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Sequencing of freshly produced RNA following exposure of cells to DNA damage-inducing UV mimetic 4-hydroxyaminoquinolone (4-NQO)

ABSTRACT: We used Illumina-HiSeq4000 to sequence 4sU-labelled RNA samples isolated from unchallenged and DNA damaged HeLa Flp-In cells, which revealed the nature of transcriptional response folowing genotoxic stress and the contribution of P-TEFb kinase in DNA damage-induced gene transcription.

ORGANISM(S): Homo sapiens

PROVIDER: GSE110272 | GEO | 2019/04/09

REPOSITORIES: GEO

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Sequencing of freshly produced RNA following exposure of cells to DNA damage-inducing UV mimetic 4-hydroxyaminoquinolone (4-NQO)

Project description:Sequencing of freshly produced RNA following exposure of cells to DNA damage-inducing UV mimetic 4-hydroxyaminoquinolone (4-NQO)

| PRJNA433357 | ENA

Effect of 4sU labeling concentrations on quantification bias in nucleotide conversion RNA-seq data

Project description:To investigate the effect of increasing 4sU labeling concentrations on quantification bias in nucleotide conversion RNA-seq, we labeled 3 different cell lines with increasing concentrations of 4sU. We then measured 4sU dropout in 4sU samples compared to 4sU naive samples.

2024-02-06 | GSE229504 | GEO

Genome-wide FLP/MYB88 binding sites in Arabidopsis thaliana

Project description:FLP and MYB88 are two paralogous MYB proteins, regulating the symmetric division of guard mother cell during Arabidopsis stomatal development. To understand their molecular functions, we performed genome-wide identification of FLP/MYB88 binding targets using ChIP-chip with FLP/MYB88 antibody. By comparing ChIP-chip between wild-type and flp-1 myb88 lines, a total genes were identified as putative direct targets for FLP/MYB88.

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Effect of 4sU labeling durations on quantification bias in nucleotide conversion RNA-seq data

Project description:To investigate the effect of labeling durations on quantification bias in nucleotide conversion RNA-seq, we labeled NIH cells with 4sU. We then measured 4sU dropout in 4sU samples compared to 4sU naive samples.

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Genome-wide FLP/MYB88 binding sites in Arabidopsis thaliana

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Effect of TUC-seq protocol versus SLAM-seq on quantification bias in nucleotide conversion RNA-seq data

Project description:To investigate the effect of TUC-seq versus SLAM-seq on quantification bias in nucleotide conversion RNA-seq, we performed SLAM-seq and TUC-seq on NIH cells. We then measured 4sU dropout in 4sU samples compared to 4sU naive samples.

2024-02-06 | GSE253169 | GEO

Explore the effect of m6A reader YTHDF1 on RNAs half-life

Project description:In order to evaluate mRNA dynamic, we performed 4SU-TT-seq to estimate RNA synthesis and degradation rates in HEK293 cell line. After 1h exposure to the nucleoside analog 4-thiouridine (4SU), 4sU is incorporated into newly transcribed RNA, and the resulting 4sU-labeled RNAs are isolated and sequenced. The sequencing results revealed that parts of mRNAs in YTHDF1 deficient cells tends to be more stable than mRNAs from wild type

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NELF-A phosphorylation site identification

Project description:NELF-A phosphorylation by P-TEFb is a key event in the pausing release. We conduct IMAC-LC-MS-MS to identified NELF-A phosphorylation site by activation P-TEFb kinase.

2016-03-23 | PXD003433 | Pride

Study of the Evolution of Pigments from Freshly Pressed to 'On-the-Shelf' Extra-Virgin Olive Oils by Means of Near-UV Visible Spectroscopy.

Project description:Spectroscopic non-destructive methods have high potentialities as fast, cheap and easy-to-be-used approaches to address olive oil quality and authenticity. Based on previous research where near-UV Visible spectroscopy was used to investigate extra-virgin olive oils (EVOOs) and their main pigments' content (i.e., β-carotene, lutein, pheophytin a and pheophytin b), we have implemented the spectral deconvolution method in order to follow the EVOO's life, from 'freshly pressed' to 'on-the-shelf' EVOO samples at different storage time. In the first part of the manuscript, the new implemented deconvolution spectroscopic method aimed to quantify two additional pigments, namely chlorophyll a and chlorophyll b, is described and tested on 'ad hoc' samples with known concentrations of chlorophylls. The effect of light exposure and acidification was investigated to test the reliability and robustness of the spectral deconvolution. In the second part of the work, this approach was used to study the kinetic of pigments' degradation in several monocultivar fresh EVOO samples under optimal storage's conditions. The results here reported show that this spectroscopic deconvolution approach is a good method to study fresh EVOOs too; moreover, the proposed method revealed to be sensitive to detect eventual stresses of olive oil samples stored in not-good conditions.

| S-EPMC8394633 | biostudies-literature

Stable and inducible expression of Fbxo25 in Flp-In-293 cells: control vs. tetracycline treatment

Project description:Expression profile of human Flp-In-293-WT-FBXO25 or Flp-In-293-∆F-FBXO25 cells comparing non treated cells vs. tetraciclyne treated for 24 and 48 hours. Flp-In-293-∆F-FBXO25 cells when induced express the non functional protein (without F-box domain). The objective of the study was to identify genes up or down-regulated when Fbxo25 wild-type or Fbxo25 lacking F-box domain is superexpressed.

2012-05-15 | GSE37380 | GEO

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