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: Environmental Science and Pollution Research International

Article Title: The cytocompatibility of graphene oxide as a platform to enhance the effectiveness and safety of silver nanoparticles through in vitro studies

doi: 10.1007/s11356-023-30151-1

Figure Lengend Snippet: A549 and HFFF2 cells viability 24 h after incubation with nanomaterials, measured by three different assays. Statistically significant difference between a group and the control is marked as * p < 0.05, ** p < 0.0021, *** p < 0.0002, p **** < 0.0001. MTT and NR results are presented as % of control (mean with standard variation). Blue bars, GO; red bars, Ag; purple, GO:Ag. Notes: MTT is based on mitochondrial succinate dehydrogenase activity; NR is based on lysosomal uptake of neutral red. LDH is based on leakage of cytosol lactic dehydrogenase

Article Snippet: HFFF2, human fetal foreskin fibroblasts, from the European Collection of Authenticated Cell Cultures, catalogue no 86031405, is a cell line isolated from a 14 to 18 week old male fetus.

Techniques: Incubation, Control, Activity Assay

Journal: Environmental Science and Pollution Research International

Article Title: The cytocompatibility of graphene oxide as a platform to enhance the effectiveness and safety of silver nanoparticles through in vitro studies

doi: 10.1007/s11356-023-30151-1

Figure Lengend Snippet: A549 and HFFF2 cell proliferation rate after 24 h and 48 h of incubation with nanomaterials, measured by colorimetric BrdU assay. Statistically significant difference between a group and the control is marked as * p < 0.05, **** p < 0.0001. Results are presented as % of control (mean with standard variation). Blue bars, GO; red bars, Ag; purple, GO:Ag

Article Snippet: HFFF2, human fetal foreskin fibroblasts, from the European Collection of Authenticated Cell Cultures, catalogue no 86031405, is a cell line isolated from a 14 to 18 week old male fetus.

Techniques: Incubation, BrdU Staining, Control

Journal: Environmental Science and Pollution Research International

Article Title: The cytocompatibility of graphene oxide as a platform to enhance the effectiveness and safety of silver nanoparticles through in vitro studies

doi: 10.1007/s11356-023-30151-1

Figure Lengend Snippet: Reactive oxygen species (ROS) level in A549 and HFFF2 cells after 2 h of incubation with nanomaterials, measured by colorimetric DCF-DA fluorometric assay. Statistically significant difference between a group and the control is marked as ** p < 0.0021, *** p < 0.0002, p **** < 0.0001. Results are presented as mean fluorescence intensity (MFI) with standard deviation. Blue bars, GO; red bars, Ag; purple, GO:Ag

Article Snippet: HFFF2, human fetal foreskin fibroblasts, from the European Collection of Authenticated Cell Cultures, catalogue no 86031405, is a cell line isolated from a 14 to 18 week old male fetus.

Techniques: Incubation, Control, Fluorescence, Standard Deviation

Journal: Environmental Science and Pollution Research International

Article Title: The cytocompatibility of graphene oxide as a platform to enhance the effectiveness and safety of silver nanoparticles through in vitro studies

doi: 10.1007/s11356-023-30151-1

Figure Lengend Snippet: Caspase 3/7 activity in A549 and HFFF2 cells after 2 h of treatment with nanomaterials, measured by fluorometric CellEvent assay. There were no statistically significant differences. Results are presented as mean fluorescence intensity (MFI) with standard deviation. Blue bars, GO; red bars, Ag; purple, GO:Ag; green, additional controls

Article Snippet: HFFF2, human fetal foreskin fibroblasts, from the European Collection of Authenticated Cell Cultures, catalogue no 86031405, is a cell line isolated from a 14 to 18 week old male fetus.

Techniques: Activity Assay, Fluorescence, Standard Deviation

Journal: Environmental Science and Pollution Research International

Article Title: The cytocompatibility of graphene oxide as a platform to enhance the effectiveness and safety of silver nanoparticles through in vitro studies

doi: 10.1007/s11356-023-30151-1

Figure Lengend Snippet: Confocal imaging of HFFF2 cells combined with caspase 3/7 activity detection after treatment with nanomaterials for 2 h. Additional positive control: ketoconazole. Scale bar 450 µm. Notes: Nuclei were stained with DAPI (blue), caspase- 3/7 activity was visualized using a CellEvent probe (green) which stains nuclei in the presence of active caspases; actin F was stained with phalloidin conjugated with Alexa Fluor 633 (red)

Article Snippet: HFFF2, human fetal foreskin fibroblasts, from the European Collection of Authenticated Cell Cultures, catalogue no 86031405, is a cell line isolated from a 14 to 18 week old male fetus.

Techniques: Imaging, Activity Assay, Positive Control, Staining

Journal: Environmental Science and Pollution Research International

Article Title: The cytocompatibility of graphene oxide as a platform to enhance the effectiveness and safety of silver nanoparticles through in vitro studies

doi: 10.1007/s11356-023-30151-1

Figure Lengend Snippet: Selected magnified pictures from confocal imaging of A549 and HFFF2 cells combined with caspase- 3/7 activity detection after treatment with nanomaterials for 2 h. Additional positive controls: miconazole (A549) and ketoconazole (HFFF2). Scale bar 450 µm. Notes: Nuclei were stained with DAPI (blue); caspase 3/7 activity was visualized using a CellEvent probe (green, bright nuclei) which stains nuclei in the presence of active caspases; actin F was stained with phalloidin conjugated with Alexa Fluor 633 (red)

Article Snippet: HFFF2, human fetal foreskin fibroblasts, from the European Collection of Authenticated Cell Cultures, catalogue no 86031405, is a cell line isolated from a 14 to 18 week old male fetus.

Techniques: Imaging, Activity Assay, Staining

Journal: Environmental Science and Pollution Research International

Article Title: The cytocompatibility of graphene oxide as a platform to enhance the effectiveness and safety of silver nanoparticles through in vitro studies

doi: 10.1007/s11356-023-30151-1

Figure Lengend Snippet: Live imaging of A549 (upper row) and HFFF2 (lower row) cells after 7 days of treatment with nanomaterials, which were introduced into the culture medium after cell adhesion

Article Snippet: HFFF2, human fetal foreskin fibroblasts, from the European Collection of Authenticated Cell Cultures, catalogue no 86031405, is a cell line isolated from a 14 to 18 week old male fetus.

Techniques: Imaging

Journal: Environmental Science and Pollution Research International

Article Title: The cytocompatibility of graphene oxide as a platform to enhance the effectiveness and safety of silver nanoparticles through in vitro studies

doi: 10.1007/s11356-023-30151-1

Figure Lengend Snippet: Live imaging of HFFF2 cells after seeding on tissue culture plates coated with nanomaterials. Cells were grown for 24 h. Agglomerates of thicker GO flakes are visible. Scale bar 200 µm

Article Snippet: HFFF2, human fetal foreskin fibroblasts, from the European Collection of Authenticated Cell Cultures, catalogue no 86031405, is a cell line isolated from a 14 to 18 week old male fetus.

Techniques: Imaging

Journal: Environmental Science and Pollution Research International

Article Title: The cytocompatibility of graphene oxide as a platform to enhance the effectiveness and safety of silver nanoparticles through in vitro studies

doi: 10.1007/s11356-023-30151-1

Figure Lengend Snippet: May–Grünwald and Giemsa staining of A549 (upper row) and HFFF2 (lower row) cells after 24 days after seeding on tissue culture plates coated with nanomaterials (selected images). Agglomerates of thicker GO flakes are visible in the A549 cell line; stained large and thin flakes are visible in the HFFF2 cell line. Scale bar 200 µm

Article Snippet: HFFF2, human fetal foreskin fibroblasts, from the European Collection of Authenticated Cell Cultures, catalogue no 86031405, is a cell line isolated from a 14 to 18 week old male fetus.

Techniques: Staining