Project description:To assess the timing and scope of IRF4–dependent reprogramming in vivo, CTV-labeled IRF4–sufficient and –deficient B cells were transferred into mMT hosts. One day later, hosts were challenged with 50 mg LPS. Three days post-LPS challenge, transferred cells were recovered and sorted from divisions 0, 1, 3, 4, 5, and 6 as determined by CTV dilution for ATAC–seq.
Project description:To assess the timing and scope of IRF4–dependent reprogramming in vivo, CTV-labeled IRF4–sufficient and –deficient B cells were transferred into mMT hosts. One day later, hosts were challenged with 50 mg LPS. Three days post-LPS challenge, transferred cells were recovered and sorted from divisions 0, 1, 3, 4, 5, and 6 as determined by CTV dilution for RNA–seq.
Project description:To determine the impact of a low Mg(2+)/pH defined growth medium (MgM) on the proteome of Salmonella enterica serotype Typhimurium, researchers cultured S. Typhimurium cells in the medium under two different conditions termed MgM Shock and MgM Dilution and then comparatively analyzed the bacterial cells harvested from these conditions by a global proteomic approach.
Project description:Pyruvate fermentation pathway and energetics of Desulfovibrio alaskensis strain G20 under syntrophic coculture and fermentative monoculture conditions Expression data for Desulfovibrio alaskensis strain G20 grown in chemostats on pyruvate under respiratory conditions (sulfate-limited and pyruvate-limited monoculture, dilution rate 0.047 and 0.027 h-1), fermentative conditions (monoculture, dilution rate 0.036 h-1), and syntrophic conditions (coculture with Methanococcus maripaludis or Methanospirillum hungatei, dilution rate of 0.047 and 0.027 h-1)
Project description:mESCs were cultured at least 2 weeks in medium medium: N2B27 for SILAC (DMEM/F12 for SILAC (AthenaES), Neurobasal for SILAC (AthenaES), Sodium Pyruvate (40 mg/mL), N2 (1X), B27 (0.5X), Pen/Strep (1%), L-glutamine (2 mM), beta-mercaptoethanol (50 µM)) + 2i/LIF supplemented with (medium) 13C6 15N4 L-arginine (0.65 mM), (medium) 13C6 L-arginine (0.55 mM), and L-Proline (200 mg/L)84. Before switching from light to heavy medium, cells were treated with 0.05 µg/mL CHX or equivalent dilution of DMSO in 6-well plates. We treated the cells with 0.05 µg/mL CHX. At timepoint 0 h, we replaced medium medium with pre-warmed heavy medium: N2B27 for SILAC (Thermo scientific) supplemented with (heavy) 13C6 15N2 L-Lysine-2HCl (0.65 mM), (heavy) 13C6 15N4 L-Arginine-HCl (0.55 mM), and L-Proline (200 mg/L) for mESC.
Project description:NIH/3T3 cells were cultured at least 2 weeks in light medium: DMEM for SILAC (Thermo scientific) supplemented with PS, dialyzed FBS (Thermo scientific), (light) L-Lysine-2HCl (0.666 mM), (light) L-Arginine-HCl (0.399 mM)44, and L-Proline (200 mg/L). Before switching from light to heavy medium, cells were treated with 0.05 µg/mL CHX or equivalent dilution of DMSO in 6-well plates. At timepoint 0 h, we replaced light medium with pre-warmed heavy medium: DMEM for SILAC (Thermo scientific) supplemented with PS, dialyzed FBS (Thermo scientific), (heavy) 13C6 15N2 L-Lysine-2HCl (0.666 mM), (heavy) 13C6 15N4 L-Arginine-HCl (0.399 mM), and L-Proline (200 mg/L) for NIH/3T3.
Project description:H1299 cells were collected and lysed using M-PER lysis reagent (Thermo, 78501), and the cell lysates were incubated with compound 10 or DMSO (100 μM) for 1 h at room temperature. The lysates were equally divided and degraded with a 1:30 dilution of protease (Sigma, 10165921001, 1.25 mg/ml) for 30 min. Treated protein samples were sent to DARTS detection.