic DNA degradation in 20 kb windows, turquoise: degraded DNA segments; O) log2 ratio scores of H4K8 acetylation profile in 20 kb windows, blue: hyperacetylation, grey: hypoacetylation; P) red curve representing the sum of all intrachromosomal interaction counts/bin divided by the median number of interactions for all bins of chromosome 7; Q) percentage of interactions categorised according to their interaction span size ; light grey: <0.5 Mb, grey: 0.5-1 Mb, light blue: 1–5 Mb, light brown: 5–10 Mb, dark grey: 10–25 Mb, black: ≥25 Mb. Gaps in this plot are due to alignment problems of Hi-C data in regions harbouring SDs with high sequence similarity.

Article Snippet: Human fetal lung fibroblast cell lines IMR91L (male) and IMR90 (female) were obtained from the Coriell Institute for Medical Research.

Techniques: Derivative Assay, Sequencing, Binding Assay, ChIA Pet Assay, Hi-C

Journal: BMC Genomics

Article Title: Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7

doi: 10.1186/1471-2164-15-537

Figure Lengend Snippet: Cross-species comparison showing that SDs next to the WBS locus have inserted at topological domain borders. Hi-C interactions and topological domains in the human fetal fibroblast cell line IMR90 are shown in dark green in the upper part as triangle view and bars, respectively. SDs with sequence similarity of 98%-99% and above 99%, respectively, (shown in yellow and orange in the SDs track) coincide with gaps within the Hi-C data. SD distribution and Hi-C data of the corresponding region in mouse are given in the lower part of the image. The position of FKBP6 and WBSCR16 , the human orthologues of the two genes next to the murine topological domain borders are highlighted in green and red, respectively. The intervals commonly affected in WBS and the distal 7q11.23 syndrome are indicated by pale red bars. Note that the region distal to SRRM3 including the distal SD block are homologous to a different mouse chromosome.

Article Snippet: Human fetal lung fibroblast cell lines IMR91L (male) and IMR90 (female) were obtained from the Coriell Institute for Medical Research.

Techniques: Comparison, Hi-C, Sequencing, Blocking Assay

Journal: Nanoscale Advances

Article Title: Drug delivery with a pH-sensitive star-like dextran-graft polyacrylamide copolymer

doi: 10.1039/d2na00353h

Figure Lengend Snippet: Viability of the normal human lung fibroblast HEL299 cells, treated for 48 h with: (a) – free Dox or D- g -PAAan-Dox in Dox-equivalent concentrations, (b) – free Cis or D- g -PAAan-Cis in Cis-equivalent concentrations; * p < 0.05 compared to free drugs.

Article Snippet: Lung carcinoma human A549 and normal human lung fibroblast HEL299 cell lines were purchased from AddexBio Technologies (San Diego, CA, USA).

Techniques:

Journal: Nanoscale Advances

Article Title: Drug delivery with a pH-sensitive star-like dextran-graft polyacrylamide copolymer

doi: 10.1039/d2na00353h

Figure Lengend Snippet: IC 50 of free drugs and drug-loaded D- g -PAAan nanoparticles on HEL299 cell viability

Article Snippet: Lung carcinoma human A549 and normal human lung fibroblast HEL299 cell lines were purchased from AddexBio Technologies (San Diego, CA, USA).

Techniques:

Journal: Inflammation

Article Title: The Priming Potential of Interferon Lambda-1 for Antiviral Defense in the Oral Mucosa

doi: 10.1007/s10753-022-01624-1

Figure Lengend Snippet: Type III IFN receptor expression in human gingival keratinocytes. A : Detection of IL10R2 , IFNLR1 , and GAPDH mRNA in various keratinocytes and fibroblasts with (+) or without (-) cDNA by RT-PCR. M, marker. B : Quantitative analysis of IFNLR1 mRNA expression by real-time PCR in various keratinocytes and fibroblasts. Data represent the mean ± standard deviation (SD) of triplicate assays. C : Detection of cell surface IFN-λR1 by flow cytometry. The black line represents IFN-λR1, and the gray area shows the isotype control. A representative histogram from three independent experiments is shown. Values are the mean fluorescence intensity of IFN-λR1 expression and shown as a fold increase in IFN-λR1 expression from that with the control. D : HGK were treated with the indicated concentrations of IFN-λ1 for 30 min. Whole-cell lysates prepared from these cells were immunoblotted with anti-phospho-STAT1 (pSTAT1), anti-STAT1, or anti-GAPDH antibodies. A representative blot is shown. The bar graph shows the integrated signal intensities of the pSTAT1/STAT1 ratio. Data represent the mean ± SD of triplicate assays. * P < 0.05 and ** P < 0.01 versus untreated cells (0) (Dunnett’s multiple comparison test). E : Human gingival sections were stained with an isotype and anti-IFN-λR1 antibody. Sections were counterstained with hematoxylin. Representative images of 3 samples each are shown. The right image is a high-magnification image of the square area. A-D : Data show a representative of at least three independent experiments. OBA-9; an immortalized human gingival keratinocyte cell line. HGK; human primary gingival keratinocytes. HaCaT; an immortalized human skin keratinocyte cell line. HEK; human primary epidermal keratinocytes. HGF; human primary gingival fibroblasts. HFL-III; normal human lung fibroblasts.

Article Snippet: Normal human lung fibroblasts were provided by the Japanese Collection of Research Bioresources Cell Bank.

Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Marker, Real-time Polymerase Chain Reaction, Standard Deviation, Flow Cytometry, Control, Fluorescence, Comparison, Staining