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The respective cell samples were analyzed for size (forward-scatter, FSC) and granularity (side-scatter, SSC).
Stained cell samples were analyzed with a four-color FACS flow cytometer (FACSCalibur, Becton Dickinson) using CellQuest software (Becton Dickinson).
Cell samples were analyzed on a FACSCalibur™ using Cellquest™ software or on a FACSAria™ using FACSDiva™ software (all from BD Biosciences).
Cell samples were analyzed on a MoFlo (Beckman Coulter) cell sorter, and emission was collected through a 610 nm long pass dichroic mirror (DCLP) to a 620 nm long pass (LP) filter for the Hoechst red collection and a 424/44 nm band pass (BP) filter for the Hoechst blue collection.
Media and cell samples were analyzed by quantitative westerns.
Cell culture medium was changed and cell samples were analyzed on a daily basis.
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The DNA content of the cell samples was analyzed by FACScan Scanford flow cytometer (BD Biosciences, San Jose, CA) with an argon laser turned to 488 nm for excitation.
After treatment, the cell samples were collected and the activity of NF- κB in cell samples was analyzed by TD-20/20 TD-20/20ter (Turner BioSystems, Sunnyvaluminometer) wiTurner BioSystemsaSunnyvaleer assay system (Promega, Madison, WI, USA).
After detection of CK19-positive cells, samples were analyzed by fluorescence microscopy to identify CD44-positive cells (red staining).
To detect whether GSE treatments cause DNA double strand break (DSB) in Ca9-22 cellsamplesles were analyzed using flow cytometry to quantify levels of the phosphorylated γH2AX protein.
In the first dataset (GEO Accession number GSE39981), DNA methylation profiles of 46 samples (6 CD19+ B cells samples, 8 granulocytes samples, 5 CD14+ monocytes samples, 11 CD56+ NK cells samples, 8 cellsD4+T cellsampleses, 2 CD3+CD8+ T cells samples, 1 CD3+CD56+ NK sample and 5 CD3+ T cells samples) were analyzed by the Infinium 27k.
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