ewing sarcoma tc 71 cell line  (DSMZ)

Journal: Cell reports

Article Title: Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation

doi: 10.1016/j.celrep.2022.111761

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Ewing sarcoma cell line TC-71 , DSMZ, Braunschweig, Germany , RRID: CVCL_2213.

Techniques: Plasmid Preparation, Polymer, Virus, In Vivo, Recombinant, Reverse Transcription, DNA Methylation Assay, Knockdown, Gene Expression, Microarray, shRNA, Software

Journal: Cancer cell

Article Title: STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and EWSR1-FLI1 activity in Ewing sarcoma.

doi: 10.1016/j.ccell.2021.04.001

Figure Lengend Snippet: Figure 1. STAG2 knockout profoundly alters the transcriptomic landscape (A) Representative western blotting in cellular extracts from isogenic STAG2 knockout (KO) (generated with two independent sgRNAs: SA2m#1 and SA2m#2), STAG1 KO (sgRNA: SA1m#1), STAG2 rescued (sgRNA: SA2r) and STAG2 knockdown (KD) at 48 h (generated with two independent siRNAs: siSA2#6 and siSA2#8) Ewing sarcoma cells. Color code for sgRNA isogenic models is indicated for each model and kept identical throughout the article. (B) Scaled Venn diagram for modulated genes between STAG2 WT and KO conditions (n = 3); total modulated genes for each condition represent the sum of intra- circle numbers; universe includes expressed genes (n = 13,780). p value for intersection was calculated with the SuperExact test. (C) Boxplots of log2 fold change for up-, un-, and downregulated genes in STAG2 KO and STAG2 rescued cells as compared with A673 or TC71 parental cells (n = 3 for each model); number of genes is indicated for each category. p values: two-tailed paired Wilcoxon test. Boxes represent the central 50% of data points (interquartile range). Upper and lower whiskers represent the largest and smallest observed values within 1.5 times the interquartile range from the ends of the box. (D) Heatmap for the core set of commonly upregulated (left panel) and downregulated (right panel) genes identified in (B and C) for STAG2 KO and KD Ewing cell lines. Time after siRNA transfection is indicated at the top, sgRNA and siRNA identifiers at the bottom. See also Figures S1 and S2, Table S1.

Article Snippet: The Ewing sarcoma A673 cell line was obtained from the American Type Culture Collection (ATCC) and the Ewing sarcoma TC71 cell line was obtained from the German Collection of Microorganisms and Cell Cultures (DSMZ).

Techniques: Knock-Out, Western Blot, Generated, Knockdown, Two Tailed Test, Transfection

Journal: Cancer cell

Article Title: STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and EWSR1-FLI1 activity in Ewing sarcoma.

doi: 10.1016/j.ccell.2021.04.001

Figure Lengend Snippet: Figure 5. STAG2 mutation is globally associated with decreased cis-promoter-enhancer and enhancer-enhancer interactions within loops (A–D) Color-coded boxplots of comparative analysis of (A–B) H3K27ac ChIP-seq peak intensities and (C–D) H3K27ac HiChIP interactions along promoter- enhancer chains between STAG2 WT and KO as well as between STAG2 KO and rescued cells. p values: two-tailed Wilcoxon test. P (promoter) and E (enhancer) positions in the chain are shown for ranks 1 to 5. (E) Color-coded boxplots of comparative analysis of intra super-enhancer interactions in H3K27ac HiChIP data between STAG2 WT and KO or rescued cells. p values: two-tailed t test. (A–E) Boxes represent the central 50% of data points (interquartile range). Upper and lower whiskers represent the largest and smallest observed values within 1.5 times the interquartile range from the ends of the box. The n value for each condition is indicated. (F) Top, curve of cumulative percentage of loop presence upon genomic distance (log10 scale) in A673 and TC71 (STAG2 WT). Loop size threshold: 75% of cumulative loops corresponding to 595 kb for A673 (red line) and 340 kb (green line) for TC71. Numbers of loop and median loop size for each cell line is indicated. Bottom, percentage of cis-interaction read pairs upon genomic distance between STAG2 WT, KO, and rescued conditions in CTCF and H3K27ac HiChIP data. A threshold of 20 kb used for H3K27ac chain detection is displayed (blue dashed line). Right, zoom in CTCF and H3K27ac HiChIP plots flanking lower and top thresholds (highlighted in gray). See also Figures S7 and S8, Tables S4, S5, and S6.

Article Snippet: The Ewing sarcoma A673 cell line was obtained from the American Type Culture Collection (ATCC) and the Ewing sarcoma TC71 cell line was obtained from the German Collection of Microorganisms and Cell Cultures (DSMZ).

Techniques: Mutagenesis, ChIP-sequencing, HiChIP, Two Tailed Test