Dataset Information

IDR-Targeting Compounds Suppress HPV Genome Replication via Disruption of Phospho-BRD4 Association with DNA Damage Response Factors

ABSTRACT: Sample name abbreviation is below. Cell State: Prol for proliferation, Diff for differentiation Compound (cpd) treatment: DMSO for DMSO-only treatment, 14 or 90 for compound pNPS14 or pNPS90 treatment BRD4-L IP: L1, L2, and L3 for anti-BRD4-L IP samples 1, 2, and 3 BRD4-S IP: S1, S2, and S3 for anti-BRD4-S IP samples 1, 2, and 3 IgG IP: Ig1, Ig2, and Ig3 for IgG IP samples 1, 2, and 3 Sample ID vs. sample name is listed below. 967246 / Prol_DMSO_L1, 967247 / Prol_DMSO_L2, 967248 / Prol_DMSO_L3 967249 / Prol_14_L1, 967250 / Prol_14_L2, 967251 / Prol_14_L3 967252 / Prol_10_L1, 967253 / Prol_10_L2, 967254 / Prol_10_L3 967255 / Prol_DMSO_S1, 967256 / Prol_DMSO_S2, 967257 / Prol_DMSO_S3 967258 / Prol_14_S1, 967259 / Prol_14_S2, 967260 / Prol_14_S3 967261 / Prol_10_S1, 967262 / Prol_10_S2, 967263 / Prol_10_S3 967264 / Diff_DMSO_L1, 967265 / Diff_DMSO_L2, 967266 / Diff_DMSO_L3 967267 / Diff_14_L1, 967268 / Diff_14_L2, 967269 / Diff_14_L3 967270 / Diff_10_L1, 967271 / Diff_10_L2, 967272 / Diff_10_L3 967273 / Diff_DMSO_S1, 967274 / Diff_DMSO_S2, 967275 / Diff_DMSO_S3 967276 / Diff_14_S1, 967277 / Diff_14_S2, 967278 / Diff_14_S3 967279 / Diff_10_S1, 967280 / Diff_10_S2, 967281 / Diff_10_S3 967282 / Prol_DMSO_Ig1, 967283 / Prol_DMSO_Ig2, 967284 / Prol_DMSO_Ig3 967285 / Diff_DMSO_Ig1, 967286 / Diff_DMSO_Ig2, 967287 / Diff_DMSO_Ig3

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Cheng-Ming Chiang

PROVIDER: MSV000091570 | MassIVE | Tue Mar 28 07:49:00 BST 2023

REPOSITORIES: MassIVE

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Project description:Mass spectrometry-based proteomics was applied to unravel Erk signaling in mouse embryonic stem cells (ESCs). A previously described engineered ESCs system for Erk induction via a drug-inducible cRAF-ErT2 fusion (Hamilton, W. B. & Brickman, J. M., Cell Rep 2014) was used in two different setups measuring the phosphoproteome in an 11-plex tandem mass tag (TMT)-based approach as described below. Fgf4 stimulation and MEK inhibition: ESCs were stimulated with Fgf4 (40 nM, recombinant, mouse, 5 minutes) following pretreatment (30 minutes) with either DMSO (1:10000) or MEK inhibition (MEKi: 1 microM PD0325901): The experimental treatment conditions and TMT11-plex labeling are specified below: 126: DMSO, unstimulated control replicate 1 127N: DMSO, unstimulated control replicate 2 127C: DMSO, unstimulated control replicate 3 128N: DMSO + Fgf4 replicate 1 128C: DMSO + Fgf4 replicate 2 129N: DMSO + Fgf4 replicate 3 129C: MEKi + Fgf4 replicate 1 130N: MEKi + Fgf4 replicate 2 130C: MEKi + Fgf4 replicate 3 131N: MEKi replicate 1 131C: MEKi replicate 2 Analog sensitive Erk2 setup: In the ESC system the ERK2-/- ESCs (Hamilton et al., PloS ONE, 2013) were engineered to stably express an inducible cRAF-ErT2 fusion protein expressed from the same transgene as a FLAG-tagged analogue sensitive Erk2Q103A. Erk1 was subsequently removed by CRISPR-Cas9 mutagenesis using sgRNAs flanking exon 2. Cells were pre-treated for 30 minutes with either the ATP-mimetic compound 1-NM-PP1 (2 microM) (Endo et al., Biochem Biophys Res Commun 2006), the Mek1 inhibitor PD0325901 (1 microM), or DMSO (0.01%), followed by induction or not of the cRAF-ErT2 fusion by (Z)-4-Hydroxytamoxifen (4OHT) (250 nM) for 2 hours as indicated. The experimental treatment conditions and TMT11-plex labeling are specified below: 126: DMSO pretreatment, non-induced control, replicate 1 127N: DMSO pretreatment, non-induced control, replicate 2 127C: DMSO pretreatment, non-induced control, replicate 3 128N: DMSO pretreatment, 4OHT-induction, replicate 1 128C: DMSO pretreatment, 4OHT-induction, replicate 2 129N: DMSO pretreatment, 4OHT-induction, replicate 3 129C: PP1 pretreatment, 4OHT-induction, replicate 1 130N: PP1 pretreatment, 4OHT-induction, replicate 2 130C: PP1 pretreatment, 4OHT-induction, replicate 3 131N: MEKi pretreatment, 4OHT-induction, replicate 1 131C: MEKi pretreatment, 4OHT-induction, replicate 2

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IDR-Targeting Compounds Suppress HPV Genome Replication via Disruption of Phospho-BRD4 Association with DNA Damage Response Factors

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