Journal: PLoS ONE

Article Title: A Novel Histone Deacetylase Inhibitor Exhibits Antitumor Activity via Apoptosis Induction, F-Actin Disruption and Gene Acetylation in Lung Cancer

doi: 10.1371/journal.pone.0012417

Figure Lengend Snippet: ( A ) Chemical structure of OSU-HDAC-44 and SAHA. ( B ) Molecular docking analysis of OSU-HDAC-44 and SAHA. The structures of OSU-HDAC-44 and SAHA were calculated and the docking mode on catalytic domain of HDAC8 was predicted using the docking program GOLD 4.0.1. ( C ) Dose-dependent effects of OSU-HDAC-44 ( left ) and SAHA ( right ) on cell viability in IMR90, H1299, A549 and CL1-1 cells. Cells were treated with 0.5–10 µM of OSU-HDAC-44 or SAHA for 48 h, and cell viability was assessed by trypan blue exclusion assay. ( D ) OSU-HDAC-44 synergized with cisplatin to suppress cell proliferation. Cells were exposed to cisplatin (Cis) alone for 4 h, OSU-HDAC-44 (HDAC-44) alone for 48 h, or pretreated with OSU-HDAC-44 for 48 h before cisplatin treatment for 4 h, and then drug were withdrew and cells were incubated with drug-free media for additional 48 h. Cell viability was assessed by trypan blue exclusion assay. CL1-1 cells were treated with 4.4 µM cisplatin or 0.3 µM OSU-HDAC-44. A549 cells were treated with 1.6 µM cisplatin or 0.2 µM OSU-HDAC-44. Data represent mean ± SEM from three independent experiments. * P <0.05; ** P <0.01; *** P <0.001.

Article Snippet: Human normal lung cell line IMR90 and human NSCLC cell lines A549 and H1299 were obtained from the American Type Culture Collection (ATCC, Manassas, VA), and the human NSCLC cell line CL1-1 was kindly provided by Dr. P-C Yang (Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan) .

Techniques: Trypan Blue Exclusion Assay, Incubation

Journal: bioRxiv

Article Title: A Fractal-Dimension Framework for Quantifying Self-Similarity in Chromatin Folding

doi: 10.64898/2026.05.06.723123

Figure Lengend Snippet: Illustrative Hi-C contact maps for chromosomes 1–4 at 500 kb and 100 kb resolution in the IMR90 cell line. For visualization, contact counts are displayed on the log(count + 1) scale. The maps reveal clear multiscale structure and strong diagonal organization, consistent with spatial proximity between nearby genomic loci.

Article Snippet: In this work, we analyze intrachromosomal Hi-C contact matrices from the IMR90 cell line obtained from the Gene Expression Omnibus (GEO) database of the National Center for Biotechnology Information (NCBI), accession GSE63525, associated with the high-resolution in situ Hi-C study of Rao et al. [ ].

Techniques: Hi-C

Journal: Bioinformatics

Article Title: De novo pattern discovery enables robust assessment of functional consequences of non-coding variants

doi: 10.1093/bioinformatics/bty826

Figure Lengend Snippet: Different genomics patterns of DVAR-clusters C1∼C5 in 2 000 000 non-coding variants randomly sampled from the 1000 Genomes Project. (a) The percentage of each cluster of the non-coding variants. (b) The distributions of DVAR-scores of non-coding variants in different clusters. (c) Enrichment of DVAR-clusters with gene-based regions: Splice, 3′ UTR, 5′ UTR, Enhancer, Promoter Intron and Intergenic region, extracted from UCSC database. The darkness of the blue color indicates the relative enrichment with darker blue representing higher significance [−10log10 (Fisher exact P-value)] and vice versa. (d) Enrichment with chromatin states of GM12878 cell line identified by ChromHMM. (e) The boxplot of the numbers of active epigenomes in DVAR-clusters C1-C5 across 127 Roadmap epigenomes. (f) The boxplot of the numbers of active tissue-groups in DVAR-clusters C1∼C5 across 15 Roadmap tissue-groups (Color version of this figure is available at Bioinformatics online.)

Article Snippet: To test that, we grouped the cell types into 17 tissues according to the grouping by the Roadmap Epigenomics (‘IMR90’, ‘ES cell’, ‘iPSC’, ‘ES-deriv’, ‘Blood &T cell’, ‘HSC &B cell’, ‘Mesench’, ‘Myosat’, ‘Epithelial’, ‘Neurosph’, ‘Brain’, ‘Adipose’, ‘Muscle’, ‘Heart’, ‘Smooth muscle’ and ‘Digestive’).

Techniques: