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Synthetic circuits for tracking human cell fate

ABSTRACT: Cells respond heterogeneously to DNA damage. We engineered genetic circuits to detect differential responses in a population that persist for many days post-stimulus. We used microarrays to compare memory and non-memory subpopulations 3 days after DNA damage or doxycycline exposure. MD12/p53R2-RE and MD10/TetOx2 cells were either exposed to UV (10uJ/m^2) or doxycycline (1 ug/mL, 24 hours) and allowed to recover 3 days before sortng of memory and non-memory cells and RNA extraction. Two replicates were submitted for each condition (UV memory, UV non-memory, dox memory, dox non-memory)

ORGANISM(S): Homo sapiens

SUBMITTER: Mara Inniss

PROVIDER: E-GEOD-38189 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Synthetic circuits for tracking human cell fate

Project description:Cells respond heterogeneously to DNA damage. We engineered genetic circuits to detect differential responses in a population that persist for many days post-stimulus. We used microarrays to compare memory and non-memory subpopulations 3 days after DNA damage or doxycycline exposure.

2012-05-24 | GSE38189 | GEO

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Expression data from YAP-S127A Villin-rtTA crypts

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Analysis of oncogenic Kras-induced changes in the RNA-bound proteome of PDAC cells

Project description:In order to reveal the impact of oncogenic KRAS signaling on the RNA-bound proteome of Pancreatic Ductal Adenocarcinoma (PDAC), we carried out quantitative whole Transcriptome RNA Interactome Capture (RIC) analysis in tumour cells from an inducible mouse model of PDAC (iKras PDAC) (Ying et al., 2012). In this model, oncogenic Kras (G12D) expression can be controlled by administration of doxycycline (Dox). For RIC, we employed Orthogonal Organic Phase Separation (OOPS)(Queiroz et al., 2019). In this method, UV-C crosslinking coupled with phenol-chloroform based phase separation is used to isolate RNA-crosslinked proteins, which concentrate in the interface fraction, whilst free proteins concentrate in the organic fraction. SILAC was employed for quantitative analysis of Dox induced (24hrs) changes in the RNA-bound proteome. To assess the impact of ERK signalling, an independent experiment was carried out in which Trametinib (10nM) was added to the cells at the same time as Dox (both with or without Dox cells). A total of 6 biological replicates without Trametinib, and 4 biological replicates with Trametinib, were conducted, with switching the Heavy and Light SILAC labels for +Dox and -Dox conditions. Both the Interface as well as the organic phase fractions were analysed by mass spectrometry. In a separate experiment, the total proteome changes in response to dox (24hrs) were quantified from two reciprocally SILAC labelled mixes of heavy and light iKras PDAC whole cell lysates (See the READ ME.XLS for details of the experimental conditions).

2023-02-12 | PXD030825 | Pride

CPSF-160 iCLIP

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