Journal: Genome Research

Article Title: RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells

doi: 10.1101/gr.255851.119

Figure Lengend Snippet: HCT116 ex vivo tree for method validation. Colored clones were utilized for RETrace validation. Important microsatellite and methylation statistics per analyzed single cell are highlighted above .

Article Snippet: In order to build the ex vivo single-cell culture tree, we obtained HCT116 colorectal carcinoma cell line from Coriell Institute and initially cultured cells in McCoy's 5A media (ATCC) with 1% penicillin-streptomycin (Thermo Fisher Scientific) and 15% FBS (Thermo Fisher Scientific).

Techniques: Ex Vivo, Biomarker Discovery, Clone Assay, Methylation

Journal: Genome Research

Article Title: RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells

doi: 10.1101/gr.255851.119

Figure Lengend Snippet: Retrospective lineage tracing accuracy based on microsatellite capture of single cells from the HCT116 ex vivo tree. ( A ) Diagram of complete phylogenetic tree with colors corresponding to clones from the original ex vivo tree. ( B ) Accuracy of tree calling, as determined by the rate of topologically correct triplets reconstructed, based on the varying number of estimated cell division differences between each clone. An overall tree accuracy of 88% was observed by using all possible triplets from the tree. ( C ) Overall tree accuracy as a function of maximum cell divisions recapitulated in the ex vivo tree compared to existing methods for phylogenetic tree mapping. Arrow indicates optimal desired results of maximizing accuracy at lower cell division differences.

Article Snippet: In order to build the ex vivo single-cell culture tree, we obtained HCT116 colorectal carcinoma cell line from Coriell Institute and initially cultured cells in McCoy's 5A media (ATCC) with 1% penicillin-streptomycin (Thermo Fisher Scientific) and 15% FBS (Thermo Fisher Scientific).

Techniques: Ex Vivo, Clone Assay

Journal: Genome Research

Article Title: RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells

doi: 10.1101/gr.255851.119

Figure Lengend Snippet: RETrace methylation characterization of HCT116 single cells. ( A ) Heat map utilizing z-scores of pairwise dissimilarity against ENCODE reference cell lines for each single cell. Column colors above the heat map denote the clone from which each single cell was derived. ( B ) Plot of pairwise dissimilarity between single cells and HCT116 versus the number of shared CpG sites. Colors correspond to the outgroup identified in the pairwise dissimilarity heat map. Higher pairwise dissimilarity from HCT116 was most likely due to lower coverage of informative CpG sites. ( C ) UMAP of all CpGs within the Ensembl regulatory build windows for all analyzed single cells (colors indicate ex vivo cell clone).

Article Snippet: In order to build the ex vivo single-cell culture tree, we obtained HCT116 colorectal carcinoma cell line from Coriell Institute and initially cultured cells in McCoy's 5A media (ATCC) with 1% penicillin-streptomycin (Thermo Fisher Scientific) and 15% FBS (Thermo Fisher Scientific).

Techniques: Methylation, Derivative Assay, Ex Vivo

Journal: Saudi Journal of Biological Sciences

Article Title: Antioxidant, anticancer, apoptosis properties and chemical composition of black truffle Terfezia claveryi

doi: 10.1016/j.sjbs.2016.01.031

Figure Lengend Snippet: Cytotoxic activities of T. claveryi extracts.

Article Snippet: Human brain carcinoma cell line U-87 MG (HTB-14); human colorectal carcinoma cell line HT29 (CCL-247) and human hormone sensitive and invasive breast cancer cell line MCF-7 (HTB-22) were purchased from ScienCell USA.

Techniques: Inhibition